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Escherichia coli DH1 is a plasmid host strain with a high frequency of transformation. It is a common laboratory strain and will be used for comparative analysis.","n_reactions":2732,"n_metabolites":1940,"n_genes":1564,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.70503.json.json","assembly_accession":"GCA_016775825.1","genome_id":"562.70503","genome_name":"Escherichia coli strain RIVM_C029952","strain":"strain RIVM_C029952","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5280943.0,"gc_content":50.645218,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5318.0,"refseq_cds":4987.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"National Institute for Public Health and the Environment","completion_date":"2021-02-01T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA691727","biosample_accession":"SAMN17373197","genbank_accessions":"CP068821","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:chromosome","comments":"OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2752,"n_metabolites":2027,"n_genes":1742,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"GCF_016942505.1.json.json","assembly_accession":"GCF_016942505.1","genome_id":"GCF_016942505.1","genome_name":"Escherichia coli","strain":"BS90R-A","serovar":"","phylogroup":"B1","MLST":654,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN16387358","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1936,"n_genes":1521,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1441627.14.json.json","assembly_accession":"GCF_001610755.1","genome_id":"1441627.14","genome_name":"Escherichia coli str. 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Three replicates were created for each compound, generating BZKR1, BZKR2, BZKR3, CETR1, CETR2, and CETR3, as well as an unadapted wild-type. At the end of the experiment, the BZK-adapted bacteria were tolerant to 72-144 ug/ml of BZK, and the CET-adapted bacteria were tolerant to 240 ug/ml of CET.;Benzalkonium adapted E.coli bioreplicate 2 BW25113","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.63852.json.json","assembly_accession":"GCA_014169995.1","genome_id":"562.63852","genome_name":"Escherichia coli strain IDR1900005638-01-02","strain":"strain IDR1900005638-01-02","serovar":"","phylogroup":"B1","MLST":2178,"mash_cluster":26,"isolation_source":"Rectal swab","isolation_country":"USA","geographic_location":"USA:Maine","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4779842.0,"gc_content":50.8176,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4659.0,"refseq_cds":4432.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore MiniION","sequencing_depth":"234x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Wadsworth Center, New York State Department of Health","completion_date":"2020-08-12T00:00:00Z","collection_date":"Jan-2019","bioproject_accession":"PRJNA636827","biosample_accession":"SAMN15086849","genbank_accessions":"CP054282,CP054284,CP054283","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Maine Center for Disease Control and Prevention","comments":"Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the U.S. and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the blaKPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.","n_reactions":2731,"n_metabolites":1935,"n_genes":1511,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.51573.json.json","assembly_accession":"GCA_008807155.1","genome_id":"562.51573","genome_name":"Escherichia coli strain YPE12","strain":"strain YPE12","serovar":"","phylogroup":"A","MLST":761,"mash_cluster":22,"isolation_source":"Pork","isolation_country":"China","geographic_location":"China: Yangzhou","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5070189.0,"gc_content":50.701385,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5191.0,"refseq_cds":4946.0,"sequencing_platform":"Oxford Nanopore MinION, Illumina","sequencing_depth":"80X","assembly_method":"Unicycler v. v0.4.4","sequencing_centers":"Yangzhou University","completion_date":"2019-10-03T00:00:00Z","collection_date":"Jun-2019","bioproject_accession":"PRJNA553293","biosample_accession":"SAMN12233489","genbank_accessions":"CP041442,CP041443,CP041439,CP041441,CP041440","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Xiaoyu Lu","comments":"The emergence of plasmid-mediated tet(X) genes conferring resistance to tigecycline pose a public health concern. This project amis to investigate the underlying genomic basis of tigecycline resistance among E. coli strains.","n_reactions":2711,"n_metabolites":1877,"n_genes":1437,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"GCF_021496405.1.json.json","assembly_accession":"GCF_021496405.1","genome_id":"GCF_021496405.1","genome_name":"Escherichia coli","strain":"1162C","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN14611938","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1943,"n_genes":1472,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.77122.json.json","assembly_accession":"GCA_019039795.1","genome_id":"562.77122","genome_name":"Escherichia coli strain Q4552","strain":"strain Q4552","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":22,"isolation_source":"pig","isolation_country":"France","geographic_location":"France: Avignon","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4972251.0,"gc_content":50.9136,"contigs":9.0,"chromosomes":1.0,"plasmids":8.0,"patric_cds":5603.0,"refseq_cds":4716.0,"sequencing_platform":"Illumina MiSeq; 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With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2711,"n_metabolites":1877,"n_genes":1455,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.30435.json.json","assembly_accession":"GCA_003288455.1","genome_id":"562.30435","genome_name":"Escherichia coli strain AR_451","strain":"strain AR_451","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5165626.0,"gc_content":50.764168,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":5168.0,"refseq_cds":5016.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"10.03x","assembly_method":"canu v. 1.4; SPAdes v. 3.6.0","sequencing_centers":"FDA/CDC","completion_date":"2018-07-05T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA316321","biosample_accession":"SAMN07291544","genbank_accessions":"CP030337,CP030335,CP030340,CP030339,CP030336,CP030338,CP030333,CP030334","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"Susceptible;Resistant;Intermediate;Not defined","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The AR Isolate Bank is a centralized repository of microbial pathogens with well-characterized resistance profiles that are assembled by CDC in collaboration with the Food and Drug Administration (FDA). The AR Bank is available to support and advance development of diagnostic devices and antimicrobial drug products. The AR Isolate Bank also supports the National Action Plan for Combating Antibiotic Resistance Bacteria by advancing the development of diagnostic tests to identify and characterize resistant bacteria, and by accelerating research and development for new antibiotics.The AR Isolate Bank includes collections of bacterial pathogens that are associated with known or emerging resistance mechanisms. Since its launch in July 2015, the AR Bank continues to grow and will eventually include genera and species such as Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus, Enterococcus, Streptococcus, Salmonella, and Neisseria gonorrhoeae.Each pathogen listed on this web site includes information regarding its susceptibility and/or resistance profile(s), known resistance biomarkers, isolate characteristics, and associated data in PDF.Use this web site to search through pathogen panels, find additional information about the available isolates, and find procedures for requesting panels.","n_reactions":2711,"n_metabolites":1877,"n_genes":1399,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.50638.json.json","assembly_accession":"GCA_007998125.1","genome_id":"562.50638","genome_name":"Escherichia coli strain NCYU-21-79 strain not 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Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. 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Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2730,"n_metabolites":1929,"n_genes":1224,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"2491692.3.json.json","assembly_accession":"GCA_015571735.1","genome_id":"2491692.3","genome_name":"Escherichia coli O39:H21 strain Res13-Lact-PEB08-01","strain":"O39:H21 strain Res13-Lact-PEB08-01","serovar":"O39:H21","phylogroup":"B1","MLST":101,"mash_cluster":26,"isolation_source":"feces","isolation_country":"Canada","geographic_location":"Canada: Quebec","host_name":"Pig, Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5017694.0,"gc_content":50.702354,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5037.0,"refseq_cds":4741.0,"sequencing_platform":"Oxford Nanopore MinION and Illumina MiSeq","sequencing_depth":"1.00x","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Government of Canada","completion_date":"2020-11-18T00:00:00Z","collection_date":"13-Mar-2017","bioproject_accession":"PRJNA662792","biosample_accession":"SAMN16304199","genbank_accessions":"CP062865,CP062866,CP062867","refseq_accessions":"","genome_status":"Complete","taxon_id":2491692.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Agriculture and Agri-Food Canada","comments":"The majority of antibiotics sold are administered to livestock, presumably promoting the development and spread of antibiotic resistance genes in food-borne pathogens such as Enterobacteriaceae producing extended spectrum beta-lactamases (ESBL). 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These long read sequenced isolates include Escherichia coli O104:H4 str. 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With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2733,"n_metabolites":1946,"n_genes":1453,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.63854.json.json","assembly_accession":"GCA_014170595.1","genome_id":"562.63854","genome_name":"Escherichia coli strain 276.2","strain":"strain 276.2","serovar":"","phylogroup":"G","MLST":117,"mash_cluster":2,"isolation_source":"Turkey's","isolation_country":"Canada","geographic_location":"Canada","host_name":"Turkey","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5325828.0,"gc_content":50.711494,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5785.0,"refseq_cds":5101.0,"sequencing_platform":"Oxford Nanopore MinION","sequencing_depth":"60.8x","assembly_method":"Flye v. 2.6","sequencing_centers":"University of Guelph","completion_date":"2020-08-12T00:00:00Z","collection_date":"2016/2017","bioproject_accession":"PRJNA596173","biosample_accession":"SAMN13613902","genbank_accessions":"CP059904,CP059905,CP059906","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from Turkey's in Canada","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:fecal","comments":"Chromosomes and plasmids were assembled from E. coli isolated from Turkey's in Canada. Both long reads (Oxford Nanopore) and short reads (Illumina) were used.","n_reactions":2735,"n_metabolites":1945,"n_genes":1488,"n_exchange":331,"n_with_gpr":2289,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.72333.json.json","assembly_accession":"GCA_017355085.1","genome_id":"562.72333","genome_name":"Escherichia coli strain P3","strain":"strain P3","serovar":"","phylogroup":"A","MLST":165,"mash_cluster":22,"isolation_source":"Cattle hide","isolation_country":"USA","geographic_location":"USA: South Central","host_name":"cattle","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4876886.0,"gc_content":50.78027,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4849.0,"refseq_cds":4563.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore","sequencing_depth":"151.0x","assembly_method":"Unicycler v. DECEMBER-2019","sequencing_centers":"Texas A&M","completion_date":"2021-03-15T00:00:00Z","collection_date":"2005","bioproject_accession":"PRJNA669528","biosample_accession":"SAMN16454214","genbank_accessions":"CP063956,CP063957","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from cattle isolates at Iowa State University","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:https://doi.org/10.4315/0362-028x-68.12.2580","comments":"This is a non-pathogenic/toxigenic E. coli strain that has been recommended by the USDA for use as a surrogate indicator organism to measure changes in microbial counts. This isolate was originally isolated from cattle isolates at Iowa State University. It has been verified to lack by the E. coli Reference Center of Pennsylvania State University, as well as has been reported by the depositor to express no cytotoxicity when cultured with African green monkey kidney (Vero) cells. Further analysis incorporating whole genome sequencing by the current submitter also demonstrates a lack of virulence. This isolate was purchased from the American Type Culture Collection (ATCC), and the current sequence data was generated by both the Illumina MiSeq and Oxford Nanopore MinION platforms.For further information please see the following:https://www.atcc.org/products/all/BAA-1428.aspx#generalinformationhttps://doi.org/10.4315/0362-028x-68.12.2580","n_reactions":2732,"n_metabolites":1938,"n_genes":1529,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.63042.json.json","assembly_accession":"GCA_013426115.1","genome_id":"562.63042","genome_name":"Escherichia coli strain 005008","strain":"strain 005008","serovar":"","phylogroup":"A","MLST":3835,"mash_cluster":21,"isolation_source":"abdominal drainage","isolation_country":"China","geographic_location":"China: Chengdu, Sichuan","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5121313.0,"gc_content":50.66931,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5185.0,"refseq_cds":4854.0,"sequencing_platform":"Illumina HiSeq; Oxford Nanopore MiniION","sequencing_depth":"150.0x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"West China Hospital, Sichuan University","completion_date":"2020-07-20T00:00:00Z","collection_date":"30-Nov-2012","bioproject_accession":"PRJNA418674","biosample_accession":"SAMN15447143","genbank_accessions":"CP058661,CP058665,CP058662,CP058663,CP058664","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:pure culture","comments":"The Genome sequencing and assembly of Escherichia spp.","n_reactions":2732,"n_metabolites":1938,"n_genes":1528,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.45436.json.json","assembly_accession":"GCA_004138625.1","genome_id":"562.45436","genome_name":"Escherichia coli strain Ec-20Lar","strain":"strain Ec-20Lar","serovar":"","phylogroup":"F","MLST":648,"mash_cluster":9,"isolation_source":"Clinical material","isolation_country":"Greece","geographic_location":"Greece","host_name":"Human, Homo sapiens","host_health":"Colonization","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5083560.0,"gc_content":50.611908,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5087.0,"refseq_cds":4862.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"533.0x","assembly_method":"HGAP v. 4","sequencing_centers":"University Hospital of Larissa","completion_date":"2019-02-05T00:00:00Z","collection_date":"2018","bioproject_accession":"PRJNA515400","biosample_accession":"SAMN10754569","genbank_accessions":"CP035317","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:University Hospital of Larissa","comments":"ST648 Escherichia coli from a Greek hospital","n_reactions":2733,"n_metabolites":1944,"n_genes":1512,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GRC","country":"Greece"},{"gem_file":"376725.3.json.json","assembly_accession":"GCA_005037795.2","genome_id":"376725.3","genome_name":"Escherichia coli O103:H2 strain FWSEC0007","strain":"O103:H2 strain FWSEC0007","serovar":"O103:H2","phylogroup":"B1","MLST":17,"mash_cluster":26,"isolation_source":"Clinical: Human (Homo sapiens)","isolation_country":"Canada","geographic_location":"Canada:Manitoba,Winnipeg","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5470829.0,"gc_content":50.687874,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5856.0,"refseq_cds":5741.0,"sequencing_platform":"Illumina MiSeq;Oxford Nanopore MinION","sequencing_depth":"103.12x;58.53x","assembly_method":"Unicycler;Canu v. 0.4.4.0;1.7","sequencing_centers":"National Microbiology Laboratory","completion_date":"2019-05-03T00:00:00Z","collection_date":"2004","bioproject_accession":"PRJNA287560","biosample_accession":"SAMN08768108","genbank_accessions":"NJGQ01000000","refseq_accessions":"","genome_status":"Complete","taxon_id":376725.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"is from Environmental, animal husbandry, food samples, and medical isolates","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"Mesophilic","optimal_temperature":"37 C","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"collected_by:National Microbiology Laboratory: Public Health Agency of Canada","comments":"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.","n_reactions":2732,"n_metabolites":1939,"n_genes":1531,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.34086.json.json","assembly_accession":"GCA_003571685.1","genome_id":"562.34086","genome_name":"Escherichia coli strain AR_0013","strain":"strain AR_0013","serovar":"","phylogroup":"F","MLST":62,"mash_cluster":7,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5481110.0,"gc_content":50.75948,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5800.0,"refseq_cds":5632.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"160x","assembly_method":"canu v. 1.6","sequencing_centers":"Centers for Disease Control and Prevention","completion_date":"2018-09-16T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA292901","biosample_accession":"SAMN04014854","genbank_accessions":"CP032204,CP032205","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"Susceptible;Resistant;Susceptible-dose dependent;Not defined","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Collection of bacterial pathogens that demonstrate a range of carbapenem susceptibility","n_reactions":2733,"n_metabolites":1948,"n_genes":1532,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.28563.json.json","assembly_accession":"GCA_002999075.1","genome_id":"562.28563","genome_name":"Escherichia coli strain AR_0374","strain":"strain AR_0374","serovar":"","phylogroup":"B1","MLST":156,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5022669.0,"gc_content":50.848305,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":4914.0,"refseq_cds":4834.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"18.16x","assembly_method":"SMRT v. 2.3.0; HGAP v. 3.0; SPAdes v.","sequencing_centers":"FDA/CDC","completion_date":"2018-04-25T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA316321","biosample_accession":"SAMN07291517","genbank_accessions":"CP027126,CP027128,CP027127,CP027125","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"Susceptible;Resistant;Not defined","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The AR Isolate Bank is a centralized repository of microbial pathogens with well-characterized resistance profiles that are assembled by CDC in collaboration with the Food and Drug Administration (FDA). The AR Bank is available to support and advance development of diagnostic devices and antimicrobial drug products. The AR Isolate Bank also supports the National Action Plan for Combating Antibiotic Resistance Bacteria by advancing the development of diagnostic tests to identify and characterize resistant bacteria, and by accelerating research and development for new antibiotics.The AR Isolate Bank includes collections of bacterial pathogens that are associated with known or emerging resistance mechanisms. Since its launch in July 2015, the AR Bank continues to grow and will eventually include genera and species such as Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus, Enterococcus, Streptococcus, Salmonella, and Neisseria gonorrhoeae.Each pathogen listed on this web site includes information regarding its susceptibility and/or resistance profile(s), known resistance biomarkers, isolate characteristics, and associated data in PDF.Use this web site to search through pathogen panels, find additional information about the available isolates, and find procedures for requesting panels.","n_reactions":2712,"n_metabolites":1879,"n_genes":1464,"n_exchange":331,"n_with_gpr":2266,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.70517.json.json","assembly_accession":"GCA_016776045.1","genome_id":"562.70517","genome_name":"Escherichia coli strain RIVM_C018563","strain":"strain RIVM_C018563","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5180503.0,"gc_content":50.52519,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5129.0,"refseq_cds":4845.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"National Institute for Public Health and the Environment","completion_date":"2021-02-01T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA691727","biosample_accession":"SAMN17373180","genbank_accessions":"CP068804","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:chromosome","comments":"OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2731,"n_metabolites":1936,"n_genes":1517,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"2778656.3.json.json","assembly_accession":"GCA_015571715.1","genome_id":"2778656.3","genome_name":"Escherichia coli O20:H12 strain Res13-Lact-PEB17-18","strain":"O20:H12 strain Res13-Lact-PEB17-18","serovar":"O20:H12","phylogroup":"C","MLST":88,"mash_cluster":25,"isolation_source":"feces","isolation_country":"Canada","geographic_location":"Canada: Quebec","host_name":"Pig, Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5190756.0,"gc_content":50.688164,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5247.0,"refseq_cds":4922.0,"sequencing_platform":"Oxford Nanopore MinION and Illumina MiSeq","sequencing_depth":"1.00x","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Government of Canada","completion_date":"2020-11-18T00:00:00Z","collection_date":"08-May-2017","bioproject_accession":"PRJNA662792","biosample_accession":"SAMN16304208","genbank_accessions":"CP062855,CP062856,CP062857,CP062858","refseq_accessions":"","genome_status":"Complete","taxon_id":2778656.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Agriculture and Agri-Food Canada","comments":"The majority of antibiotics sold are administered to livestock, presumably promoting the development and spread of antibiotic resistance genes in food-borne pathogens such as Enterobacteriaceae producing extended spectrum beta-lactamases (ESBL). Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. The major goal of the study was to characterize cefotaxime-resistant bacteria isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2732,"n_metabolites":1936,"n_genes":1529,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.13964.json.json","assembly_accession":"GCF_900096845.1","genome_id":"562.13964","genome_name":"Escherichia coli strain 106","strain":"strain 106","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4638126.0,"gc_content":50.83,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4520.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UNIVERSITY OF EXETER","completion_date":"2017-01-02T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB15352","biosample_accession":"SAMEA4444107","genbank_accessions":"LT615377","refseq_accessions":"NZ_LT615377.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli\u2019s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a \u2018trade-up\u2019 is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic\\; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.","n_reactions":2732,"n_metabolites":1935,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.60277.json.json","assembly_accession":"GCA_012934765.1","genome_id":"562.60277","genome_name":"Escherichia coli strain SCU-387","strain":"strain SCU-387","serovar":"","phylogroup":"B2","MLST":14,"mash_cluster":6,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5514160.0,"gc_content":50.49032,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5666.0,"refseq_cds":5241.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"18x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-04-30T00:00:00Z","collection_date":"2018","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609795","genbank_accessions":"CP051688,CP051689,CP051690,CP051691","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2733,"n_metabolites":1947,"n_genes":1469,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.70732.json.json","assembly_accession":"GCA_016889185.1","genome_id":"562.70732","genome_name":"Escherichia coli strain FDAARGOS_1257 strain Not applicable","strain":"","serovar":"","phylogroup":"B2","MLST":127,"mash_cluster":6,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5311839.0,"gc_content":50.402073,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5311.0,"refseq_cds":4972.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"996.18x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-15T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357399","genbank_accessions":"CP069480,CP069481","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1257","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2752,"n_metabolites":2023,"n_genes":1659,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.495.json.json","assembly_accession":"GCA_017165335.1","genome_id":"83334.495","genome_name":"Escherichia coli O157:H7 strain Z892","strain":"O157:H7 strain Z892","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5603028.0,"gc_content":50.47867,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5816.0,"refseq_cds":5418.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"106.36268104023735x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327590","genbank_accessions":"CP062758,CP062759,CP062760","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:IPRAVE Consortium","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1485,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_020881875.1.json.json","assembly_accession":"GCF_020881875.1","genome_id":"GCF_020881875.1","genome_name":"Escherichia 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The isolates included demonstrate varied susceptibility patterns to antibiotics. These susceptibility patterns are representative of the diversity of susceptibility identified in surveillance isolates collected in the United States.","n_reactions":2731,"n_metabolites":1938,"n_genes":1488,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.69647.json.json","assembly_accession":"GCA_016592875.1","genome_id":"562.69647","genome_name":"Escherichia coli strain 2018-18.25PC","strain":"strain 2018-18.25PC","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":22,"isolation_source":"rectal swab","isolation_country":"Viet Nam","geographic_location":"Viet Nam:Thai Binh","host_name":"Pig, Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4694979.0,"gc_content":50.861633,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4571.0,"refseq_cds":4359.0,"sequencing_platform":"Miseq","sequencing_depth":"691x","assembly_method":"Canu v. 1.8","sequencing_centers":"Osaka Institute of Public Health","completion_date":"2020-12-08T00:00:00Z","collection_date":"2018-08-08","bioproject_accession":"PRJDB8858","biosample_accession":"SAMD00233763","genbank_accessions":"AP023286","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The purpose of the study is to investigate the antimicrobial-resistant bacteria in food, livestock-, and human-feces samples using genetic analysis for clarifying the dissemination of resistant bacteria in a community.","n_reactions":2734,"n_metabolites":1934,"n_genes":1527,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"VNM","country":"Vietnam"},{"gem_file":"562.63856.json.json","assembly_accession":"GCA_014170635.1","genome_id":"562.63856","genome_name":"Escherichia coli strain 81.1","strain":"strain 81.1","serovar":"","phylogroup":"G","MLST":3258,"mash_cluster":2,"isolation_source":"Turkey's","isolation_country":"Canada","geographic_location":"Canada","host_name":"Turkey","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5474731.0,"gc_content":50.758015,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5584.0,"refseq_cds":5208.0,"sequencing_platform":"Oxford Nanopore MinION","sequencing_depth":"139x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"University of Guelph","completion_date":"2020-08-12T00:00:00Z","collection_date":"2016/2017","bioproject_accession":"PRJNA596173","biosample_accession":"SAMN13613899","genbank_accessions":"CP059913,CP059914,CP059915,CP059916","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from Turkey's in Canada","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:fecal","comments":"Chromosomes and plasmids were assembled from E. coli isolated from Turkey's in Canada. Both long reads (Oxford Nanopore) and short reads (Illumina) were used.","n_reactions":2733,"n_metabolites":1943,"n_genes":1485,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.77537.json.json","assembly_accession":"GCA_910664945.1","genome_id":"562.77537","genome_name":"Escherichia coli strain TA321 / Oneg:H31 / fimH31 / 6968 (ST Warwick) strain TA321 / Oneg:H31 / fimH31 / 6968 (ST Warwick) strain TA321 / Oneg:H31 / fimH31 / 6968 (ST Warwick)","strain":"strain TA321 / Oneg:H31 / fimH31 / 6968 (ST Warwick) strain TA321 / Oneg:H31 / fimH31 / 6968 (ST Warwick) strain TA321 / Oneg:H31 / fimH31 / 6968 (ST Warwick)","serovar":"","phylogroup":"E","MLST":6968,"mash_cluster":20,"isolation_source":"phylogroupE","isolation_country":"Australia","geographic_location":"Australia","host_name":"Trichosurus vulpecula","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5322337.0,"gc_content":50.532227,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5321.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UMR 1137 IAME","completion_date":"2021-07-06T00:00:00Z","collection_date":"1995","bioproject_accession":"PRJEB39628","biosample_accession":"SAMEA8952633","genbank_accessions":"OU349846","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"host_health_state:healthy","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PhylogroupE","n_reactions":2730,"n_metabolites":1936,"n_genes":1486,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"585035.6.json.json","assembly_accession":"GCA_000026285.1","genome_id":"585035.6","genome_name":"Escherichia coli S88","strain":"S88","serovar":"serovar O45","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"case of neonatal meningitis","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Gastroenteritis","genome_length":5166121.0,"gc_content":50.6,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5120.0,"refseq_cds":4832.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Genoscope","completion_date":"2008-12-18T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA33375","biosample_accession":"SAMEA3138231","genbank_accessions":"CU928161,CU928146","refseq_accessions":"NC_011742,NC_011747","genome_status":"Complete","taxon_id":585035.0,"organism_name":"Escherichia coli S88","pathovar":"ExPEC","antimicrobial_resistance":"","culture_collection":"","publication":"19165319,19307211","isolation_comments":"isolated from a case of neonatal meningitis and will be used for comparative analysis","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"Yes","temperature_range":"Mesophilic","optimal_temperature":"-","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"Escherichia coli S88. Escherichia coli S88 is a serotype O45:K1 strain isolated from a case of neonatal meningitis and will be used for comparative analysis.","n_reactions":2732,"n_metabolites":1944,"n_genes":1453,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"364106.45.json.json","assembly_accession":"GCA_014930875.1","genome_id":"364106.45","genome_name":"Escherichia coli UTI89","strain":"UTI89","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"urine","isolation_country":"India","geographic_location":"India: Thanjavur","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5065741.0,"gc_content":50.604206,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4941.0,"refseq_cds":"","sequencing_platform":"Illumina MiSeq","sequencing_depth":"10.0x","assembly_method":"BRESEQ v. 0.33.1","sequencing_centers":"SASTRA University","completion_date":"2020-10-25T00:00:00Z","collection_date":"20-Sep-2018","bioproject_accession":"PRJNA666979","biosample_accession":"SAMN16339622","genbank_accessions":"CP062985","refseq_accessions":"","genome_status":"Complete","taxon_id":364106.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Bacterial culture","comments":"From uropathogenic E.coli UTI89 strain we are able to get variant matrix producing colonies. 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These sequence will help to understand the variants between ancestral strain and variant strain.","n_reactions":2733,"n_metabolites":1946,"n_genes":1454,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"IND","country":"India"},{"gem_file":"562.70516.json.json","assembly_accession":"GCA_016776065.1","genome_id":"562.70516","genome_name":"Escherichia coli strain RIVM_C017997","strain":"strain RIVM_C017997","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5174511.0,"gc_content":50.45663,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5112.0,"refseq_cds":4820.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"National Institute for Public Health and the Environment","completion_date":"2021-02-01T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA691727","biosample_accession":"SAMN17373173","genbank_accessions":"CP068800","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:chromosome","comments":"OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2752,"n_metabolites":2027,"n_genes":1742,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"562.15199.json.json","assembly_accession":"GCF_002012065.1","genome_id":"562.15199","genome_name":"Escherichia coli strain Ecol_656","strain":"strain Ecol_656","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"USA","geographic_location":"USA: Caguas","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5405139.0,"gc_content":50.8,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5758.0,"refseq_cds":5690.0,"sequencing_platform":"PacBio","sequencing_depth":"XX","assembly_method":"HGAP v. unspecified","sequencing_centers":"University of Oxford","completion_date":"2017-03-03T00:00:00Z","collection_date":"2012","bioproject_accession":"PRJNA316786","biosample_accession":"SAMN05511161","genbank_accessions":"CP018979,CP018978,CP018977","refseq_accessions":"NZ_CP018979.1,NZ_CP018978.1,NZ_CP018977.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART)","comments":"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.","n_reactions":2711,"n_metabolites":1877,"n_genes":1409,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.28398.json.json","assembly_accession":"GCA_002952955.1","genome_id":"562.28398","genome_name":"Escherichia coli strain 2_0","strain":"2_0","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4651848.0,"gc_content":50.804993,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4545.0,"refseq_cds":"","sequencing_platform":"illumina","sequencing_depth":"100x","assembly_method":"unknown v. not applicable","sequencing_centers":"University of Texas at Austin","completion_date":"2018-02-01T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA430697","biosample_accession":"SAMN08380003","genbank_accessions":"CP026359","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:not applicable","comments":"We have carried out directed evolution experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine across from amber codons, creating a 21 amino acid genetic code in which the amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.51584.json.json","assembly_accession":"GCA_008926145.1","genome_id":"562.51584","genome_name":"Escherichia coli strain ERL06-2497","strain":"strain ERL06-2497","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"bovine","isolation_country":"New Zealand","geographic_location":"New Zealand","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5663907.0,"gc_content":50.497757,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":6077.0,"refseq_cds":5795.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"351x","assembly_method":"HGAP v. 2.3.0","sequencing_centers":"United State Department of Agriculture","completion_date":"2019-10-09T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA494713","biosample_accession":"SAMN10177965","genbank_accessions":"CP032797,CP032798,CP032799,CP032800","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Not collected","comments":"The aim of this project is to provided complete closed Shiga toxin-containing Escherichia coli O157:H7 genomes from New Zealand to use for genomic comparison with STEC O157:H7 strains from other countries.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NZL","country":"New Zealand"},{"gem_file":"562.29129.json.json","assembly_accession":"GCA_003018275.1","genome_id":"562.29129","genome_name":"Escherichia coli strain 2014C-3097","strain":"strain 2014C-3097","serovar":"O181:H49","phylogroup":"B1","MLST":173,"mash_cluster":26,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5285744.0,"gc_content":50.80159,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5278.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"60.29x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Aug-2013","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08579582","genbank_accessions":"CP027449,CP027450,CP027451","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2732,"n_metabolites":1937,"n_genes":1513,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.60613.json.json","assembly_accession":"GCA_013201215.1","genome_id":"562.60613","genome_name":"Escherichia coli strain CP61_Sichuan","strain":"strain CP61_Sichuan","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":22,"isolation_source":"slaughterhouse","isolation_country":"China","geographic_location":"China: Sichuan","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4763818.0,"gc_content":50.929676,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4774.0,"refseq_cds":4482.0,"sequencing_platform":"Illumina; Oxford Nanopore MiniION","sequencing_depth":"100x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Yangzhou University","completion_date":"2020-05-31T00:00:00Z","collection_date":"July-2016","bioproject_accession":"PRJNA633463","biosample_accession":"SAMN14944004","genbank_accessions":"CP053730,CP053729,CP053728","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Comprehensive genomic understanding of coevolution of mcr genes in E. coli strains via nanopore sequencing","n_reactions":2711,"n_metabolites":1877,"n_genes":1464,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.19210.json.json","assembly_accession":"GCA_002310715.1","genome_id":"562.19210","genome_name":"Escherichia coli strain 1223","strain":"strain 1223","serovar":"","phylogroup":"A","MLST":744,"mash_cluster":21,"isolation_source":"urinary tract infections","isolation_country":"United Kingdom","geographic_location":"United Kingdom: Scotland, Edinburgh","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":4951571.0,"gc_content":50.63,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5159.0,"refseq_cds":5057.0,"sequencing_platform":"PacBio","sequencing_depth":"20x","assembly_method":"De-novo v. Celera Assembler 8.3","sequencing_centers":"The Roslin Institute","completion_date":"2017-09-18T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA402083","biosample_accession":"SAMN07618122","genbank_accessions":"CP023383,CP023384,CP023385","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from urinary tract infections in dogs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.","n_reactions":2733,"n_metabolites":1938,"n_genes":1525,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"83334.293.json.json","assembly_accession":"GCA_005885915.1","genome_id":"83334.293","genome_name":"Escherichia coli O157:H7 strain ECP17-1298","strain":"O157:H7 strain ECP17-1298","serovar":"serovar Typhimurium","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:NY","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5550459.0,"gc_content":50.465195,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5840.0,"refseq_cds":5521.0,"sequencing_platform":"PacBio","sequencing_depth":"270x","assembly_method":"HGAP v. 3","sequencing_centers":"FDA Center for Food Safety and Applied Nutrition","completion_date":"2019-05-29T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA507262","biosample_accession":"SAMN11787763","genbank_accessions":"CP040570,CP040571","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CDC","comments":"Whole genome sequencing of cultured foodborne bacterial pathogens collected from the 2017 GenomeTrakr/PulseNet proficiency testing exercise. Six isolates were distributed for sequencing: 4 Salmonella enterica subsp. enterica serovar Typhimurium and 2 E.coli O157:H7 isolates.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.5742.json.json","assembly_accession":"GCA_000801185.1","genome_id":"562.5742","genome_name":"Escherichia coli 94-3024","strain":"94-3024","serovar":"","phylogroup":"B1","MLST":672,"mash_cluster":26,"isolation_source":"Montana milk 1994 outbreak strain fromCDC","isolation_country":"USA","geographic_location":"USA: Montana","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5064032.0,"gc_content":50.66,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4880.0,"refseq_cds":4557.0,"sequencing_platform":"Sequence generated by Ion Torrent and","sequencing_depth":">30x","assembly_method":"CLC Genomics Workbench v. 7.0; Celera","sequencing_centers":"USDA-ARS","completion_date":"2014-12-15T00:00:00Z","collection_date":"1994","bioproject_accession":"PRJNA253936","biosample_accession":"SAMN03262652","genbank_accessions":"CP009106.1,CP009107.1","refseq_accessions":"NZ_CP009106.1,NZ_CP009107.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Complete Genome Sequence and Comparison of Two Shiga Toxin-Producing Escherichia coli O104 Strains","n_reactions":2732,"n_metabolites":1939,"n_genes":1520,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_000010385.1.json.json","assembly_accession":"GCF_000010385.1","genome_id":"GCF_000010385.1","genome_name":"Escherichia coli SE11","strain":"SE11","serovar":"","phylogroup":"B1","MLST":156,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMD00061087","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":409438.0,"organism_name":"Escherichia coli SE11","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1937,"n_genes":1527,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.53935.json.json","assembly_accession":"GCA_009671125.1","genome_id":"562.53935","genome_name":"Escherichia coli strain 1919D62","strain":"strain 1919D62","serovar":"","phylogroup":"A","MLST":7131,"mash_cluster":22,"isolation_source":"feces","isolation_country":"China","geographic_location":"China:Henan","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4969394.0,"gc_content":50.522034,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4930.0,"refseq_cds":4664.0,"sequencing_platform":"Illumina MiSeq; PacBio","sequencing_depth":"432.0x","assembly_method":"A5-miseeq v. v20150522; CANU v. v1.4","sequencing_centers":"Henan Agricultural University","completion_date":"2019-11-19T00:00:00Z","collection_date":"2019-07-01","bioproject_accession":"PRJNA588386","biosample_accession":"SAMN13242790","genbank_accessions":"CP046009,CP046007,CP046008","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:mixed culture","comments":"The goal of this project is to identify Escherichia coli strain 1919D62","n_reactions":2711,"n_metabolites":1877,"n_genes":1459,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"1248823.7.json.json","assembly_accession":"GCA_000671295.1","genome_id":"1248823.7","genome_name":"Escherichia coli O145:H28 str. RM12581","strain":"O145:H28 str. 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Escherichia coli O145:H28 strain RM12581 was originally isolated from bagged romaine lettuce. 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Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2732,"n_metabolites":1941,"n_genes":1512,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"83334.368.json.json","assembly_accession":"GCA_013167815.1","genome_id":"83334.368","genome_name":"Escherichia coli O157:H7 strain F1273","strain":"O157:H7 strain F1273","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"beef","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5723703.0,"gc_content":50.482265,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":6064.0,"refseq_cds":5780.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"433x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11229487","genbank_accessions":"CP038376,CP038379,CP038377,CP038378","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.74541.json.json","assembly_accession":"GCA_017598885.1","genome_id":"562.74541","genome_name":"Escherichia coli strain GDQ20D15","strain":"strain GDQ20D15","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"fecal sample","isolation_country":"China","geographic_location":"China:Guangdong, Zhaoqing","host_name":"duck","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5136696.0,"gc_content":50.417,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5183.0,"refseq_cds":4843.0,"sequencing_platform":"PacBio","sequencing_depth":"85.12x","assembly_method":"HGAP v. 4","sequencing_centers":"SouthChina Agriculture University","completion_date":"2021-03-28T00:00:00Z","collection_date":"2020-08-02","bioproject_accession":"PRJNA716615","biosample_accession":"SAMN18440216","genbank_accessions":"JAGFYB010000001,JAGFYB010000003,JAGFYB010000002","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"direct submission","n_reactions":2733,"n_metabolites":1939,"n_genes":1534,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.72332.json.json","assembly_accession":"GCA_017355125.1","genome_id":"562.72332","genome_name":"Escherichia coli strain P68","strain":"strain P68","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"Cattle hide","isolation_country":"USA","geographic_location":"USA: South Central","host_name":"cattle","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4889555.0,"gc_content":50.736465,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4873.0,"refseq_cds":4601.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore","sequencing_depth":"135.0x","assembly_method":"Unicycler v. DECEMBER-2019","sequencing_centers":"Texas A&M","completion_date":"2021-03-15T00:00:00Z","collection_date":"2005","bioproject_accession":"PRJNA669524","biosample_accession":"SAMN16454191","genbank_accessions":"CP063958","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from cattle isolates at Iowa State University","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:https://doi.org/10.4315/0362-028x-68.12.2580","comments":"This is a non-pathogenic/toxigenic E. coli strain that has been recommended by the USDA for use as a surrogate indicator organism to measure changes in microbial counts. This isolate was originally isolated from cattle isolates at Iowa State University. It has been verified to lack by the E. coli Reference Center of Pennsylvania State University, as well as has been reported by the depositor to express no cytotoxicity when cultured with African green monkey kidney (Vero) cells. Further analysis incorporating whole genome sequencing by the current submitter also demonstrates a lack of virulence. This isolate was purchased from the American Type Culture Collection (ATCC), and the current sequence data was generated by both the Illumina MiSeq and Oxford Nanopore MinION platforms.For further information please see the following:https://www.atcc.org/products/all/BAA-1431.aspx#generalinformationhttps://doi.org/10.4315/0362-028x-68.12.2580","n_reactions":2732,"n_metabolites":1939,"n_genes":1549,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83333.104.json.json","assembly_accession":"GCF_000974465.1","genome_id":"83333.104","genome_name":"Escherichia coli K-12 strain ER3440","strain":"K-12 strain ER3440","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4604543.0,"gc_content":50.81,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4630.0,"refseq_cds":4369.0,"sequencing_platform":"PacBio","sequencing_depth":"50-200","assembly_method":"SMRT Analysis v. 2.3","sequencing_centers":"New England Biolabs","completion_date":"2015-04-21T00:00:00Z","collection_date":"Jun-14","bioproject_accession":"PRJNA271807","biosample_accession":"SAMN03277613","genbank_accessions":"CP010439","refseq_accessions":"NZ_CP010439.1","genome_status":"Complete","taxon_id":83333.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"fhuA2::IS2 _(lacZ)4826 glnX44 trpE31 _(hisG)1 gyrA96 recA::cat(FRT)(CmR) recD1014 rpsL104(StrR) xyl-7 mtlA2(Fs) metB1(FS) _(yjiT-mrr)::npt(KnR) serB28","substrain":"","additional_metadata":"identified_by:Anthony Kingston;sample_type:Cell Culture","comments":"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.","n_reactions":2731,"n_metabolites":1936,"n_genes":1558,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1038927.45.json.json","assembly_accession":"GCA_005014075.1","genome_id":"1038927.45","genome_name":"Escherichia coli O104:H4 strain FWSEC0009","strain":"O104:H4 strain FWSEC0009","serovar":"O104:H4","phylogroup":"B1","MLST":678,"mash_cluster":26,"isolation_source":"Clinical: Human (Homo sapiens)","isolation_country":"Germany","geographic_location":"Germany","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5442997.0,"gc_content":50.65053,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5768.0,"refseq_cds":5654.0,"sequencing_platform":"Illumina MiSeq;Oxford Nanopore MinION","sequencing_depth":"65.55x;110.27x","assembly_method":"Unicycler;Canu v. 0.4.4.0;1.7","sequencing_centers":"National Microbiology Laboratory","completion_date":"2019-05-01T00:00:00Z","collection_date":"2011","bioproject_accession":"PRJNA287560","biosample_accession":"SAMN08768110","genbank_accessions":"CP031902,CP031903,CP031904,CP031905","refseq_accessions":"","genome_status":"Complete","taxon_id":1038927.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"is from Environmental, animal husbandry, food samples, and medical isolates","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"Mesophilic","optimal_temperature":"37 C","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"collected_by:Laboratory for Foodborne Zoonoses: Public Health Agency of Canada","comments":"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.","n_reactions":2753,"n_metabolites":2027,"n_genes":1741,"n_exchange":331,"n_with_gpr":2307,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"562.48251.json.json","assembly_accession":"GCA_900622685.1","genome_id":"562.48251","genome_name":"Escherichia coli strain MS14387","strain":"strain MS14387","serovar":"","phylogroup":"D","MLST":69,"mash_cluster":13,"isolation_source":"blood","isolation_country":"Australia","geographic_location":"Australia","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5232331.0,"gc_content":50.759193,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5157.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Bioplatforms Australia","completion_date":"2019-01-10T00:00:00Z","collection_date":"2009-09-03","bioproject_accession":"PRJEB29930","biosample_accession":"SAMEA5128445","genbank_accessions":"LR130564,LR130565,LR130566","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"102.100.100.25769","publication":"","isolation_comments":"","other_clinical":"host_health_state:diseased","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Escherichia coli.","n_reactions":2732,"n_metabolites":1940,"n_genes":1497,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"562.50518.json.json","assembly_accession":"GCA_007109325.1","genome_id":"562.50518","genome_name":"Escherichia coli strain 131","strain":"strain 131","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5316481.0,"gc_content":50.85747,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5512.0,"refseq_cds":5274.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"50x","assembly_method":"HGAP v. 4","sequencing_centers":"Duke University","completion_date":"2019-07-18T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA551684","biosample_accession":"SAMN12163092","genbank_accessions":"CP041556,CP041557,CP041558","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Deverick Anderson","comments":"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2731,"n_metabolites":1937,"n_genes":1468,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.408.json.json","assembly_accession":"GCA_015353135.1","genome_id":"83334.408","genome_name":"Escherichia coli O157:H7 strain Wll001","strain":"O157:H7 strain Wll001","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"China","geographic_location":"China: Wuhan","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5586104.0,"gc_content":50.4885,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5830.0,"refseq_cds":5405.0,"sequencing_platform":"PacBio","sequencing_depth":"120.0x","assembly_method":"HGAP v. 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This strain was isolated from the stool of a food-poisoned patient in Seoul, Korea.","n_reactions":2732,"n_metabolites":1942,"n_genes":1520,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"KOR","country":"South Korea"},{"gem_file":"562.66856.json.json","assembly_accession":"GCA_014679325.1","genome_id":"562.66856","genome_name":"Escherichia coli strain HUE1","strain":"strain HUE1","serovar":"","phylogroup":"A","MLST":48,"mash_cluster":22,"isolation_source":"urinary catheter","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4742352.0,"gc_content":50.81833,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":4671.0,"refseq_cds":4462.0,"sequencing_platform":"Illumina MiSeq; Nanopore MinION","sequencing_depth":"220x","assembly_method":"Unicycler v. 0.4.8-beta","sequencing_centers":"Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Department of Veterinary Medicine, Rakuno Gakuen University","completion_date":"2020-09-09T00:00:00Z","collection_date":"2008","bioproject_accession":"PRJDB10417","biosample_accession":"SAMD00241721","genbank_accessions":"AP023427,AP023428,AP023429,AP023430,AP023431,AP023432","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Antimicrobial-resistant bacteria have spread rapidly all over the world and are an important global health issue. Inappropriate use of antibiotics is one of the reasons of their occurrence. In this context, phage therapy, by using bacteriophages which specifically infect to bacteria, has been received significant attention as an alternative approach to classical antibiotic therapy. On the other hand, further understandings of interaction between bacteria and phages are required to develop phage therapy because bacteria can acquire phage-resistance in the therapy. To investigate mechanisms underlying phage infection to the host and identify the receptors, whole genome information is necessary. This study will facilitate the understandings of life cycle of phage and phage-resistance.","n_reactions":2731,"n_metabolites":1941,"n_genes":1519,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_016404015.2.json.json","assembly_accession":"GCF_016404015.2","genome_id":"GCF_016404015.2","genome_name":"Escherichia 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In this study, we employed a combination of a lytic K1 capsule-specific phage, saturated Tn5 transposon mutagenesis, and high-throughput transposon directed insertion-site sequencing (TraDIS) to identify genes associated with K1 capsule production in the clinical urosepsis isolate PA45B.","n_reactions":2732,"n_metabolites":1944,"n_genes":1459,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"562.76468.json.json","assembly_accession":"GCA_018884585.1","genome_id":"562.76468","genome_name":"Escherichia coli strain LSN03-016011/A","strain":"strain LSN03-016011/A","serovar":"","phylogroup":"C","MLST":88,"mash_cluster":25,"isolation_source":"feces","isolation_country":"Turkey","geographic_location":"Turkey","host_name":"Homo 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coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.28408.json.json","assembly_accession":"GCA_002953775.1","genome_id":"562.28408","genome_name":"Escherichia coli strain 7A","strain":"7A","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4651842.0,"gc_content":50.804928,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4545.0,"refseq_cds":"","sequencing_platform":"illumina","sequencing_depth":"100x","assembly_method":"unknown v. not applicable","sequencing_centers":"University of Texas at Austin","completion_date":"2018-02-01T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA430697","biosample_accession":"SAMN08380017","genbank_accessions":"CP026347","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:not applicable","comments":"We have carried out directed evolution experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine across from amber codons, creating a 21 amino acid genetic code in which the amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1446701.4.json.json","assembly_accession":"GCA_002741495.1","genome_id":"1446701.4","genome_name":"Escherichia coli O169:H41 strain F6326-C1","strain":"O169:H41 strain F6326-C1","serovar":"O169:H41","phylogroup":"E","MLST":182,"mash_cluster":20,"isolation_source":"","isolation_country":"United States","geographic_location":"United States","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5157150.0,"gc_content":50.26,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5125.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"78.0x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2017-11-02T00:00:00Z","collection_date":"1998","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN07656210","genbank_accessions":"CP024263,CP024264,CP024265","refseq_accessions":"","genome_status":"Complete","taxon_id":1446701.0,"organism_name":"","pathovar":"ETEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2731,"n_metabolites":1933,"n_genes":1506,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_000017745.1.json.json","assembly_accession":"GCF_000017745.1","genome_id":"GCF_000017745.1","genome_name":"Escherichia coli O139:H28 str. 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WGS was performed to determine genetic determinants in E.coli for different levels of heat resistance and determine the evolution regarding the emergence of heat resistant strains of E.coli in a meat plant setting.","n_reactions":2735,"n_metabolites":1949,"n_genes":1524,"n_exchange":331,"n_with_gpr":2289,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.13782.json.json","assembly_accession":"GCF_001901405.1","genome_id":"562.13782","genome_name":"Escherichia coli strain S50","strain":"strain S50","serovar":"","phylogroup":"B1","MLST":517,"mash_cluster":26,"isolation_source":"forest soil","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4981720.0,"gc_content":50.71,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5121.0,"refseq_cds":4805.0,"sequencing_platform":"Illumina Miseq; Roche 454 GS Junior","sequencing_depth":"30-80x","assembly_method":"Newbler v. 2.7","sequencing_centers":"Nanjing Agricultural University","completion_date":"2016-12-12T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA269191","biosample_accession":"SAMN03252457","genbank_accessions":"CP010238,CP010239","refseq_accessions":"NZ_CP010238.1,NZ_CP010239.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"env_biome:soil","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments","n_reactions":2730,"n_metabolites":1936,"n_genes":1458,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.29038.json.json","assembly_accession":"GCA_003028775.1","genome_id":"562.29038","genome_name":"Escherichia coli strain E24377A","strain":"strain E24377A","serovar":"","phylogroup":"B1","MLST":453,"mash_cluster":26,"isolation_source":"urine","isolation_country":"Pakistan","geographic_location":"Pakistan: Sheikh Zaid Hospital, Lahore","host_name":"Human, Homo sapiens","host_health":"Urinary tract infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4721864.0,"gc_content":50.736443,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4636.0,"refseq_cds":"","sequencing_platform":"Illumina MiSeq","sequencing_depth":"30X","assembly_method":"SPAdes v. 3.10.1","sequencing_centers":"Rehman Medical Institute","completion_date":"2018-04-02T00:00:00Z","collection_date":"06-Dec-2016","bioproject_accession":"PRJNA389368","biosample_accession":"SAMN07196154","genbank_accessions":"CP028308","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Asma Manzoor, Nabila Ishaq","comments":"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","n_reactions":2732,"n_metabolites":1937,"n_genes":1519,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"PAK","country":"Pakistan"},{"gem_file":"562.19202.json.json","assembly_accession":"GCA_002310555.1","genome_id":"562.19202","genome_name":"Escherichia coli strain 1943","strain":"strain 1943","serovar":"","phylogroup":"B1","MLST":539,"mash_cluster":26,"isolation_source":"urinary tract infections","isolation_country":"United Kingdom","geographic_location":"United Kingdom: Scotland, Edinburgh","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":5000721.0,"gc_content":50.75,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5148.0,"refseq_cds":5046.0,"sequencing_platform":"PacBio","sequencing_depth":"20x","assembly_method":"De-novo v. Celera Assembler 8.8","sequencing_centers":"The Roslin Institute","completion_date":"2017-09-18T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA402083","biosample_accession":"SAMN07618127","genbank_accessions":"CP023359,CP023360,CP023361,CP023362","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from urinary tract infections in dogs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.","n_reactions":2732,"n_metabolites":1939,"n_genes":1512,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_020535205.1.json.json","assembly_accession":"GCF_020535205.1","genome_id":"GCF_020535205.1","genome_name":"Escherichia coli","strain":"EC20","serovar":"","phylogroup":"A","MLST":361,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN21906625","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1937,"n_genes":1528,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.61490.json.json","assembly_accession":"GCA_013315675.1","genome_id":"562.61490","genome_name":"Escherichia coli strain SCU-176","strain":"strain SCU-176","serovar":"","phylogroup":"B2","MLST":550,"mash_cluster":6,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5088045.0,"gc_content":50.5315,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":5107.0,"refseq_cds":4797.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"100x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-06-10T00:00:00Z","collection_date":"2017","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14943547","genbank_accessions":"CP054345,CP054346,CP054347,CP054348,CP054349,CP054350,CP054351,CP054352","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2732,"n_metabolites":1945,"n_genes":1457,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.29112.json.json","assembly_accession":"GCA_003018715.1","genome_id":"562.29112","genome_name":"Escherichia coli strain 2013C-3277","strain":"strain 2013C-3277","serovar":"E. coli O26:H11","phylogroup":"B1","MLST":29,"mash_cluster":23,"isolation_source":"Stool","isolation_country":"United States","geographic_location":"United States","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"0-4","body_sample_site":"","disease":"","genome_length":5687465.0,"gc_content":50.638203,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":6018.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"44.034x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Oct-2012","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN02991240","genbank_accessions":"CP027331,CP027332,CP027333,CP027334","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CDC","comments":"PulseNet STEC genome reference library","n_reactions":2733,"n_metabolites":1941,"n_genes":1518,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.70512.json.json","assembly_accession":"GCA_016776145.1","genome_id":"562.70512","genome_name":"Escherichia coli strain RIVM_C028568","strain":"strain RIVM_C028568","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5210247.0,"gc_content":50.67468,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5212.0,"refseq_cds":4882.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"National Institute for Public Health and the Environment","completion_date":"2021-02-01T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA691727","biosample_accession":"SAMN17373187","genbank_accessions":"CP068811","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:chromosome","comments":"OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2732,"n_metabolites":1938,"n_genes":1518,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"2126982.6.json.json","assembly_accession":"GCA_004771135.1","genome_id":"2126982.6","genome_name":"Escherichia coli O18:H1 strain CFSAN067215","strain":"O18:H1 strain CFSAN067215","serovar":"","phylogroup":"B2","MLST":73,"mash_cluster":5,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:CA","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5242835.0,"gc_content":50.63415,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5484.0,"refseq_cds":5362.0,"sequencing_platform":"PacBio","sequencing_depth":"405.0x","assembly_method":"HGAP v. 3.0","sequencing_centers":"FDA/CFSAN","completion_date":"2019-04-11T00:00:00Z","collection_date":"2000","bioproject_accession":"PRJNA230969","biosample_accession":"SAMN08737532","genbank_accessions":"CP028320,CP028321,CP028322,CP028323","refseq_accessions":"","genome_status":"Complete","taxon_id":2126982.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Dudley Lab/Penn State","comments":"Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.","n_reactions":2733,"n_metabolites":1946,"n_genes":1452,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.250.json.json","assembly_accession":"GCA_003028755.1","genome_id":"83334.250","genome_name":"Escherichia coli O157:H7 strain Sakai","strain":"O157:H7 strain Sakai","serovar":"","phylogroup":"B1","MLST":453,"mash_cluster":26,"isolation_source":"urine","isolation_country":"Pakistan","geographic_location":"Pakistan: Sheikh Zaid Hospital, Lahore","host_name":"Human, Homo sapiens","host_health":"Urinary tract infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4709905.0,"gc_content":50.763325,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4637.0,"refseq_cds":"","sequencing_platform":"Illumina MiSeq","sequencing_depth":"30X","assembly_method":"SPAdes v. 3.10.1","sequencing_centers":"Rehman Medical Institute","completion_date":"2018-04-02T00:00:00Z","collection_date":"06-Dec-2016","bioproject_accession":"PRJNA389368","biosample_accession":"SAMN07196155","genbank_accessions":"CP028307","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Asma Manzoor, Nabila Ishaq","comments":"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","n_reactions":2732,"n_metabolites":1936,"n_genes":1512,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"PAK","country":"Pakistan"},{"gem_file":"562.13963.json.json","assembly_accession":"GCF_900096835.1","genome_id":"562.13963","genome_name":"Escherichia coli strain 109","strain":"strain 109","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4638126.0,"gc_content":50.83,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4512.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UNIVERSITY OF EXETER","completion_date":"2017-01-02T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB15352","biosample_accession":"SAMEA4444110","genbank_accessions":"LT615376","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli\u2019s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a \u2018trade-up\u2019 is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic\\; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.","n_reactions":2732,"n_metabolites":1935,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13772.json.json","assembly_accession":"GCF_001901065.1","genome_id":"562.13772","genome_name":"Escherichia coli strain M6","strain":"strain M6","serovar":"","phylogroup":"B1","MLST":278,"mash_cluster":26,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Mouse, Mus 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genes.Scientific treatment and rational drug use of civets for farmers to cure diarrhea diseases are of great significance.","n_reactions":2711,"n_metabolites":1877,"n_genes":1486,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"1412834.4.json.json","assembly_accession":"GCF_000765435.1","genome_id":"1412834.4","genome_name":"Escherichia coli FAP1","strain":"FAP1","serovar":"","phylogroup":"B1","MLST":453,"mash_cluster":26,"isolation_source":"Pig (faeces)","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5254632.0,"gc_content":50.53,"contigs":5.0,"chromosomes":"","plasmids":4.0,"patric_cds":5403.0,"refseq_cds":5011.0,"sequencing_platform":"PacBio","sequencing_depth":"77.0x","assembly_method":"HGAP (part of Pacific 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FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. 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The aim is to define reservoirs and transmission pathways relating to the acquisition of Escherichia coli producing extended-spectrum ?-lactamases (ESBL-EC) in a haematology cohort. The overall approach will be to identify numerous reservoirs of ESBL-EC in a geographically defined area, and use bacterial sequencing combined with mathematical modelling to predict transmission routes between them and the hospital cohort. The hypothesis is that interventions to reduce ESBL-EC carriage and disease in humans are reliant on an understanding of these transmission pathways.","n_reactions":2733,"n_metabolites":1943,"n_genes":1522,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.70602.json.json","assembly_accession":"GCA_016803875.1","genome_id":"562.70602","genome_name":"Escherichia coli strain FHI_NMBU_11","strain":"strain FHI_NMBU_11","serovar":"O128ab:H2","phylogroup":"B1","MLST":25,"mash_cluster":26,"isolation_source":"feces","isolation_country":"Norway","geographic_location":"Norway:South-east","host_name":"Homo sapiens","host_health":"Diarrhea","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5565139.0,"gc_content":50.610416,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5732.0,"refseq_cds":5344.0,"sequencing_platform":"Oxford Nanopore MiniION; 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benzalkonium (BZK), cetrimide (CET), chlorhexidine (CHX), and colistin (COL). Three replicates were created for each compound, generating BZKR1G40, BZKR2G40, BZKR3G40, CETR1G40, CETR2G40, CETR3G40, CHXR1G20, CHXR2G20, CHXR3G20, COLR1G32, COLR2G32, COLR3G32 as well as an unadapted wild-type (WTG40). At the end of the experiment, the BZK-adapted bacteria were tolerant to 72-144 ug/ml of BZK, the CET-adapted bacteria were tolerant to 240 ug/ml of CET, the CHX-adapted bacteria were tolerant to 4.8-9.6 ug/ml of CHX, and the COL-adapted bacteria were tolerant to >300 ug/ml.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"386585.9.json.json","assembly_accession":"GCA_000008865.1","genome_id":"386585.9","genome_name":"Escherichia coli O157:H7 str. Sakai","strain":"O157:H7 str. 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EHEC attaches and effaces to cells in the large intestine.There are numerous differences that distinguish O157:H7 from K-12, hundreds of them associated with genomic islands in either strain, including at least 9 large PAIs in O157:H7 that encode virulence factors. A type III secretion system, the locus of enterocyte effacement, numerous toxins and adhesins, as well as fimbrial gene clusters and iron uptake systems are found in these PAIs. Pathogenicity genes are also found on the plasmid pO157.Escherichia coli O157:H7 strain Sakai. This strain of O157:H7 was isolated in a 1997 outbreak in Sakai, Japan.","n_reactions":2711,"n_metabolites":1877,"n_genes":1426,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"JPN","country":"Japan"},{"gem_file":"562.22326.json.json","assembly_accession":"GCA_002736085.1","genome_id":"562.22326","genome_name":"Escherichia coli strain UFU_EC98","strain":"strain UFU_EC98","serovar":"","phylogroup":"B1","MLST":156,"mash_cluster":26,"isolation_source":"urine","isolation_country":"Brazil","geographic_location":"Brazil: Minas Gerais","host_name":"Human, Homo sapiens","host_health":"Urinary tract infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5017436.0,"gc_content":50.59,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5123.0,"refseq_cds":5048.0,"sequencing_platform":"Illumina HiSeq","sequencing_depth":"134.0x","assembly_method":"CLC Genomics Workbench v. v10","sequencing_centers":"Londrina State University","completion_date":"2017-10-30T00:00:00Z","collection_date":"29-jul-2014","bioproject_accession":"PRJNA413419","biosample_accession":"SAMN07746131","genbank_accessions":"CP024092,CP024093,CP024094,CP024095","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from human urine in 2014","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Federal University of Uberlandia","comments":"Escherichia coli EC98 was isolated from human urine in 2014. The antibiotic resistance is a main characteristic of this strain.","n_reactions":2733,"n_metabolites":1941,"n_genes":1528,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BRA","country":"Brazil"},{"gem_file":"562.74540.json.json","assembly_accession":"GCA_017598855.1","genome_id":"562.74540","genome_name":"Escherichia coli strain GDQ20D112","strain":"strain GDQ20D112","serovar":"","phylogroup":"F","MLST":457,"mash_cluster":11,"isolation_source":"liver sample","isolation_country":"China","geographic_location":"China:Guangdong, Zhaoqing","host_name":"duck","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5637399.0,"gc_content":50.162582,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5673.0,"refseq_cds":5314.0,"sequencing_platform":"PacBio","sequencing_depth":"85.12x","assembly_method":"HGAP v. 4","sequencing_centers":"SouthChina Agriculture University","completion_date":"2021-03-28T00:00:00Z","collection_date":"2020-08-02","bioproject_accession":"PRJNA716615","biosample_accession":"SAMN18440217","genbank_accessions":"JAGFYA010000002,JAGFYA010000003,JAGFYA010000005,JAGFYA010000004,JAGFYA010000001","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:tissue sample","comments":"direct submission","n_reactions":2711,"n_metabolites":1877,"n_genes":1453,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.70770.json.json","assembly_accession":"GCA_016904115.1","genome_id":"562.70770","genome_name":"Escherichia coli strain FDAARGOS_1290 strain Not applicable","strain":"","serovar":"","phylogroup":"D","MLST":69,"mash_cluster":13,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5206932.0,"gc_content":50.695976,"contigs":9.0,"chromosomes":1.0,"plasmids":8.0,"patric_cds":5165.0,"refseq_cds":4883.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"1253.22x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357432","genbank_accessions":"CP070048,CP070049,CP070050,CP070051,CP070052,CP070053,CP070054,CP070055,CP070056","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1290","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2753,"n_metabolites":2026,"n_genes":1730,"n_exchange":331,"n_with_gpr":2307,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"1446746.6.json.json","assembly_accession":"GCA_002741515.1","genome_id":"1446746.6","genome_name":"Escherichia coli O6:H16 strain F6699","strain":"O6:H16 strain F6699","serovar":"O6:H16","phylogroup":"A","MLST":2353,"mash_cluster":22,"isolation_source":"","isolation_country":"United States","geographic_location":"United 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The genomes were assembled using a combination of Nanopore R9.4 and Illumina sequencing data.","n_reactions":2731,"n_metabolites":1938,"n_genes":1452,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.67018.json.json","assembly_accession":"GCA_014863625.1","genome_id":"562.67018","genome_name":"Escherichia coli strain AML001_ev03","strain":"strain AML001_ev03","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"not applicable","isolation_country":"USA","geographic_location":"USA: Boston","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4631469.0,"gc_content":50.778664,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4507.0,"refseq_cds":"","sequencing_platform":"Illumina NextSeq","sequencing_depth":"50x","assembly_method":"breseq v. 0.35.1","sequencing_centers":"Boston University","completion_date":"2020-10-08T00:00:00Z","collection_date":"06-Aug-2020","bioproject_accession":"PRJNA666010","biosample_accession":"SAMN16090674","genbank_accessions":"CP062239","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolate from each separate evolution experiment and the parent strains are provided here","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"Cm resistance","substrain":"","additional_metadata":"sample_type:cell culture;biomaterial_provider:M.J. Dunlop, Boston University, 44 Cummington Mall, Boston, MA 02226;collected_by:A.M. Langevin;passage_history:72 h turbidostat with 1\ufffdg/mL Cm","comments":"In this work, we evolved strains of Escherichia coli with different genotypes related to the AcrAB-TolC efflux pump. Parent strains were either wild type, had the pump overexpressed, or had the pump knocked out. We evolved these three strains under different levels of chloramphenicol. Each parent strain was evolved in an evolution experiment using three biological replicates. The most resistant isolate from each separate evolution experiment and the parent strains are provided here. The goal of this work was to identify which chloramphenicol concentrations promote the evolution of antibiotic resistance and how the presence of the AcrAB-TolC pump impacts this evolution.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.77530.json.json","assembly_accession":"GCA_910664785.1","genome_id":"562.77530","genome_name":"Escherichia coli strain B185 / O148:H10 / fimH562 / 3577 (ST Warwick) strain B185 / O148:H10 / fimH562 / 3577 (ST Warwick) strain B185 / O148:H10 / fimH562 / 3577 (ST Warwick)","strain":"strain B185 / O148:H10 / fimH562 / 3577 (ST Warwick) strain B185 / O148:H10 / fimH562 / 3577 (ST Warwick) strain B185 / O148:H10 / fimH562 / 3577 (ST Warwick)","serovar":"","phylogroup":"E","MLST":3577,"mash_cluster":20,"isolation_source":"phylogroupE","isolation_country":"Australia","geographic_location":"Australia","host_name":"Turdus merula","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5156958.0,"gc_content":50.595005,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5010.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UMR 1137 IAME","completion_date":"2021-07-06T00:00:00Z","collection_date":"2001","bioproject_accession":"PRJEB39628","biosample_accession":"SAMEA8952621","genbank_accessions":"OU349838","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"host_health_state:healthy","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PhylogroupE","n_reactions":2711,"n_metabolites":1877,"n_genes":1422,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"562.19211.json.json","assembly_accession":"GCA_002310735.1","genome_id":"562.19211","genome_name":"Escherichia coli strain 1283","strain":"strain 1283","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"urinary tract infections","isolation_country":"United Kingdom","geographic_location":"United Kingdom: Scotland, Edinburgh","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":4920052.0,"gc_content":50.75,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5103.0,"refseq_cds":5032.0,"sequencing_platform":"PacBio","sequencing_depth":"20x","assembly_method":"De-novo v. Celera Assembler 8.5","sequencing_centers":"The Roslin Institute","completion_date":"2017-09-18T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA402083","biosample_accession":"SAMN07618124","genbank_accessions":"CP023371,CP023372,CP023374,CP023373,CP023375,CP023376","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from urinary tract infections in dogs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.","n_reactions":2732,"n_metabolites":1937,"n_genes":1528,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.58149.json.json","assembly_accession":"GCA_010365465.1","genome_id":"562.58149","genome_name":"Escherichia coli strain 124","strain":"strain 124","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"environment","isolation_country":"Switzerland","geographic_location":"Switzerland","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4910586.0,"gc_content":50.58545,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":4958.0,"refseq_cds":4644.0,"sequencing_platform":"Oxford Nanopore/illumina minniseq","sequencing_depth":"80x","assembly_method":"unicycler v. 0.4.8","sequencing_centers":"University of Zurich","completion_date":"2020-02-09T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA604100","biosample_accession":"SAMN13951920","genbank_accessions":"CP048344,CP048345,CP048346,CP048347,CP048348","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated and completely sequenced","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Carbapenemase-producing Enterobacteriaceae from different environmental sources in Switzerland were isolated and completely sequenced.","n_reactions":2733,"n_metabolites":1939,"n_genes":1534,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHE","country":"Switzerland"},{"gem_file":"GCF_003667405.1.json.json","assembly_accession":"GCF_003667405.1","genome_id":"GCF_003667405.1","genome_name":"Escherichia coli","strain":"W2-5","serovar":"","phylogroup":"B1","MLST":162,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN10230267","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1944,"n_genes":1529,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.28407.json.json","assembly_accession":"GCA_002953755.1","genome_id":"562.28407","genome_name":"Escherichia coli strain 8FA","strain":"8FA","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4651849.0,"gc_content":50.805004,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4538.0,"refseq_cds":"","sequencing_platform":"illumina","sequencing_depth":"100x","assembly_method":"unknown v. not applicable","sequencing_centers":"University of Texas at Austin","completion_date":"2018-02-01T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA430697","biosample_accession":"SAMN08380020","genbank_accessions":"CP026344","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:not applicable","comments":"We have carried out directed evolution experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine across from amber codons, creating a 21 amino acid genetic code in which the amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1055538.8.json.json","assembly_accession":"GCA_014607575.1","genome_id":"1055538.8","genome_name":"Escherichia coli O145 strain RM12522-C8","strain":"O145 strain RM12522-C8","serovar":"","phylogroup":"D","MLST":-1,"mash_cluster":20,"isolation_source":"feces","isolation_country":"USA","geographic_location":"USA: CA","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5505797.0,"gc_content":50.68044,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5795.0,"refseq_cds":5414.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"69.54x","assembly_method":"HGAP v. RS_HGAP Assembly.3","sequencing_centers":"USDA, ARS, WRRC","completion_date":"2020-09-16T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA483500","biosample_accession":"SAMN10887318","genbank_accessions":"CP035767,CP035766","refseq_accessions":"","genome_status":"Complete","taxon_id":1055538.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Complete Genomes of Environmental Shiga Toxin- Producing Escherichia coli O145","n_reactions":2711,"n_metabolites":1877,"n_genes":1425,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.16426.json.json","assembly_accession":"GCA_002116715.2","genome_id":"562.16426","genome_name":"Escherichia coli strain HB-Coli0","strain":"strain HB-Coli0","serovar":"","phylogroup":"B1","MLST":602,"mash_cluster":26,"isolation_source":"intestine","isolation_country":"China","geographic_location":"China: Baoding","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5078176.0,"gc_content":50.7,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5259.0,"refseq_cds":5152.0,"sequencing_platform":"PacBio","sequencing_depth":"300.0x","assembly_method":"SMRT portal v. Version 3.2.0","sequencing_centers":"Agricultural University of Hebei Province","completion_date":"2017-05-01T00:00:00Z","collection_date":"2017-04-21","bioproject_accession":"PRJNA383767","biosample_accession":"SAMN06819205","genbank_accessions":"CP020933,CP020934,CP020935,CP020936","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:single cell","comments":"Analysis of assembling and annotation of whole genome of avian multoyage resistant Escherichia","n_reactions":2733,"n_metabolites":1940,"n_genes":1520,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"83334.491.json.json","assembly_accession":"GCA_017165315.1","genome_id":"83334.491","genome_name":"Escherichia coli O157:H7 strain Z887","strain":"O157:H7 strain Z887","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5625781.0,"gc_content":50.50207,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5856.0,"refseq_cds":5446.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"171.56585192349294x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327589","genbank_accessions":"CP062761,CP062762","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:IPRAVE Consortium","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.17622.json.json","assembly_accession":"GCA_002193095.1","genome_id":"562.17622","genome_name":"Escherichia coli strain H105","strain":"strain H105","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"vaginal swab","isolation_country":"Germany","geographic_location":"Germany","host_name":"Homo sapiens; 55 year old","host_health":"","host_gender":"","host_age":"55 years","body_sample_site":"","disease":"","genome_length":5113241.0,"gc_content":50.78,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5306.0,"refseq_cds":5212.0,"sequencing_platform":"PacBio","sequencing_depth":"86.0x","assembly_method":"HGAP v. 2.3.0","sequencing_centers":"Institute of Medical Microbiology , Justus Liebig University Giessen","completion_date":"2017-06-14T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA387731","biosample_accession":"SAMN07162922","genbank_accessions":"CP021454,CP021871","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Escherichia coli H105","n_reactions":2732,"n_metabolites":1943,"n_genes":1473,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"562.63083.json.json","assembly_accession":"GCA_902810275.1","genome_id":"562.63083","genome_name":"Escherichia coli strain SC422","strain":"strain SC422","serovar":"","phylogroup":"B1","MLST":58,"mash_cluster":26,"isolation_source":"Sediment","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5003951.0,"gc_content":50.625656,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4953.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"MASSEY UNIVERSITY","completion_date":"2020-06-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB36951","biosample_accession":"SAMEA6595219","genbank_accessions":"LR778143","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Mike Sadowsky","comments":"Here we report the complete genomes of 47 Escherichia coli natural isolates, sampled from watersheds located at (46\u00b042\u203204\"N, 92\u00b012\u203226\"W) in Duluth, Minnesota. The genomes were assembled using a combination of Nanopore R9.4 and Illumina sequencing data.","n_reactions":2732,"n_metabolites":1937,"n_genes":1526,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.45710.json.json","assembly_accession":"GCA_004368015.1","genome_id":"562.45710","genome_name":"Escherichia coli strain FORC_081","strain":"strain FORC_081","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"chicken","isolation_country":"South Korea","geographic_location":"South Korea","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5135611.0,"gc_content":50.575016,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5281.0,"refseq_cds":5270.0,"sequencing_platform":"PacBio","sequencing_depth":"","assembly_method":"PacBio SMRT v. 2.3.0","sequencing_centers":"Food-borne Pathogen Omics Research Center,FORC","completion_date":"2019-03-25T00:00:00Z","collection_date":"2007-02-09","bioproject_accession":"PRJNA437355","biosample_accession":"SAMN08660891","genbank_accessions":"CP029057,CP029058,CP029059,CP029060,CP029061","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from chicken in South Korea","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Seoul National University","comments":"Escherichia coli FORC_081 Complete genome sequencingEscherichia coli is one of the well-known food-borne pathogen. It was isolated from chicken in South Korea.","n_reactions":2733,"n_metabolites":1938,"n_genes":1541,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"KOR","country":"South Korea"},{"gem_file":"562.70757.json.json","assembly_accession":"GCA_016903335.1","genome_id":"562.70757","genome_name":"Escherichia coli strain FDAARGOS_1295 strain Not applicable","strain":"","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5142344.0,"gc_content":50.62275,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5138.0,"refseq_cds":4845.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"881.44x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357437","genbank_accessions":"CP069890,CP069891","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1295","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2711,"n_metabolites":1877,"n_genes":1388,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"2848143.3.json.json","assembly_accession":"GCA_018986775.1","genome_id":"2848143.3","genome_name":"Escherichia coli O85:H1 strain 03-3638","strain":"O85:H1 strain 03-3638","serovar":"O85:H1","phylogroup":"B2","MLST":706,"mash_cluster":6,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5163097.0,"gc_content":50.494915,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5184.0,"refseq_cds":4907.0,"sequencing_platform":"Illumina MiSeq/NextSeq and Oxford","sequencing_depth":"61x (Illumina)/x","assembly_method":"Unicycler (normal mode) using PE Illumina","sequencing_centers":"Health Canada","completion_date":"2021-06-22T00:00:00Z","collection_date":"2003","bioproject_accession":"PRJNA735700","biosample_accession":"SAMN19011648","genbank_accessions":"CP076714,CP076715,CP076716,CP076717","refseq_accessions":"","genome_status":"Complete","taxon_id":2848143.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Health Canada - Bureau of Microbial Hazards","comments":"Characterization of shiga toxin (stx) genes in E. coli including novel stx variants/subtypes","n_reactions":2733,"n_metabolites":1942,"n_genes":1443,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.71839.json.json","assembly_accession":"GCA_017088465.1","genome_id":"562.71839","genome_name":"Escherichia coli strain 65COLEC","strain":"strain 65COLEC","serovar":"","phylogroup":"A","MLST":2705,"mash_cluster":22,"isolation_source":"feces","isolation_country":"Singapore","geographic_location":"Singapore","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5055327.0,"gc_content":50.527573,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5041.0,"refseq_cds":4737.0,"sequencing_platform":"Illumina NovaSeq Oxford Nanopore MiniION","sequencing_depth":"363x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Temasek Life Sciences Laboratory Limited","completion_date":"2021-03-01T00:00:00Z","collection_date":"2019-02","bioproject_accession":"PRJNA599529","biosample_accession":"SAMN17807535","genbank_accessions":"CP070914,CP070915,CP070916,CP070917,CP070918,CP070919","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Bacterial pure culture","comments":"In this project, we isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore. Their genomes were sequenced and analysed to identify resistance mechanisms, plasmids and mode of antibiotic resistance gene acquisition.","n_reactions":2734,"n_metabolites":1939,"n_genes":1535,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"SGP","country":"Singapore"},{"gem_file":"GCF_014168855.1.json.json","assembly_accession":"GCF_014168855.1","genome_id":"GCF_014168855.1","genome_name":"Escherichia coli","strain":"WP3-W18-ESBL-08","serovar":"","phylogroup":"D","MLST":-1,"mash_cluster":15,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMD00194414","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1936,"n_genes":1519,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"2778653.3.json.json","assembly_accession":"GCA_015571915.1","genome_id":"2778653.3","genome_name":"Escherichia coli O112ab:H8 strain Res13-Lact-EA06-22","strain":"O112ab:H8 strain Res13-Lact-EA06-22","serovar":"O112ab:H8","phylogroup":"B1","MLST":75,"mash_cluster":26,"isolation_source":"feces","isolation_country":"Canada","geographic_location":"Canada: Quebec","host_name":"Pig, Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5353630.0,"gc_content":50.503902,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5427.0,"refseq_cds":5088.0,"sequencing_platform":"Oxford Nanopore MinION and Illumina MiSeq","sequencing_depth":"1.00x","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Government of Canada","completion_date":"2020-11-18T00:00:00Z","collection_date":"10-Apr-2017","bioproject_accession":"PRJNA662792","biosample_accession":"SAMN16304114","genbank_accessions":"CP062910,CP062911,CP062912,CP062913,CP062914,CP062915","refseq_accessions":"","genome_status":"Complete","taxon_id":2778653.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Agriculture and Agri-Food Canada","comments":"The majority of antibiotics sold are administered to livestock, presumably promoting the development and spread of antibiotic resistance genes in food-borne pathogens such as Enterobacteriaceae producing extended spectrum beta-lactamases (ESBL). Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. The major goal of the study was to characterize cefotaxime-resistant bacteria isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2731,"n_metabolites":1938,"n_genes":1506,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"GCF_900635325.1.json.json","assembly_accession":"GCF_900635325.1","genome_id":"GCF_900635325.1","genome_name":"Escherichia coli","strain":"NCTC10444","serovar":"","phylogroup":"E","MLST":57,"mash_cluster":20,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMEA3529258","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2730,"n_metabolites":1938,"n_genes":1511,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.28805.json.json","assembly_accession":"GCA_003073955.1","genome_id":"562.28805","genome_name":"Escherichia coli strain AR434","strain":"strain AR434","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4793375.0,"gc_content":50.646404,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4742.0,"refseq_cds":4653.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"22.26x","assembly_method":"canu v. 1.4","sequencing_centers":"FDA/CDC","completion_date":"2018-04-30T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA316321","biosample_accession":"SAMN07291527","genbank_accessions":"CP029122,CP029123","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"Susceptible;Resistant;Not defined","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The AR Isolate Bank is a centralized repository of microbial pathogens with well-characterized resistance profiles that are assembled by CDC in collaboration with the Food and Drug Administration (FDA). The AR Bank is available to support and advance development of diagnostic devices and antimicrobial drug products. The AR Isolate Bank also supports the National Action Plan for Combating Antibiotic Resistance Bacteria by advancing the development of diagnostic tests to identify and characterize resistant bacteria, and by accelerating research and development for new antibiotics.The AR Isolate Bank includes collections of bacterial pathogens that are associated with known or emerging resistance mechanisms. Since its launch in July 2015, the AR Bank continues to grow and will eventually include genera and species such as Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus, Enterococcus, Streptococcus, Salmonella, and Neisseria gonorrhoeae.Each pathogen listed on this web site includes information regarding its susceptibility and/or resistance profile(s), known resistance biomarkers, isolate characteristics, and associated data in PDF.Use this web site to search through pathogen panels, find additional information about the available isolates, and find procedures for requesting panels.","n_reactions":2733,"n_metabolites":1939,"n_genes":1528,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"2605619.5.json.json","assembly_accession":"GCA_008124145.1","genome_id":"2605619.5","genome_name":"Escherichia coli O16:H48 strain PG20180170","strain":"O16:H48 strain PG20180170","serovar":"O16:H48","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"mouse gut","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4699346.0,"gc_content":50.77198,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4747.0,"refseq_cds":4472.0,"sequencing_platform":"Illumina MiSeq and Nanopore","sequencing_depth":"587x","assembly_method":"Unicycler v. 0.4.3","sequencing_centers":"National Microbiology Laboratory at Guelph","completion_date":"2019-08-29T00:00:00Z","collection_date":"11-Jan-2019","bioproject_accession":"PRJNA560883","biosample_accession":"SAMN12603269","genbank_accessions":"CP043187,CP043188","refseq_accessions":"","genome_status":"Complete","taxon_id":2605619.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Canadian Food Inspection Agency","comments":"Humans and farm animals commonly consume food- or waterborne bacteria that harbour antibiotic resistance genes. The fate and potential horizontal gene transfer of those genes into the host microbiome will have a crucial bearing on the eventual health risk of exposure to antibiotic resistance genes. In the present study, the effects of antibiotics on the in vivo transfer of \ud835\udefd-lactam resistance genes were evaluated in a mouse model by characterizing the microbiome in excreted feces. Mice were dosed with Escherichia coli, Salmonella enterica serovars Heidelberg or Bredeney referred to as donors. The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1936,"n_genes":1547,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1055538.13.json.json","assembly_accession":"GCA_014623225.1","genome_id":"1055538.13","genome_name":"Escherichia coli O145 strain RM9154-C1","strain":"O145 strain RM9154-C1","serovar":"","phylogroup":"D","MLST":32,"mash_cluster":20,"isolation_source":"feces","isolation_country":"USA","geographic_location":"USA: CA","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5576061.0,"gc_content":50.588543,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5842.0,"refseq_cds":5494.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"177.27x","assembly_method":"HGAP v. 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Dunlop, Boston University, 44 Cummington Mall, Boston, MA 02215;collected_by:A.M. Langevin","comments":"In this work, we evolved strains of Escherichia coli with different genotypes related to the AcrAB-TolC efflux pump. Parent strains were either wild type, had the pump overexpressed, or had the pump knocked out. We evolved these three strains under different levels of chloramphenicol. Each parent strain was evolved in an evolution experiment using three biological replicates. The most resistant isolate from each separate evolution experiment and the parent strains are provided here. The goal of this work was to identify which chloramphenicol concentrations promote the evolution of antibiotic resistance and how the presence of the AcrAB-TolC pump impacts this evolution.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83333.111.json.json","assembly_accession":"GCF_000981485.1","genome_id":"83333.111","genome_name":"Escherichia coli K-12","strain":"K-12","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4638126.0,"gc_content":50.83,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4581.0,"refseq_cds":4165.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UNIVERSITY OF EXETER","completion_date":"2015-04-02T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB7832","biosample_accession":"SAMEA3143339","genbank_accessions":"LN832404","refseq_accessions":"NZ_LN832404.1","genome_status":"Complete","taxon_id":83333.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Escherichia coli K12 (AG100) was targeted with two antibiotics, erythromycin (a macrolide, ERY) and doxycycline (a tetracycline, DOX) that bind to different ribosomal RNA subunits, thereby inhibiting translation. Two treatment of 8 seasons of 12 hours at dosages corresponding to the IC50 of each drug were sequenced\\; IC50 denotes the antibiotic concentration that reduces bacterial density by a factor of 50% relative to that produced without antibiotic in one season. We studied one 50-50 combination using a half-dose of both drug for each season, and the EDEDEDED treatment, writing 'E' for a season of ERY and D for DOX. Library preparation method: DNA was fragmented by sonication using a Biorupter for 30s on, 90s off, using low power for 10 minutes on ice. Libraries were prepared using SPRIworks cartridges for Illumina (Beckman Coulter) and Nextflex indexed adapters, with 300-600 bp size selection, amplified with 8 cycles PCR using Kapa HiFi DNA polymerase and purified using GeneRead kit (Qiagen). Concentrations were determined using a Bioanalyser 7500 DNA chip. Libraries were pooled in equimolar amounts, denatured, diluted to 6.5 pMol and clustered on a flowcell using a cBot (Illumina). 100 paired end sequencing with a custom barcode read was completed on a HiSeq 2500 using Truseq SBS v3 reagents Illumina).","n_reactions":2732,"n_metabolites":1935,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.58277.json.json","assembly_accession":"GCA_011022275.1","genome_id":"562.58277","genome_name":"Escherichia coli strain 190693","strain":"strain 190693","serovar":"","phylogroup":"D","MLST":315,"mash_cluster":15,"isolation_source":"Blood culture","isolation_country":"United Kingdom","geographic_location":"United Kingdom: Liverpool","host_name":"Human, Homo sapiens","host_health":"Bacteremia","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5151952.0,"gc_content":50.643017,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5127.0,"refseq_cds":4827.0,"sequencing_platform":"Oxford Nanopore MiniION; Illumina MiSeq","sequencing_depth":"76.0x","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Liverpool School of Tropical Medicine","completion_date":"2020-02-26T00:00:00Z","collection_date":"2016-11-15","bioproject_accession":"PRJNA607545","biosample_accession":"SAMN14137859","genbank_accessions":"CP048934","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:The Royal Liverpool University Hospital","comments":"Clonal pair of clinical isolates of E. coli, one isolate is TZP susceptible and one isolate is TZP resistant","n_reactions":2731,"n_metabolites":1937,"n_genes":1517,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.52722.json.json","assembly_accession":"GCA_009650035.1","genome_id":"562.52722","genome_name":"Escherichia coli strain AUSMDU00014361","strain":"strain AUSMDU00014361","serovar":"","phylogroup":"B1","MLST":29,"mash_cluster":23,"isolation_source":"","isolation_country":"Australia","geographic_location":"Australia","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5774445.0,"gc_content":50.653336,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":6165.0,"refseq_cds":5675.0,"sequencing_platform":"Oxford Nanopore GridION; Illumina NextSeq","sequencing_depth":"89.0x","assembly_method":"Unicycler v. 0.4.8b","sequencing_centers":"Microbiological Diagnostic Unit","completion_date":"2019-11-12T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA556438","biosample_accession":"SAMN11008224","genbank_accessions":"CP045827,CP045828,CP045829,CP045830","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.","n_reactions":2731,"n_metabolites":1939,"n_genes":1515,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"GCF_020541005.1.json.json","assembly_accession":"GCF_020541005.1","genome_id":"GCF_020541005.1","genome_name":"Escherichia coli","strain":"P27_L1_05.20","serovar":"","phylogroup":"B1","MLST":-1,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN22251400","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2734,"n_metabolites":1938,"n_genes":1521,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.70726.json.json","assembly_accession":"GCA_016888965.1","genome_id":"562.70726","genome_name":"Escherichia coli strain FDAARGOS_1261 strain Not applicable","strain":"","serovar":"","phylogroup":"B2","MLST":2604,"mash_cluster":6,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5050101.0,"gc_content":50.42483,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4973.0,"refseq_cds":4673.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"738.22x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-15T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357403","genbank_accessions":"CP069441","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1261","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2732,"n_metabolites":1944,"n_genes":1452,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.77493.json.json","assembly_accession":"GCA_019334665.1","genome_id":"562.77493","genome_name":"Escherichia coli strain GB2005-delet-a-f","strain":"strain GB2005-delet-a-f","serovar":"","phylogroup":"A","MLST":1060,"mash_cluster":21,"isolation_source":"","isolation_country":"China","geographic_location":"China","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4553952.0,"gc_content":50.772514,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4575.0,"refseq_cds":4318.0,"sequencing_platform":"PacBio","sequencing_depth":"100.0x","assembly_method":"Celera Assembler v. 07-2021","sequencing_centers":"shandongdaxue","completion_date":"2021-07-25T00:00:00Z","collection_date":"2021-06-15","bioproject_accession":"PRJNA747615","biosample_accession":"SAMN20286395","genbank_accessions":"CP079736","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Escherichia coli GB2005-delet-a-f","n_reactions":2731,"n_metabolites":1933,"n_genes":1514,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.67513.json.json","assembly_accession":"GCA_015571775.1","genome_id":"562.67513","genome_name":"Escherichia coli strain Res13-Lact-PEA06-10","strain":"strain Res13-Lact-PEA06-10","serovar":"O-untypeable:H4","phylogroup":"A","MLST":761,"mash_cluster":22,"isolation_source":"feces","isolation_country":"Canada","geographic_location":"Canada: Quebec","host_name":"Pig, Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5115450.0,"gc_content":50.624012,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5201.0,"refseq_cds":4857.0,"sequencing_platform":"Oxford Nanopore MinION and Illumina MiSeq","sequencing_depth":"1.00x","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Government of Canada","completion_date":"2020-11-18T00:00:00Z","collection_date":"11-Apr-2017","bioproject_accession":"PRJNA662792","biosample_accession":"SAMN16304175","genbank_accessions":"CP062883,CP062884,CP062885,CP062886,CP062887,CP062888","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Agriculture and Agri-Food Canada","comments":"The majority of antibiotics sold are administered to livestock, presumably promoting the development and spread of antibiotic resistance genes in food-borne pathogens such as Enterobacteriaceae producing extended spectrum beta-lactamases (ESBL). Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. The major goal of the study was to characterize cefotaxime-resistant bacteria isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2732,"n_metabolites":1940,"n_genes":1526,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.68395.json.json","assembly_accession":"GCA_014295235.1","genome_id":"562.68395","genome_name":"Escherichia coli strain G6/7","strain":"strain G6/7","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"feces from healthy individual","isolation_country":"Germany","geographic_location":"Germany","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5434724.0,"gc_content":50.85548,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5642.0,"refseq_cds":5230.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"791x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"University of Arkansas for Medical Sciences","completion_date":"2020-08-25T00:00:00Z","collection_date":"1954","bioproject_accession":"PRJNA650131","biosample_accession":"SAMN15693149","genbank_accessions":"CP060061,CP060064,CP060063,CP060062","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:isolate;passage_history:multiple passages","comments":"Some Escherichia coli strains have been shown to provide beneficial effects on human and animal health. Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.","n_reactions":2734,"n_metabolites":1939,"n_genes":1513,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"562.7245.json.json","assembly_accession":"GCF_000988355.1","genome_id":"562.7245","genome_name":"Escherichia coli strain SQ37","strain":"strain SQ37","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"United States","geographic_location":"United 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The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2732,"n_metabolites":1940,"n_genes":1508,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.50716.json.json","assembly_accession":"GCA_008065435.1","genome_id":"562.50716","genome_name":"Escherichia coli strain RM9088","strain":"strain RM9088","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":22,"isolation_source":"cloacal swab","isolation_country":"USA","geographic_location":"USA: CA","host_name":"crow","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5524396.0,"gc_content":50.675514,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5882.0,"refseq_cds":5500.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"151.71x","assembly_method":"HGAP v. v3","sequencing_centers":"USDA, ARS, WRRC","completion_date":"2019-08-22T00:00:00Z","collection_date":"07-APR-2009","bioproject_accession":"PRJNA557687","biosample_accession":"SAMN12405405","genbank_accessions":"CP042298,CP042296,CP042297","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Complete genomes of birds isolates carrying shiga toxin producing Escherichia coli","n_reactions":2711,"n_metabolites":1877,"n_genes":1458,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.79349.json.json","assembly_accession":"GCA_020105115.1","genome_id":"562.79349","genome_name":"Escherichia coli strain SPCR2020","strain":"strain SPCR2020","serovar":"","phylogroup":"A","MLST":361,"mash_cluster":22,"isolation_source":"rectal swab of 45 year old man with liver cirrhosis returning from Russia","isolation_country":"Canada","geographic_location":"Canada: Vancouver","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5577634.0,"gc_content":50.63215,"contigs":21.0,"chromosomes":1.0,"plasmids":20.0,"patric_cds":5780.0,"refseq_cds":5360.0,"sequencing_platform":"Oxford Nanopore GridION","sequencing_depth":"120.0x","assembly_method":"metaFlye v. 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Fowler Jr.","comments":"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2752,"n_metabolites":2023,"n_genes":1759,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.58375.json.json","assembly_accession":"GCA_011045875.1","genome_id":"562.58375","genome_name":"Escherichia coli strain ZF31","strain":"strain ZF31","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":22,"isolation_source":"a feces sample of swine origin","isolation_country":"China","geographic_location":"China: Nantong, jiangsu province","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4792435.0,"gc_content":50.91996,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":4753.0,"refseq_cds":4497.0,"sequencing_platform":"Oxford Nanopore MiniION; Illumina HiSeq","sequencing_depth":"50.0x","assembly_method":"Unicycler v. v0.4.4","sequencing_centers":"Yangzhou University","completion_date":"2020-03-02T00:00:00Z","collection_date":"2018-05","bioproject_accession":"PRJNA599268","biosample_accession":"SAMN13742197","genbank_accessions":"CP047455,CP047459,CP047458,CP047457,CP047456,CP047460","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:College of Veterinary Medicine, Yangzhou University","comments":"The genomic epidemiology of tigecycline resistance gene tet(X) variants in a swine farm in Chian","n_reactions":2731,"n_metabolites":1935,"n_genes":1525,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"GCF_016404165.2.json.json","assembly_accession":"GCF_016404165.2","genome_id":"GCF_016404165.2","genome_name":"Escherichia coli","strain":"S19-651","serovar":"","phylogroup":"B1","MLST":33,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN16993361","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1947,"n_genes":1524,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.50516.json.json","assembly_accession":"GCA_007109165.1","genome_id":"562.50516","genome_name":"Escherichia coli strain 131","strain":"strain 131","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"blood","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"Bloodstream infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5440285.0,"gc_content":50.76175,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5625.0,"refseq_cds":5383.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"125x","assembly_method":"HGAP v. 4","sequencing_centers":"Duke University","completion_date":"2019-07-18T00:00:00Z","collection_date":"2006","bioproject_accession":"PRJNA551684","biosample_accession":"SAMN12163094","genbank_accessions":"CP041546,CP041547,CP041548,CP041549","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Vance G. 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In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2751,"n_metabolites":2023,"n_genes":1688,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.70077.json.json","assembly_accession":"GCA_003399945.2","genome_id":"562.70077","genome_name":"Escherichia coli strain CFSAN061772","strain":"strain CFSAN061772","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"Raw milk cheese","isolation_country":"Egypt","geographic_location":"Egypt","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5067037.0,"gc_content":50.391125,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5111.0,"refseq_cds":4840.0,"sequencing_platform":"PacBio","sequencing_depth":"500x","assembly_method":"HGAP v. 3","sequencing_centers":"FDA/CFSAN","completion_date":"2019-08-20T00:00:00Z","collection_date":"2016","bioproject_accession":"PRJNA230969","biosample_accession":"SAMN06909728","genbank_accessions":"NIYA01000000","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Laboratory of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City","comments":"Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.","n_reactions":2711,"n_metabolites":1877,"n_genes":1479,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"EGY","country":"Egypt"},{"gem_file":"GCF_003956265.1.json.json","assembly_accession":"GCF_003956265.1","genome_id":"GCF_003956265.1","genome_name":"Escherichia coli","strain":"510016","serovar":"","phylogroup":"A","MLST":1201,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN08161314","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1937,"n_genes":1511,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.79224.json.json","assembly_accession":"GCA_020023255.1","genome_id":"562.79224","genome_name":"Escherichia coli strain K-12 substr. 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To date, AB1157 is still frequently employed as an E. coli reference strain by researchers worldwide.","n_reactions":2732,"n_metabolites":1936,"n_genes":1554,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.59451.json.json","assembly_accession":"GCA_012516455.1","genome_id":"562.59451","genome_name":"Escherichia coli strain SFE8","strain":"strain SFE8","serovar":"","phylogroup":"B1","MLST":533,"mash_cluster":26,"isolation_source":"feces from pig","isolation_country":"China","geographic_location":"China:Sichuan","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5214762.0,"gc_content":50.66686,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5303.0,"refseq_cds":4963.0,"sequencing_platform":"Illumina 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FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2732,"n_metabolites":1943,"n_genes":1464,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"1048689.4.json.json","assembly_accession":"GCA_000245515.1","genome_id":"1048689.4","genome_name":"Escherichia coli O55:H7 str. RM12579","strain":"O55:H7 str. 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We chose to sequence strain RM12579 (California, 1974) due to its proximity in time and space to the first O157:H7 isolated in the US, a California isolate from 1975.","n_reactions":2732,"n_metabolites":1937,"n_genes":1492,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.9097.json.json","assembly_accession":"GCF_001566635.1","genome_id":"562.9097","genome_name":"Escherichia coli strain G749","strain":"strain G749","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"USA","geographic_location":"USA: Seattle","host_name":"Human, Homo 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The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1936,"n_genes":1547,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.79211.json.json","assembly_accession":"GCA_019973815.1","genome_id":"562.79211","genome_name":"Escherichia coli strain FUJ80155","strain":"strain FUJ80155","serovar":"","phylogroup":"F","MLST":648,"mash_cluster":9,"isolation_source":"","isolation_country":"Japan","geographic_location":"Japan:Aichi","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5527700.0,"gc_content":50.54896,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":5536.0,"refseq_cds":5191.0,"sequencing_platform":"MiSeq; MinION","sequencing_depth":"106x","assembly_method":"Unicycler v. 0.4.9b","sequencing_centers":"Microbiology, Fujita Health University School of Medicine","completion_date":"2021-09-01T00:00:00Z","collection_date":"2019-09-25","bioproject_accession":"PRJDB11569","biosample_accession":"SAMD00317523","genbank_accessions":"AP024694,AP024695,AP024696,AP024697,AP024698,AP024699,AP024700,AP024701","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Illumina and Oxford NANOPORE hybrid assembly of Eschericha coli clinical isolates producing NDM-5 and OXA-48.","n_reactions":2734,"n_metabolites":1946,"n_genes":1519,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"JPN","country":"Japan"},{"gem_file":"562.59216.json.json","assembly_accession":"GCA_012221565.1","genome_id":"562.59216","genome_name":"Escherichia coli strain 8-3-Ti3","strain":"strain 8-3-Ti3","serovar":"","phylogroup":"B1","MLST":270,"mash_cluster":24,"isolation_source":"colonoscopy","isolation_country":"Australia","geographic_location":"Australia: Canberra","host_name":"Human, Homo sapiens","host_health":"Crohn's disease","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5141082.0,"gc_content":50.823658,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5459.0,"refseq_cds":5137.0,"sequencing_platform":"Illumina NextSeq; Oxford Nanopore MiniION","sequencing_depth":"35x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Monash University","completion_date":"2020-04-09T00:00:00Z","collection_date":"2010","bioproject_accession":"PRJNA616136","biosample_accession":"SAMN14482836","genbank_accessions":"CP050865,CP050866,CP050867","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"29266651","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:David Gordon","comments":"Completion of two ST270 EIEC genomes for use as references","n_reactions":2732,"n_metabolites":1940,"n_genes":1460,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"1055542.5.json.json","assembly_accession":"GCA_003112245.1","genome_id":"1055542.5","genome_name":"Escherichia coli O111 str. 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The major serovars of STEC associated with illness have been O26, O111, O103, O121, O45, and O145, accounting for 25-50% of human illness caused by STECs and, in some cases, severe illness comparable to illness caused by E. coli O157:H7. Sequencing of STECs from the agriculturally important region of the California central coast will address the diversity of genomic content and physiology of STECs compared to E. coli O157.","n_reactions":2731,"n_metabolites":1938,"n_genes":1513,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.9021.json.json","assembly_accession":"GCF_001542545.1","genome_id":"562.9021","genome_name":"Escherichia coli strain PPECC42","strain":"strain PPECC42","serovar":"O11","phylogroup":"D","MLST":5147,"mash_cluster":18,"isolation_source":"lung","isolation_country":"China","geographic_location":"China: Hunan","host_name":"Pig, Sus scrofa","host_health":"resipiratory disease","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5019692.0,"gc_content":50.69,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5026.0,"refseq_cds":4825.0,"sequencing_platform":"Illumina HiSeq","sequencing_depth":"100.0x","assembly_method":"SOAPdenovo v. 1.05","sequencing_centers":"Huazhong Agricultural University","completion_date":"2016-02-02T00:00:00Z","collection_date":"2006","bioproject_accession":"PRJNA308786","biosample_accession":"SAMN04017854","genbank_accessions":"CM003707","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"ExPEC","antimicrobial_resistance":"","culture_collection":"","publication":"25243151","isolation_comments":"","other_clinical":"host_disease_outcome:acute disease;host_disease_stage:dying stage;host_health_state:after sampling","other_environmental":"","cell_shape":"","motility":"","temperature_range":"Thermophilic","optimal_temperature":"C","oxygen_requirement":"Aerobic","genotype":"","substrain":"","additional_metadata":"collected_by:Huazhong Agricultural University","comments":"Extraintestinal pathogenic Escherichia coli strain PPECC42 genome sequencing and assembly","n_reactions":2732,"n_metabolites":1945,"n_genes":1501,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.60271.json.json","assembly_accession":"GCA_012934595.1","genome_id":"562.60271","genome_name":"Escherichia coli strain SCU-122","strain":"strain SCU-122","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5025250.0,"gc_content":50.622257,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4992.0,"refseq_cds":4705.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"20x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-04-30T00:00:00Z","collection_date":"2016","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609782","genbank_accessions":"CP051714,CP051715","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. 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This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2732,"n_metabolites":1944,"n_genes":1456,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.79033.json.json","assembly_accession":"GCA_019844015.1","genome_id":"562.79033","genome_name":"Escherichia coli strain NDM_12_14482","strain":"strain NDM_12_14482","serovar":"","phylogroup":"A","MLST":167,"mash_cluster":21,"isolation_source":"rectal swab from neonate","isolation_country":"Tanzania","geographic_location":"Tanzania:Dar es Salaam","host_name":"Homo sapiens","host_health":"Gut colonization","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5026935.0,"gc_content":50.821304,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5064.0,"refseq_cds":4738.0,"sequencing_platform":"Illumina HiSeq; Oxford Nanopore","sequencing_depth":"49.9x","assembly_method":"Unicycler v. v0.4.8.0","sequencing_centers":"University of Bergen","completion_date":"2021-09-01T00:00:00Z","collection_date":"2018-02-18","bioproject_accession":"PRJNA756168","biosample_accession":"SAMN20857176","genbank_accessions":"CP082127,CP082128","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Joel Manyahi","comments":"NDM-5 gut colonization","n_reactions":2731,"n_metabolites":1940,"n_genes":1539,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"TZA","country":"Tanzania"},{"gem_file":"83334.365.json.json","assembly_accession":"GCA_013167795.1","genome_id":"83334.365","genome_name":"Escherichia coli O157:H7 strain F3113","strain":"O157:H7 strain F3113","serovar":"O157:H7","phylogroup":"E","MLST":5516,"mash_cluster":19,"isolation_source":"beef","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5545489.0,"gc_content":50.514896,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5805.0,"refseq_cds":5492.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"144x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11229488","genbank_accessions":"CP038374,CP038375","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1939,"n_genes":1486,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.63785.json.json","assembly_accession":"GCA_014075915.1","genome_id":"562.63785","genome_name":"Escherichia coli strain 33-6","strain":"strain 33-6","serovar":"","phylogroup":"A","MLST":48,"mash_cluster":22,"isolation_source":"","isolation_country":"China","geographic_location":"China:Sichuan","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4738982.0,"gc_content":50.738533,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":4744.0,"refseq_cds":4441.0,"sequencing_platform":"Oxford Nanopore 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This genome will be used for comparative analysis.","n_reactions":2752,"n_metabolites":2024,"n_genes":1746,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.70746.json.json","assembly_accession":"GCA_016889905.1","genome_id":"562.70746","genome_name":"Escherichia coli strain FDAARGOS_1259 strain Not applicable","strain":"","serovar":"","phylogroup":"B2","MLST":12,"mash_cluster":6,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5224343.0,"gc_content":50.61798,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5290.0,"refseq_cds":4981.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"699.36x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4, SPAdes v. 3.14.1","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-15T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357401","genbank_accessions":"CP069559,CP069560,CP069561,CP069562","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1259","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2732,"n_metabolites":1946,"n_genes":1449,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_021398995.1.json.json","assembly_accession":"GCF_021398995.1","genome_id":"GCF_021398995.1","genome_name":"Escherichia coli O25:H4","strain":"O25:H4","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN21159020","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":2067421.0,"organism_name":"Escherichia coli O25:H4","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1943,"n_genes":1465,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.19575.json.json","assembly_accession":"GCA_002220215.1","genome_id":"562.19575","genome_name":"Escherichia coli strain E62","strain":"strain E62","serovar":"","phylogroup":"B1","MLST":2521,"mash_cluster":26,"isolation_source":"feces","isolation_country":"China","geographic_location":"China","host_name":"Rat, Rattus norvegicus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4914770.0,"gc_content":50.74,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4998.0,"refseq_cds":4908.0,"sequencing_platform":"PacBio","sequencing_depth":"50x","assembly_method":"SPAdes v. 3.7.1","sequencing_centers":"Polyu","completion_date":"2017-07-17T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA389489","biosample_accession":"SAMN07251590","genbank_accessions":"CP022393","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:not applicable","comments":"Genetic status of the D-Serine Utilization Locus dsdCXA and Biofilm Adhesin Genes pgaABCD Defines Survival fitness and Resistance Formation Potential of Gut Microbiome Strains","n_reactions":2732,"n_metabolites":1935,"n_genes":1516,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"1078021.4.json.json","assembly_accession":"GCA_005171095.1","genome_id":"1078021.4","genome_name":"Escherichia coli O113:H21 strain FWSEC0011","strain":"O113:H21 strain FWSEC0011","serovar":"O113:H21","phylogroup":"B1","MLST":56,"mash_cluster":26,"isolation_source":"Domesticated, Livestock: Bovine: animal manure: agricultural - farm","isolation_country":"Canada","geographic_location":"Canada:Ontario","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5314491.0,"gc_content":50.854465,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5523.0,"refseq_cds":5428.0,"sequencing_platform":"Illumina MiSeq;Oxford Nanopore MinION","sequencing_depth":"108.45x;96.89x","assembly_method":"Unicycler;Canu v. 0.4.4.0;1.7","sequencing_centers":"National Microbiology Laboratory","completion_date":"2019-05-01T00:00:00Z","collection_date":"2004","bioproject_accession":"PRJNA287560","biosample_accession":"SAMN08768112","genbank_accessions":"CP031892,CP031893,CP031894,CP031895,CP031896,CP031897","refseq_accessions":"","genome_status":"Complete","taxon_id":1078021.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"is from Environmental, animal husbandry, food samples, and medical isolates","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"Mesophilic","optimal_temperature":"37 C","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"collected_by:Laboratory for Foodborne Zoonoses: Public Health Agency of Canada","comments":"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. 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The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.","n_reactions":2731,"n_metabolites":1938,"n_genes":1518,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"GCF_020883315.1.json.json","assembly_accession":"GCF_020883315.1","genome_id":"GCF_020883315.1","genome_name":"Escherichia coli","strain":"RIVM_C037794","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN22569033","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1942,"n_genes":1523,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"168807.7.json.json","assembly_accession":"GCA_900149915.1","genome_id":"168807.7","genome_name":"Escherichia coli O127:H6 strain EPEC E2348/69 variety 2","strain":"O127:H6 strain EPEC E2348/69 variety 2","serovar":"","phylogroup":"B2","MLST":15,"mash_cluster":6,"isolation_source":"Sanger Centre via Imperial College","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4848621.0,"gc_content":50.567574,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4906.0,"refseq_cds":4436.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"CNB/CSIC","completion_date":"2017-10-28T00:00:00Z","collection_date":"2012","bioproject_accession":"PRJEB18716","biosample_accession":"SAMEA35192668","genbank_accessions":"LT827011","refseq_accessions":"","genome_status":"Complete","taxon_id":168807.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The strain EPEC E2348/69 variety 2 was obtained from the Sanger Centre via the Imperial College. The sequence was obtained using NGS and the reads were assembled using NC_011601.1 as reference.","n_reactions":2730,"n_metabolites":1938,"n_genes":1418,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_021441965.1.json.json","assembly_accession":"GCF_021441965.1","genome_id":"GCF_021441965.1","genome_name":"Escherichia coli","strain":"PT62","serovar":"","phylogroup":"B1","MLST":6775,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN24648241","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2730,"n_metabolites":1931,"n_genes":1447,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.78132.json.json","assembly_accession":"GCA_019551815.1","genome_id":"562.78132","genome_name":"Escherichia coli strain CY708 strain not collected","strain":"","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"not collected","isolation_country":"China","geographic_location":"China:shenzhen","host_name":"not collected","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4693401.0,"gc_content":50.78522,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4697.0,"refseq_cds":4429.0,"sequencing_platform":"PacBio RSII; Illumina HiSeq","sequencing_depth":"480x","assembly_method":"SOAPdenovo v. 2.04","sequencing_centers":"Shenzhen University","completion_date":"2021-08-11T00:00:00Z","collection_date":"2019-10-09","bioproject_accession":"PRJNA689933","biosample_accession":"SAMN17256769","genbank_accessions":"CP068279,CP068280","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:culture","comments":"To date, only a few studies identified hyper-motile isolates that affect FlhDC at the post-translational level. Here we obtained this kind of hyper-motile isolates by evolving an E. coli K12 NCM3722 wild-type strain (CY598) on the soft agar plate. These isolates shared one single point mutation in ClpX, making ClpX another hot locus during evolution of bacterial motility. We then revealed the molecular mechanism of the ClpX mutant.","n_reactions":2753,"n_metabolites":2028,"n_genes":1764,"n_exchange":331,"n_with_gpr":2307,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.29127.json.json","assembly_accession":"GCA_003018315.1","genome_id":"562.29127","genome_name":"Escherichia coli strain 2013C-3513","strain":"strain 2013C-3513","serovar":"O186:H11","phylogroup":"B1","MLST":21,"mash_cluster":23,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5746114.0,"gc_content":50.552044,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":6066.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"121.607x","assembly_method":"HGAP v. 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. 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FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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Whole genome sequencing of strain U90 may contribute to better explore the pathogenic mechanism of Escherichia coli in gastroenteritis.","n_reactions":2733,"n_metabolites":1938,"n_genes":1537,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.19204.json.json","assembly_accession":"GCA_002310595.1","genome_id":"562.19204","genome_name":"Escherichia coli strain 144","strain":"strain 144","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"urinary tract infections","isolation_country":"United Kingdom","geographic_location":"United Kingdom: Scotland, Edinburgh","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":5361252.0,"gc_content":50.56,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5494.0,"refseq_cds":5356.0,"sequencing_platform":"PacBio","sequencing_depth":"20x","assembly_method":"De-novo v. Celera Assembler 8.7","sequencing_centers":"The Roslin Institute","completion_date":"2017-09-18T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA402083","biosample_accession":"SAMN07618126","genbank_accessions":"CP023364,CP023363,CP023365","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from urinary tract infections in dogs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.","n_reactions":2712,"n_metabolites":1878,"n_genes":1466,"n_exchange":331,"n_with_gpr":2266,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.29099.json.json","assembly_accession":"GCA_003019035.1","genome_id":"562.29099","genome_name":"Escherichia coli strain 2014C-3075","strain":"strain 2014C-3075","serovar":"O36:H42","phylogroup":"F","MLST":967,"mash_cluster":11,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5339468.0,"gc_content":50.58221,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5253.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"157.52x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Jun-2013","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08579581","genbank_accessions":"CP027447,CP027448","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2733,"n_metabolites":1941,"n_genes":1526,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"498388.3.json.json","assembly_accession":"GCA_002079225.1","genome_id":"498388.3","genome_name":"Escherichia coli C strain C","strain":"C strain C","serovar":"","phylogroup":"A","MLST":1721,"mash_cluster":22,"isolation_source":"","isolation_country":"United States","geographic_location":"United States","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4617024.0,"gc_content":50.96,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4665.0,"refseq_cds":4581.0,"sequencing_platform":"PacBio","sequencing_depth":"184.0x","assembly_method":"HGAP Assembly v. 2","sequencing_centers":"Drexel University College of Medicine","completion_date":"2017-04-05T00:00:00Z","collection_date":"2016-04-01","bioproject_accession":"PRJNA380607","biosample_accession":"SAMN06645125","genbank_accessions":"CP020543","refseq_accessions":"","genome_status":"Complete","taxon_id":498388.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:bacterial culture","comments":"The last laboratory strain of E. coli to be sequnced. E. coli C is a long time laboratory strain used for phage studies. Recent data shows that it forms much better biofilm than other strains and can be used as a model organism in bacterial biofilm studies.","n_reactions":2733,"n_metabolites":1940,"n_genes":1519,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"1055543.4.json.json","assembly_accession":"GCA_003112145.1","genome_id":"1055543.4","genome_name":"Escherichia coli O121 str. RM8352","strain":"O121 str. RM8352","serovar":"O121","phylogroup":"B1","MLST":655,"mash_cluster":24,"isolation_source":"creek sediment","isolation_country":"USA","geographic_location":"USA: Salinas, California","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5474275.0,"gc_content":50.63202,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5939.0,"refseq_cds":5686.0,"sequencing_platform":"PacBio; Illumina MiSeq","sequencing_depth":"133.0x","assembly_method":"HGAP v.3 as available in the SMRT","sequencing_centers":"USDA-ARS-WRRC-PSM","completion_date":"2018-05-10T00:00:00Z","collection_date":"Jul-2009","bioproject_accession":"PRJNA69933","biosample_accession":"SAMN08724618","genbank_accessions":"CP028110,CP028111","refseq_accessions":"","genome_status":"Complete","taxon_id":1055543.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USDA ARS PSM","comments":"The rise in foodborne-related outbreaks of non O157 shiga-toxin producing E. coli (STECs) emphasizes the importance of developing improved methods to rapidly detect and characterize STECs. The major serovars of STEC associated with illness have been O26, O111, O103, O121, O45, and O145, accounting for 25-50% of human illness caused by STECs and, in some cases, severe illness comparable to illness caused by E. coli O157:H7. Sequencing of STECs from the agriculturally important region of the California central coast will address the diversity of genomic content and physiology of STECs compared to E. coli O157.","n_reactions":2732,"n_metabolites":1941,"n_genes":1525,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.54032.json.json","assembly_accession":"GCA_009762475.1","genome_id":"562.54032","genome_name":"Escherichia coli strain C27A","strain":"strain C27A","serovar":"","phylogroup":"A","MLST":7369,"mash_cluster":21,"isolation_source":"Chicken meat","isolation_country":"Cambodia","geographic_location":"Cambodia","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5279451.0,"gc_content":50.669662,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5867.0,"refseq_cds":5023.0,"sequencing_platform":"Oxford Nanopore MinION; Illumina NextSeq","sequencing_depth":"20.0x","assembly_method":"Unicycler v. 2018-07-01T00:00:00","sequencing_centers":"Tufts University","completion_date":"2019-12-18T00:00:00Z","collection_date":"2016","bioproject_accession":"PRJNA566431","biosample_accession":"SAMN12789772","genbank_accessions":"CP044305,CP044307,CP044308,CP044309,CP044306","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"recovered from food and healthy, gut-colonized humans in Cambodia are described","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Institut Pasteur du Cambodge","comments":"The complete nucletotide sequences of 5 ESBL-producing E. coli recovered from food and healthy, gut-colonized humans in Cambodia are described. Hybrid assemblies (Illumina + Minion) revealed ESBL genes were primarily plasmid encoded.","n_reactions":2711,"n_metabolites":1877,"n_genes":1456,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"KHM","country":"Cambodia"},{"gem_file":"562.16414.json.json","assembly_accession":"GCA_002105735.1","genome_id":"562.16414","genome_name":"Escherichia coli strain CFSAN051542","strain":"strain CFSAN051542","serovar":"O18ac:H14","phylogroup":"Unknown","MLST":1434,"mash_cluster":22,"isolation_source":"Blue cheese in wax","isolation_country":"United States","geographic_location":"United States","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4926135.0,"gc_content":50.95,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5140.0,"refseq_cds":5031.0,"sequencing_platform":"PacBio","sequencing_depth":"400.0x","assembly_method":"HGAP v. v.3.0","sequencing_centers":"FDA","completion_date":"2017-04-24T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA312475","biosample_accession":"SAMN05414625","genbank_accessions":"CP020835,CP020836","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"C","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARL","comments":"Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of food contamination events.","n_reactions":2730,"n_metabolites":1938,"n_genes":1518,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.67512.json.json","assembly_accession":"GCA_015571655.1","genome_id":"562.67512","genome_name":"Escherichia coli strain Res13-Lact-PER02-33","strain":"strain Res13-Lact-PER02-33","serovar":"O-untypeable:H4","phylogroup":"A","MLST":761,"mash_cluster":22,"isolation_source":"feces","isolation_country":"Canada","geographic_location":"Canada: Quebec","host_name":"Pig, Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5116488.0,"gc_content":50.625565,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5200.0,"refseq_cds":4858.0,"sequencing_platform":"Oxford Nanopore MinION and Illumina MiSeq","sequencing_depth":"1.00x","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Government of Canada","completion_date":"2020-11-18T00:00:00Z","collection_date":"20-Mar-2017","bioproject_accession":"PRJNA662792","biosample_accession":"SAMN16304229","genbank_accessions":"CP062838,CP062839,CP062840,CP062841,CP062842,CP062843","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Agriculture and Agri-Food Canada","comments":"The majority of antibiotics sold are administered to livestock, presumably promoting the development and spread of antibiotic resistance genes in food-borne pathogens such as Enterobacteriaceae producing extended spectrum beta-lactamases (ESBL). Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. The major goal of the study was to characterize cefotaxime-resistant bacteria isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2732,"n_metabolites":1940,"n_genes":1526,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.22354.json.json","assembly_accession":"GCA_002764175.1","genome_id":"562.22354","genome_name":"Escherichia coli strain F5176C6","strain":"strain F5176C6","serovar":"O167:H5","phylogroup":"B1","MLST":-1,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5425513.0,"gc_content":50.58,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5589.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"86.0x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2017-11-13T00:00:00Z","collection_date":"1997","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN07656208","genbank_accessions":"CP024667,CP024668,CP024669,CP024670,CP024671","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"ETEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2734,"n_metabolites":1939,"n_genes":1522,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.77292.json.json","assembly_accession":"GCA_019211745.1","genome_id":"562.77292","genome_name":"Escherichia coli strain Sx181-0-1","strain":"strain Sx181-0-1","serovar":"","phylogroup":"B1","MLST":196,"mash_cluster":26,"isolation_source":"urine","isolation_country":"China","geographic_location":"China:Zhengzhou","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4883689.0,"gc_content":50.761707,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4829.0,"refseq_cds":4604.0,"sequencing_platform":"Illumina HiSeq; PacBio","sequencing_depth":"200.0x","assembly_method":"SOAPdenovo v. v2.04; Celera Assembler v.","sequencing_centers":"Zhengzhou University","completion_date":"2021-07-14T00:00:00Z","collection_date":"2014-10-12T14:20:50Z","bioproject_accession":"PRJNA743417","biosample_accession":"SAMN20035118","genbank_accessions":"CP078137,CP078136","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:pure culture","comments":"Study on the resistance mechanism of Escherichia coli","n_reactions":2711,"n_metabolites":1877,"n_genes":1467,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"GCF_020149605.1.json.json","assembly_accession":"GCF_020149605.1","genome_id":"GCF_020149605.1","genome_name":"Escherichia coli","strain":"NDM4","serovar":"","phylogroup":"A","MLST":167,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN21398205","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1938,"n_genes":1529,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.67699.json.json","assembly_accession":"GCA_904711305.1","genome_id":"562.67699","genome_name":"Escherichia coli strain 2016-02-324","strain":"strain 2016-02-324","serovar":"","phylogroup":"A","MLST":7036,"mash_cluster":22,"isolation_source":"Wild bird","isolation_country":"Norway","geographic_location":"Norway","host_name":"Aves","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4902355.0,"gc_content":50.995632,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4729.0,"refseq_cds":4543.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"NORWEGIAN VETERINARY INSTITUTE","completion_date":"2020-09-28T00:00:00Z","collection_date":"2016-08-21","bioproject_accession":"PRJEB40078","biosample_accession":"SAMEA7287973","genbank_accessions":"LR882050,LR882051","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"Norwegian Veterinary Institute","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The presence of quinolone resistant Escherichia coli (QREC) in the animal reservoir might be of public health concern especially related to acquired quinolone resistance genes encoded on plasmids as they might spread to more pathogenic and disease-causing bacteria. The plasmid-mediated qnrS1 gene is known to be situated on plasmids with different incompatibility (Inc) groups. In this study, the aim was to select QREC strains encoding qnrS1 situated on plasmids with different Inc-groups and to complete circular plasmid contigs. 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In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.53933.json.json","assembly_accession":"GCA_009671085.1","genome_id":"562.53933","genome_name":"Escherichia coli strain 1916D6","strain":"strain 1916D6","serovar":"","phylogroup":"A","MLST":761,"mash_cluster":22,"isolation_source":"feces","isolation_country":"China","geographic_location":"China:Henan","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4866996.0,"gc_content":50.70403,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4841.0,"refseq_cds":4596.0,"sequencing_platform":"Illumina MiniSeq; PacBio","sequencing_depth":"432.0x","assembly_method":"A5-miseeq v. v20150522; CANU v. v1.4","sequencing_centers":"Henan Agricultural University","completion_date":"2019-11-19T00:00:00Z","collection_date":"2019-07-01","bioproject_accession":"PRJNA588383","biosample_accession":"SAMN13242769","genbank_accessions":"CP046003,CP046001,CP046002","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:mixed culture","comments":"The goal of this project is to identify Escherichia coli strain 1916D6","n_reactions":2711,"n_metabolites":1877,"n_genes":1478,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.48252.json.json","assembly_accession":"GCA_900622695.1","genome_id":"562.48252","genome_name":"Escherichia coli strain MS14384","strain":"strain MS14384","serovar":"","phylogroup":"D","MLST":963,"mash_cluster":15,"isolation_source":"blood","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5186043.0,"gc_content":50.71782,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5042.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Bioplatforms Australia","completion_date":"2019-01-10T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB29930","biosample_accession":"SAMEA5128444","genbank_accessions":"LR130562,LR130563","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"102.100.100.25766","publication":"","isolation_comments":"","other_clinical":"host_health_state:diseased","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Escherichia coli.","n_reactions":2732,"n_metabolites":1942,"n_genes":1520,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.28705.json.json","assembly_accession":"GCA_003018015.1","genome_id":"562.28705","genome_name":"Escherichia coli strain 2013C-4404","strain":"strain 2013C-4404","serovar":"O91:H14","phylogroup":"B1","MLST":33,"mash_cluster":26,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5297965.0,"gc_content":50.770947,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5699.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"166.017x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Aug-2013","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08579575","genbank_accessions":"CP027376,CP027377,CP027378,CP027379","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library;many frameshifted proteins","n_reactions":2733,"n_metabolites":1948,"n_genes":1539,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.68640.json.json","assembly_accession":"GCA_016026215.1","genome_id":"562.68640","genome_name":"Escherichia coli strain FDAARGOS_945 strain Not applicable","strain":"","serovar":"","phylogroup":"A","MLST":281,"mash_cluster":24,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5569560.0,"gc_content":50.710217,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5973.0,"refseq_cds":5547.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"611x","assembly_method":"SMRT v. 6.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2020-12-14T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN13450475","genbank_accessions":"CP065611,CP065610,CP065612","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"DSM:9029","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:DSMZ","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. 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The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.","n_reactions":2732,"n_metabolites":1940,"n_genes":1514,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"GCF_900636055.1.json.json","assembly_accession":"GCF_900636055.1","genome_id":"GCF_900636055.1","genome_name":"Escherichia coli","strain":"NCTC11121","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMEA3368339","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1942,"n_genes":1474,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.72317.json.json","assembly_accession":"GCA_017352055.1","genome_id":"562.72317","genome_name":"Escherichia coli strain EcPNK006","strain":"strain EcPNK006","serovar":"","phylogroup":"A","MLST":46,"mash_cluster":22,"isolation_source":"urine","isolation_country":"USA","geographic_location":"USA: Dallas, Texas","host_name":"Homo sapiens","host_health":"Chronic Cystitis","host_gender":"female","host_age":"","body_sample_site":"","disease":"","genome_length":4622527.0,"gc_content":50.70711,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4642.0,"refseq_cds":4360.0,"sequencing_platform":"Illumina NextSeq, ONT MinION","sequencing_depth":"116x, 836x","assembly_method":"Unicycler v. v.0.4.8","sequencing_centers":"University of Texas at Dallas","completion_date":"2021-03-14T00:00:00Z","collection_date":"2017-08","bioproject_accession":"PRJNA636382","biosample_accession":"SAMN18131653","genbank_accessions":"CP071436,CP071437,CP071438","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"UPEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"host_description:Postmenopausal","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:UT Southwestern Medical Center/ UT Dallas","comments":"Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of ten UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.","n_reactions":2752,"n_metabolites":2025,"n_genes":1725,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.70737.json.json","assembly_accession":"GCA_016889525.1","genome_id":"562.70737","genome_name":"Escherichia coli strain EA7","strain":"strain EA7","serovar":"","phylogroup":"A","MLST":7122,"mash_cluster":22,"isolation_source":"liver","isolation_country":"China","geographic_location":"China:Henan","host_name":"pig","host_health":"gastroenteritis","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4697386.0,"gc_content":50.96247,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4647.0,"refseq_cds":4423.0,"sequencing_platform":"Illumina HiSeq","sequencing_depth":"60.0x","assembly_method":"unicycler v. v.0.4.4","sequencing_centers":"Henan Agricultural University","completion_date":"2021-02-15T00:00:00Z","collection_date":"2016-10","bioproject_accession":"PRJNA700503","biosample_accession":"SAMN17833015","genbank_accessions":"CP069709,CP069708","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Yingying Liu","comments":"Escherichia coli strain A7 chromosome, complete genome","n_reactions":2711,"n_metabolites":1880,"n_genes":1381,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"679895.114.json.json","assembly_accession":"GCA_016811895.1","genome_id":"679895.114","genome_name":"Escherichia coli BW25113 strain not applicable","strain":"not applicable","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada: Manitoba","host_name":"not applicable","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4631469.0,"gc_content":50.778908,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4594.0,"refseq_cds":4339.0,"sequencing_platform":"Illumina","sequencing_depth":"30x","assembly_method":"Geneious v. 11.1.5","sequencing_centers":"University of Manitoba","completion_date":"2021-02-07T00:00:00Z","collection_date":"2018","bioproject_accession":"PRJNA646979","biosample_accession":"SAMN17570630","genbank_accessions":"CP069134","refseq_accessions":"","genome_status":"Complete","taxon_id":679895.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:pure culture","comments":"These isolates were created by gradually adapting an Escherichia coli K-12 BW25113 strain to four cationic antimicrobials\\; benzalkonium (BZK), cetrimide (CET), chlorhexidine (CHX), and colistin (COL). Three replicates were created for each compound, generating BZKR1G40, BZKR2G40, BZKR3G40, CETR1G40, CETR2G40, CETR3G40, CHXR1G20, CHXR2G20, CHXR3G20, COLR1G32, COLR2G32, COLR3G32 as well as an unadapted wild-type (WTG40). At the end of the experiment, the BZK-adapted bacteria were tolerant to 72-144 ug/ml of BZK, the CET-adapted bacteria were tolerant to 240 ug/ml of CET, the CHX-adapted bacteria were tolerant to 4.8-9.6 ug/ml of CHX, and the COL-adapted bacteria were tolerant to >300 ug/ml.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.58451.json.json","assembly_accession":"GCA_011403355.1","genome_id":"562.58451","genome_name":"Escherichia coli strain 2017.15.01CC","strain":"strain 2017.15.01CC","serovar":"","phylogroup":"B1","MLST":201,"mash_cluster":26,"isolation_source":"human stool","isolation_country":"Viet Nam","geographic_location":"Viet Nam:Thai Binh","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4869407.0,"gc_content":50.795097,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4752.0,"refseq_cds":4511.0,"sequencing_platform":"Illumina HiSeq2500; ONT MinION","sequencing_depth":"416x","assembly_method":"Canu v. 1.7","sequencing_centers":"Osaka Institute of Public Health","completion_date":"2020-02-11T00:00:00Z","collection_date":"2017-11","bioproject_accession":"PRJDB8858","biosample_accession":"SAMD00190256","genbank_accessions":"AP021890","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The purpose of the study is to investigate the antimicrobial-resistant bacteria in food, livestock-, and human-feces samples using genetic analysis for clarifying the dissemination of resistant bacteria in a community.","n_reactions":2732,"n_metabolites":1936,"n_genes":1515,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"VNM","country":"Vietnam"},{"gem_file":"562.7071.json.json","assembly_accession":"GCF_000931565.1","genome_id":"562.7071","genome_name":"Escherichia coli strain MNCRE44","strain":"strain MNCRE44","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"sputum","isolation_country":"USA","geographic_location":"USA: Minnesota","host_name":"Human, Homo sapiens","host_health":"sepsis","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5292269.0,"gc_content":50.75,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5509.0,"refseq_cds":5134.0,"sequencing_platform":"Illumina MiSeq 2x300; PacBio","sequencing_depth":"125x; 100x","assembly_method":"CLC Genomics Workbench v. 7; HGAP v. 3","sequencing_centers":"University of Minnesota","completion_date":"2015-04-15T00:00:00Z","collection_date":"Apr-2012","bioproject_accession":"PRJNA272863","biosample_accession":"SAMN03287565","genbank_accessions":"CP010876,CP010877,CP010878,CP010879,CP010880,CP010881,CP010882","refseq_accessions":"NZ_CP010876.1,NZ_CP010877.1,NZ_CP010878.1,NZ_CP010879.1,NZ_CP010880.1,NZ_CP010881.1,NZ_CP010882.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"UPEC","antimicrobial_resistance":"","culture_collection":"","publication":"25858844","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Health care provider","comments":"Sequencing of multiple CRE isolates from Minnesota for genomic comparisons","n_reactions":2751,"n_metabolites":2021,"n_genes":1667,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.64237.json.json","assembly_accession":"GCA_013694325.1","genome_id":"562.64237","genome_name":"Escherichia coli strain C9","strain":"strain C9","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"water","isolation_country":"Italy","geographic_location":"Italy: Lodi","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5139934.0,"gc_content":50.727013,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5206.0,"refseq_cds":4865.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"490.0x","assembly_method":"Microbial Assembly v. SMRT Link v.8","sequencing_centers":"Charles University in Prague","completion_date":"2020-07-26T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA646833","biosample_accession":"SAMN15566562","genbank_accessions":"CP059281,CP059282","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:University of Pavia","comments":"OXA-244 producing E.coli","n_reactions":2734,"n_metabolites":1943,"n_genes":1478,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia 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The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.","n_reactions":2732,"n_metabolites":1941,"n_genes":1525,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"83334.356.json.json","assembly_accession":"GCA_013167555.1","genome_id":"83334.356","genome_name":"Escherichia coli O157:H7 strain Gim1-1","strain":"O157:H7 strain Gim1-1","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle feces","isolation_country":"USA","geographic_location":"USA:Nebraska","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5501393.0,"gc_content":50.46711,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5771.0,"refseq_cds":5432.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"191x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"1999","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN05360205","genbank_accessions":"CP038344,CP038345","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1939,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.62716.json.json","assembly_accession":"GCA_013376895.1","genome_id":"562.62716","genome_name":"Escherichia coli strain 357900 strain not applicable","strain":"","serovar":"","phylogroup":"B1","MLST":-1,"mash_cluster":26,"isolation_source":"","isolation_country":"Bangladesh","geographic_location":"Bangladesh","host_name":"Human, Homo sapiens","host_health":"diarrhea","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4875596.0,"gc_content":50.679077,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4832.0,"refseq_cds":4633.0,"sequencing_platform":"Illumina MiSeq","sequencing_depth":"71.0x","assembly_method":"Geneious v. 6.1.7","sequencing_centers":"University of Colroado Anschutz Medical Campus","completion_date":"2020-06-30T00:00:00Z","collection_date":"10-Jun-1985","bioproject_accession":"PRJNA320137","biosample_accession":"SAMN04917416","genbank_accessions":"CP038859","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"LT-IIc1 EplBA","substrain":"","additional_metadata":"collected_by:Peter Echeverria","comments":"representative isolates producing type II heat-labile enterotoxin variants","n_reactions":2732,"n_metabolites":1939,"n_genes":1509,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BGD","country":"Bangladesh"},{"gem_file":"168807.6.json.json","assembly_accession":"GCA_900149875.1","genome_id":"168807.6","genome_name":"Escherichia coli O127:H6 strain EPEC1","strain":"O127:H6 strain EPEC1","serovar":"","phylogroup":"B2","MLST":15,"mash_cluster":6,"isolation_source":"Artificial construct derived from EPEC E2348/69 variety 2","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4792490.0,"gc_content":50.7,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4844.0,"refseq_cds":4407.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"CNB/CSIC","completion_date":"2017-10-28T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJEB18717","biosample_accession":"SAMEA35194168","genbank_accessions":"LT903847","refseq_accessions":"","genome_status":"Complete","taxon_id":168807.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"derived from EPEC E2348/69 variety 2, artificially constructed in vitro deleting all known effectors of T3SS except Tir","other_clinical":"host_health_state:not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Genome of mutant EPEC1, strain derived from EPEC E2348/69 variety 2, artificially constructed in vitro deleting all known effectors of T3SS except Tir. 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Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.","n_reactions":2734,"n_metabolites":1939,"n_genes":1513,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"37762.5.json.json","assembly_accession":"GCF_001559615.1","genome_id":"37762.5","genome_name":"Escherichia coli B strain C2566","strain":"B strain C2566","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"laboratory","isolation_country":"United States","geographic_location":"United States","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4478948.0,"gc_content":50.81,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4491.0,"refseq_cds":4309.0,"sequencing_platform":"PacBio","sequencing_depth":"400x","assembly_method":"HGAP.3/Quiver v. 2.3.0","sequencing_centers":"New England Biolabs","completion_date":"2016-02-11T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA309539","biosample_accession":"SAMN04435507","genbank_accessions":"CP014268","refseq_accessions":"","genome_status":"Complete","taxon_id":37762.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"C","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Complete genome sequences of E. coli SHuffle-K-12 and SHuffle-B and their parental strains, DHB4 and C2566, respectively.","n_reactions":2731,"n_metabolites":1931,"n_genes":1506,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_014169595.1.json.json","assembly_accession":"GCF_014169595.1","genome_id":"GCF_014169595.1","genome_name":"Escherichia coli","strain":"WP8-S17-ESBL-05","serovar":"","phylogroup":"B1","MLST":641,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMD00194597","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1937,"n_genes":1514,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13544.json.json","assembly_accession":"GCF_001886535.1","genome_id":"562.13544","genome_name":"Escherichia coli strain MRSN352231","strain":"strain MRSN352231","serovar":"","phylogroup":"A","MLST":617,"mash_cluster":21,"isolation_source":"Clinical","isolation_country":"Germany","geographic_location":"Germany","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5200916.0,"gc_content":50.75,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5310.0,"refseq_cds":5057.0,"sequencing_platform":"PacBio; 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The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.","n_reactions":2731,"n_metabolites":1937,"n_genes":1514,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"562.58452.json.json","assembly_accession":"GCA_011404215.1","genome_id":"562.58452","genome_name":"Escherichia coli strain 2017.01.04CC","strain":"strain 2017.01.04CC","serovar":"","phylogroup":"A","MLST":206,"mash_cluster":22,"isolation_source":"human stool","isolation_country":"Viet Nam","geographic_location":"Viet Nam:Thai Binh","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4615626.0,"gc_content":50.900745,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4498.0,"refseq_cds":4280.0,"sequencing_platform":"Illumina HiSeq2500; ONT MinION","sequencing_depth":"785x","assembly_method":"Canu v. 1.7","sequencing_centers":"Osaka Institute of Public Health","completion_date":"2020-02-11T00:00:00Z","collection_date":"2017-11","bioproject_accession":"PRJDB8858","biosample_accession":"SAMD00190245","genbank_accessions":"AP021891","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The purpose of the study is to investigate the antimicrobial-resistant bacteria in food, livestock-, and human-feces samples using genetic analysis for clarifying the dissemination of resistant bacteria in a community.","n_reactions":2732,"n_metabolites":1935,"n_genes":1506,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"VNM","country":"Vietnam"},{"gem_file":"562.13775.json.json","assembly_accession":"GCF_001901125.1","genome_id":"562.13775","genome_name":"Escherichia coli strain M10","strain":"strain M10","serovar":"","phylogroup":"B1","MLST":6994,"mash_cluster":26,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Mouse, Mus musculus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4954801.0,"gc_content":50.81,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":4974.0,"refseq_cds":4726.0,"sequencing_platform":"Il;lumina Miseq; 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Three replicates were created for each compound, generating BZKR1, BZKR2, BZKR3, CETR1, CETR2, and CETR3, as well as an unadapted wild-type. At the end of the experiment, the BZK-adapted bacteria were tolerant to 72-144 ug/ml of BZK, and the CET-adapted bacteria were tolerant to 240 ug/ml of CET.;Benzalkonium adapted E.coli bioreplicate 1 derived from BW25113","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.77538.json.json","assembly_accession":"GCA_910664865.1","genome_id":"562.77538","genome_name":"Escherichia coli strain M708 / Oneg:H25 / fimH25 / 57 (ST Warwick) strain M708 / Oneg:H25 / fimH25 / 57 (ST Warwick) strain M708 / Oneg:H25 / fimH25 / 57 (ST Warwick)","strain":"strain M708 / Oneg:H25 / fimH25 / 57 (ST Warwick) strain M708 / Oneg:H25 / fimH25 / 57 (ST Warwick) strain M708 / Oneg:H25 / fimH25 / 57 (ST Warwick)","serovar":"","phylogroup":"E","MLST":57,"mash_cluster":20,"isolation_source":"phylogroupE","isolation_country":"Australia","geographic_location":"Australia","host_name":"Sarcophilus harrisii","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5042123.0,"gc_content":50.68369,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4963.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UMR 1137 IAME","completion_date":"2021-07-06T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJEB39628","biosample_accession":"SAMEA8952629","genbank_accessions":"OU349845","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"host_health_state:healthy","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PhylogroupE","n_reactions":2751,"n_metabolites":2015,"n_genes":1724,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"562.70786.json.json","assembly_accession":"GCA_016904475.1","genome_id":"562.70786","genome_name":"Escherichia coli strain FDAARGOS_1292 strain Not applicable","strain":"","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5120593.0,"gc_content":50.594257,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":5141.0,"refseq_cds":4835.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"1353.32x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357434","genbank_accessions":"CP070124,CP070125,CP070126,CP070127,CP070128,CP070129,CP070130,CP070131","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1292","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2751,"n_metabolites":2021,"n_genes":1678,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_900636125.1.json.json","assembly_accession":"GCF_900636125.1","genome_id":"GCF_900636125.1","genome_name":"Escherichia coli","strain":"NCTC9699","serovar":"","phylogroup":"A","MLST":6071,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMEA3403043","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2734,"n_metabolites":1945,"n_genes":1527,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.45430.json.json","assembly_accession":"GCA_004135165.1","genome_id":"562.45430","genome_name":"Escherichia coli strain U13A","strain":"strain U13A","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"urine","isolation_country":"USA","geographic_location":"USA:Utah","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5300616.0,"gc_content":50.77806,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5357.0,"refseq_cds":5015.0,"sequencing_platform":"PacBio RSII; Illumina NextSeq","sequencing_depth":"120.0x","assembly_method":"HGAP v. 2.3.0","sequencing_centers":"The University of Queensland","completion_date":"2019-02-03T00:00:00Z","collection_date":"2013","bioproject_accession":"PRJNA516747","biosample_accession":"SAMN10817700","genbank_accessions":"CP035477,CP035478,CP035479,CP035480,CP035481,CP035482,CP035483","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated over a 5-year period (2012-2016) from the urine and feces of a single individual","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Recurrent urinary tract infections (rUTI) are extremely common, with ~25% of all women who suffer an initial UTI experiencing a recurrence within one year of the original infection. rUTI often occurs when bacteria from the initial infection persist after treatment. Escherichia coli ST131 is a major contributor to hospital and community acquired UTI and is strongly associated with limited treatment options and high rates of recurrence. Here, using a combination of both short and long read sequencing technologies we examined the dynamics of an E. coli ST131 population isolated over a 5-year period (2012-2016) from the urine and feces of a single individual. 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In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"1045010.21.json.json","assembly_accession":"GCA_002208865.2","genome_id":"1045010.21","genome_name":"Escherichia coli O157 strain FDAARGOS_293","strain":"FDAARGOS_293","serovar":"","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:DC","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5686502.0,"gc_content":50.48,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":6234.0,"refseq_cds":5979.0,"sequencing_platform":"PacBio","sequencing_depth":"17.6648961609863x","assembly_method":"SMRT v. 2.3.0, HGAP v. 3.0","sequencing_centers":"US Food and Drug Administration","completion_date":"2017-06-27T00:00:00Z","collection_date":"26-Feb-2014","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN06173306","genbank_accessions":"CP022050,CP022051,CP022052","refseq_accessions":"","genome_status":"Complete","taxon_id":1045010.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_293","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:George Washington University","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: \u2022Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. \u2022Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). \u2022Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.30992.json.json","assembly_accession":"GCA_003308975.1","genome_id":"562.30992","genome_name":"Escherichia coli strain 2017C-4173W12","strain":"strain 2017C-4173W12","serovar":"O157:H7","phylogroup":"D","MLST":69,"mash_cluster":13,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5477116.0,"gc_content":50.67291,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5535.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"138X","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-07-10T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN09534372","genbank_accessions":"CP030768,CP030770,CP030769","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2732,"n_metabolites":1940,"n_genes":1502,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13750.json.json","assembly_accession":"GCF_001900575.1","genome_id":"562.13750","genome_name":"Escherichia coli strain C9","strain":"strain C9","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4677457.0,"gc_content":50.86,"contigs":3.0,"chromosomes":3.0,"plasmids":"","patric_cds":4736.0,"refseq_cds":4394.0,"sequencing_platform":"Illumina Miseq; Roche 454 GS Junior","sequencing_depth":"30-80x","assembly_method":"Newbler v. 2.7","sequencing_centers":"Nanjing Agricultural University","completion_date":"2016-12-12T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA269191","biosample_accession":"SAMN03252416","genbank_accessions":"CP010129,CP010130,CP010131","refseq_accessions":"NZ_CP010129.1,NZ_CP010130.1,NZ_CP010131.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"env_biome:faeces","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments","n_reactions":2730,"n_metabolites":1934,"n_genes":1491,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.46740.json.json","assembly_accession":"GCA_005222065.1","genome_id":"562.46740","genome_name":"Escherichia coli strain 118","strain":"strain 118","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5553150.0,"gc_content":50.499626,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5964.0,"refseq_cds":5798.0,"sequencing_platform":"PacBio","sequencing_depth":"163x","assembly_method":"HGAP v. RS_HGAP_Assembly.3","sequencing_centers":"United State Department of Agriculture","completion_date":"2019-05-07T00:00:00Z","collection_date":"2006","bioproject_accession":"PRJNA445267","biosample_accession":"SAMN08773030","genbank_accessions":"CP028665,CP028667,CP028666","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The aim of this project is to compare complete closed genomes with whole genome sequencing (WGS) using short reads. SNPs from WGS is used in many studies to determine relatedness of strains. These SNPs are in the core genome and don't reflect the diversity of the complete genome. This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_016944635.1.json.json","assembly_accession":"GCF_016944635.1","genome_id":"GCF_016944635.1","genome_name":"Escherichia coli","strain":"EM03-18-08","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN16387501","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2734,"n_metabolites":1941,"n_genes":1514,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"701177.3.json.json","assembly_accession":"GCA_000025165.1","genome_id":"701177.3","genome_name":"Escherichia coli O55:H7 str. CB9615","strain":"O55:H7 str. CB9615","serovar":"","phylogroup":"E","MLST":335,"mash_cluster":19,"isolation_source":"infant with diarrhea","isolation_country":"Germany","geographic_location":"Germany","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"infant","body_sample_site":"","disease":"Gastroenteritis","genome_length":5452353.0,"gc_content":50.5,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5362.0,"refseq_cds":5121.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Nankai University|Tianjin Biochip","completion_date":"2010-03-08T00:00:00Z","collection_date":"2003","bioproject_accession":"PRJNA42729","biosample_accession":"SAMN02603636","genbank_accessions":"CP001846,CP001847","refseq_accessions":"NC_013941,NC_013942","genome_status":"Complete","taxon_id":701177.0,"organism_name":"Escherichia coli O55:H7 str. CB9615","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"20090843","isolation_comments":"isolated from an infant with diarrhea in Germany in 2003 and confirmed to belong to the same multilocus sequence type (ST11) as the O157:H7 clone","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"Yes","temperature_range":"Mesophilic","optimal_temperature":"-","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"Escherichia coli O55:H7 str. CB9615. Escherichia coli O55:H7 str. CB9615 was isolated from an infant with diarrhea in Germany in 2003 and confirmed to belong to the same multilocus sequence type (ST11) as the O157:H7 clone. The O55:H7 and O157:H7 E. coli clones have been shown to be closely related and will be useful for the analysis of recombination events and mutational events. ","n_reactions":2732,"n_metabolites":1937,"n_genes":1494,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"364106.8.json.json","assembly_accession":"GCA_000013265.1","genome_id":"364106.8","genome_name":"Escherichia coli UTI89","strain":"UTI89","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":5179971.0,"gc_content":50.6,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5040.0,"refseq_cds":5166.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine","completion_date":"2006-04-05T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA16259","biosample_accession":"SAMN00000110","genbank_accessions":"CP000243,CP000244","refseq_accessions":"NC_007946,NC_007941","genome_status":"Complete","taxon_id":364106.0,"organism_name":"Escherichia coli UTI89","pathovar":"UPEC","antimicrobial_resistance":"","culture_collection":"","publication":"16585510","isolation_comments":"isolated from a woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis in a murine urinary tract infection model","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"Yes","temperature_range":"Mesophilic","optimal_temperature":"-","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"Escherichia coli strain UTI89. This strain (UTI89) is a uropathogenic strain isolated from a woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis in a murine urinary tract infection model.The genome of UTI89 showed 4 pathogenicity islands. A plasmid was found that was similar to the F plasmid but which also contained virulence genes. Comparison of a set of orthologs from this organism with other E. coli strains showed positive selection on some genes, including those for iron acquisition. Comparison with additional sequences (found in Accession Numbers DQ389000:DQ389068 and DQ440980:DQ441250) of a subset of genes from a number of isolates from patients with UTI infections and isolates from healthy individuals showed positive selection of fepE and amiA genes and some weakly positive selection for ompC.","n_reactions":2711,"n_metabolites":1877,"n_genes":1388,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.63781.json.json","assembly_accession":"GCA_014075335.1","genome_id":"562.63781","genome_name":"Escherichia coli strain 90-1","strain":"strain 90-1","serovar":"","phylogroup":"B1","MLST":-1,"mash_cluster":26,"isolation_source":"","isolation_country":"China","geographic_location":"China:Sichuan","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4943519.0,"gc_content":50.89927,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":4881.0,"refseq_cds":4627.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"100x","assembly_method":"Unicycler v. v0.3.4","sequencing_centers":"China Agricutual University","completion_date":"2020-08-05T00:00:00Z","collection_date":"2019-05-15","bioproject_accession":"PRJNA610125","biosample_accession":"SAMN14278032","genbank_accessions":"CP050047,CP050048,CP050049,CP050050,CP050051","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"tet(X4) RESEARCH","n_reactions":2732,"n_metabolites":1937,"n_genes":1511,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.61516.json.json","assembly_accession":"GCA_013341375.1","genome_id":"562.61516","genome_name":"Escherichia coli strain SCU-103","strain":"strain SCU-103","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":21,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5443100.0,"gc_content":50.912937,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":6991.0,"refseq_cds":5353.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"57x","assembly_method":"Flye, Unicycler v. 2.6, 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-06-14T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14943534","genbank_accessions":"CP054457,CP054458,CP054459,CP054460,CP054461,CP054462,CP054463,CP054464","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2737,"n_metabolites":1952,"n_genes":1602,"n_exchange":331,"n_with_gpr":2291,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.77318.json.json","assembly_accession":"GCA_019265485.1","genome_id":"562.77318","genome_name":"Escherichia coli strain Colony580","strain":"strain Colony580","serovar":"","phylogroup":"A","MLST":226,"mash_cluster":22,"isolation_source":"food","isolation_country":"Thailand","geographic_location":"Thailand","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4733683.0,"gc_content":51.14738,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4334.0,"refseq_cds":"","sequencing_platform":"Illumina HiSeq","sequencing_depth":"89.293x","assembly_method":"idba_ud v. 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Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don\u2019t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.67841.json.json","assembly_accession":"GCA_904864615.1","genome_id":"562.67841","genome_name":"Escherichia coli strain MSB1_7A-sc-2280394","strain":"strain 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With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2751,"n_metabolites":2021,"n_genes":1654,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.336.json.json","assembly_accession":"GCA_013167135.1","genome_id":"83334.336","genome_name":"Escherichia coli O157:H7 strain F8492","strain":"O157:H7 strain F8492","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"beef","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5606180.0,"gc_content":50.50471,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5909.0,"refseq_cds":5617.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"248x","assembly_method":"HGAP v. 4","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11267279","genbank_accessions":"CP038282,CP038283","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.76397.json.json","assembly_accession":"GCA_018798845.1","genome_id":"562.76397","genome_name":"Escherichia coli strain AVS0096","strain":"strain AVS0096","serovar":"","phylogroup":"B2","MLST":1193,"mash_cluster":6,"isolation_source":"river water","isolation_country":"Switzerland","geographic_location":"Switzerland: Lorze","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5092092.0,"gc_content":50.569588,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5137.0,"refseq_cds":4826.0,"sequencing_platform":"Illumina MiniSeq; Oxford Nanopore","sequencing_depth":"125.0x","assembly_method":"Unicycler v. v0.4.8","sequencing_centers":"University of Zurich","completion_date":"2021-06-09T00:00:00Z","collection_date":"2020-08","bioproject_accession":"PRJNA734472","biosample_accession":"SAMN19493560","genbank_accessions":"CP076344,CP076345,CP076346,CP076347","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:AVS","comments":"Sequencing and complete genome assembly of Escherichia coli ST1193","n_reactions":2752,"n_metabolites":2023,"n_genes":1727,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHE","country":"Switzerland"},{"gem_file":"2605619.18.json.json","assembly_accession":"GCA_008124405.1","genome_id":"2605619.18","genome_name":"Escherichia coli O16:H48 strain CV601gfp","strain":"O16:H48 strain CV601gfp","serovar":"O16:H48","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4698238.0,"gc_content":50.792725,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4738.0,"refseq_cds":4449.0,"sequencing_platform":"Illumina MiSeq and PacBio","sequencing_depth":"383x","assembly_method":"HGAP v. 3.1","sequencing_centers":"National Microbiology Laboratory at Guelph","completion_date":"2019-08-29T00:00:00Z","collection_date":"19-Dec-2016","bioproject_accession":"PRJNA560883","biosample_accession":"SAMN12603256","genbank_accessions":"CP043213","refseq_accessions":"","genome_status":"Complete","taxon_id":2605619.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Gift of K.Smalla","comments":"Humans and farm animals commonly consume food- or waterborne bacteria that harbour antibiotic resistance genes. The fate and potential horizontal gene transfer of those genes into the host microbiome will have a crucial bearing on the eventual health risk of exposure to antibiotic resistance genes. In the present study, the effects of antibiotics on the in vivo transfer of \ud835\udefd-lactam resistance genes were evaluated in a mouse model by characterizing the microbiome in excreted feces. Mice were dosed with Escherichia coli, Salmonella enterica serovars Heidelberg or Bredeney referred to as donors. The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1943,"n_genes":1551,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.62728.json.json","assembly_accession":"GCA_013389695.1","genome_id":"562.62728","genome_name":"Escherichia coli strain AH65","strain":"strain AH65","serovar":"","phylogroup":"A","MLST":1788,"mash_cluster":22,"isolation_source":"","isolation_country":"China","geographic_location":"China: Fuyang, Anhui","host_name":"Chicken, Gallus gallus","host_health":"no","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5053746.0,"gc_content":50.54328,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5072.0,"refseq_cds":4766.0,"sequencing_platform":"Illumina NovaSeq; Oxford Nanopore MiniION","sequencing_depth":"113.0x","assembly_method":"unicycler v. v0.4.8-beta","sequencing_centers":"Center for Disease Control and Prevention of PLA","completion_date":"2020-07-06T00:00:00Z","collection_date":"2018","bioproject_accession":"PRJNA639233","biosample_accession":"SAMN15229516","genbank_accessions":"CP058302,CP058303,CP058304,CP058305","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Dongdong Yin","comments":"mcr-1 positive E. coli strain AH62","n_reactions":2732,"n_metabolites":1935,"n_genes":1521,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.77348.json.json","assembly_accession":"GCA_019270155.1","genome_id":"562.77348","genome_name":"Escherichia coli strain Colony155","strain":"strain Colony155","serovar":"","phylogroup":"Unknown","MLST":131,"mash_cluster":3,"isolation_source":"Rectal swab","isolation_country":"Thailand","geographic_location":"Thailand","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4733682.0,"gc_content":51.364487,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4420.0,"refseq_cds":"","sequencing_platform":"Illumina HiSeq","sequencing_depth":"85.079x","assembly_method":"idba_ud v. V1.1.3","sequencing_centers":"Ministry of Public Health-Thailand","completion_date":"2021-07-19T00:00:00Z","collection_date":"Not collected","bioproject_accession":"PRJNA668870","biosample_accession":"SAMN17771333","genbank_accessions":"CP078583","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Department of Disease Control, Ministry of Public Health","comments":"Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand","n_reactions":2747,"n_metabolites":2014,"n_genes":1650,"n_exchange":331,"n_with_gpr":2301,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia 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Austin","completion_date":"2018-02-01T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA430697","biosample_accession":"SAMN08380011","genbank_accessions":"CP026353","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:not applicable","comments":"We have carried out directed evolution experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine across from amber codons, creating a 21 amino acid genetic code in which the amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.75686.json.json","assembly_accession":"GCA_018323825.1","genome_id":"562.75686","genome_name":"Escherichia coli strain Ec387","strain":"strain Ec387","serovar":"","phylogroup":"B1","MLST":1196,"mash_cluster":26,"isolation_source":"pigs","isolation_country":"Japan","geographic_location":"Japan:Kagoshima","host_name":"Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5153318.0,"gc_content":50.63202,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5033.0,"refseq_cds":4767.0,"sequencing_platform":"Illumina Hiseq; Nanopore Minion","sequencing_depth":"150x","assembly_method":"Flye v. 2.8.3","sequencing_centers":"Rakuno Gakuen University","completion_date":"2021-04-20T00:00:00Z","collection_date":"2012","bioproject_accession":"PRJDB11508","biosample_accession":"SAMD00297130","genbank_accessions":"AP024582,AP024583,AP024584","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from pigs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Colistin resistant Escherichia coli is world wide concerns. Colistin-resistant E. coli was isolated from pigs. And the resistant isolate have mcr-9 gene related to colistin resistance.","n_reactions":2752,"n_metabolites":2025,"n_genes":1749,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"JPN","country":"Japan"},{"gem_file":"83334.488.json.json","assembly_accession":"GCA_017165115.1","genome_id":"83334.488","genome_name":"Escherichia coli O157:H7 strain Z1723","strain":"O157:H7 strain Z1723","serovar":"O157:H7","phylogroup":"E","MLST":-1,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5825793.0,"gc_content":50.461235,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":6076.0,"refseq_cds":5672.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"205.37685889208512x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327597","genbank_accessions":"CP062739,CP062740,CP062741","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Roslin Institute","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1944,"n_genes":1497,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.70730.json.json","assembly_accession":"GCA_016889105.1","genome_id":"562.70730","genome_name":"Escherichia coli strain FDAARGOS_1254 strain Not applicable","strain":"","serovar":"","phylogroup":"B2","MLST":420,"mash_cluster":6,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4892135.0,"gc_content":50.65165,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":4849.0,"refseq_cds":4616.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"740.26x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4, SPAdes v. 3.14.1","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-15T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357396","genbank_accessions":"CP069453,CP069454,CP069455,CP069456,CP069457,CP069458","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1254","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2752,"n_metabolites":2023,"n_genes":1653,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_004010695.1.json.json","assembly_accession":"GCF_004010695.1","genome_id":"GCF_004010695.1","genome_name":"Escherichia coli","strain":"2010C-3142","serovar":"","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN04505650","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1938,"n_genes":1484,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.61464.json.json","assembly_accession":"GCA_013201505.1","genome_id":"562.61464","genome_name":"Escherichia coli strain 2-101","strain":"strain 2-101","serovar":"","phylogroup":"C","MLST":1998,"mash_cluster":25,"isolation_source":"Bird of prey","isolation_country":"Portugal","geographic_location":"Portugal","host_name":"Bird of prey","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4847710.0,"gc_content":50.618294,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4842.0,"refseq_cds":4567.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"100x","assembly_method":"flye v. 2.7.1","sequencing_centers":"CHU Clermont-ferrand","completion_date":"2020-06-01T00:00:00Z","collection_date":"2008","bioproject_accession":"PRJEB36175","biosample_accession":"SAMEA6471229","genbank_accessions":"CP053785,CP053786","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"recovered from different species of wild animals and farm animals isolated in Portugal and Spain were analyzed by whole-genome sequences","other_clinical":"host_health_state:not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Antimicrobial resistance is a global and multifaceted public health issue as the pandemic spread and evolution of highly resistant bacteria occurred similarly in the human, animal and environmental settings. Even though wild animals are not in direct contact with antibiotics, they are influenced by the excessive use in humans and veterinary medicine. A total of 45 Escherichia coli isolates recovered from different species of wild animals and farm animals isolated in Portugal and Spain were analyzed by whole-genome sequences. Of the 45 strains, 26 were ESBL-producing E. coli. The most frequent ESBL-encoding gene was the blaCTX-M-1 and it was associated to IncI1 plasmid. Therefore, ESBL-producing E. coli has disseminated in several wild animal species, including birds which migrate long distances in short periods of time and thus can be considered as multidrug-resistant bacteria spreaders.","n_reactions":2733,"n_metabolites":1939,"n_genes":1535,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"PRT","country":"Portugal"},{"gem_file":"562.64259.json.json","assembly_accession":"GCA_014170995.1","genome_id":"562.64259","genome_name":"Escherichia coli strain 98.1","strain":"strain 98.1","serovar":"","phylogroup":"B1","MLST":683,"mash_cluster":26,"isolation_source":"Turkey's","isolation_country":"Canada","geographic_location":"Canada","host_name":"Turkey","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4904970.0,"gc_content":50.841022,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4870.0,"refseq_cds":4650.0,"sequencing_platform":"Oxford Nanopore MinION","sequencing_depth":"25.9x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"University of Guelph","completion_date":"2020-08-12T00:00:00Z","collection_date":"2016/2017","bioproject_accession":"PRJNA596173","biosample_accession":"SAMN13613886","genbank_accessions":"CP059953,CP059954","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from Turkey's in Canada","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:fecal","comments":"Chromosomes and plasmids were assembled from E. coli isolated from Turkey's in Canada. Both long reads (Oxford Nanopore) and short reads (Illumina) were used.","n_reactions":2732,"n_metabolites":1937,"n_genes":1520,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.67267.json.json","assembly_accession":"GCA_015139735.1","genome_id":"562.67267","genome_name":"Escherichia coli strain THO-015","strain":"strain THO-015","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"urine","isolation_country":"Japan","geographic_location":"Japan:Tokyo","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5228148.0,"gc_content":50.685577,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5201.0,"refseq_cds":4924.0,"sequencing_platform":"Sequel; NextSeq 500","sequencing_depth":"387x","assembly_method":"flye v. 2.5; minimap v. 0.2-r124; racon v.","sequencing_centers":"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases","completion_date":"2020-10-09T00:00:00Z","collection_date":"2018-07-12","bioproject_accession":"PRJDB9036","biosample_accession":"SAMD00196013","genbank_accessions":"AP022549,AP022550,AP022551,AP022552","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"This project is related to metagenomic survey and genomic epidemiology analysis of antimicrobial resistance bacteria (in particular, carbapenem and/or beta-lactam resistant Enterobacteriaceae) in Japanese hospital sewage.","n_reactions":2732,"n_metabolites":1943,"n_genes":1472,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"JPN","country":"Japan"},{"gem_file":"562.76454.json.json","assembly_accession":"GCA_018884265.1","genome_id":"562.76454","genome_name":"Escherichia coli strain B7A","strain":"strain B7A","serovar":"","phylogroup":"B1","MLST":94,"mash_cluster":26,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Homo sapiens","host_health":"diarrhea","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5240296.0,"gc_content":50.77841,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5280.0,"refseq_cds":"","sequencing_platform":"PacBio RSII","sequencing_depth":"14.99x","assembly_method":"HGAP v. 3","sequencing_centers":"University of Maryland, School of Medicine","completion_date":"2021-06-15T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA521509","biosample_accession":"SAMN10904681","genbank_accessions":"CP035812,CP035816,CP035815,CP035814,CP035813","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates","n_reactions":2752,"n_metabolites":2025,"n_genes":1720,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.52730.json.json","assembly_accession":"GCA_009663835.1","genome_id":"562.52730","genome_name":"Escherichia coli strain INSC1001","strain":"strain INSC1001","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"USA","geographic_location":"USA: Boulder, CO","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4630646.0,"gc_content":50.789284,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4603.0,"refseq_cds":4337.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"58.67x","assembly_method":"canu v. 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This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.","n_reactions":2711,"n_metabolites":1877,"n_genes":1439,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"VNM","country":"Vietnam"},{"gem_file":"562.75650.json.json","assembly_accession":"GCA_018208275.1","genome_id":"562.75650","genome_name":"Escherichia coli strain 179","strain":"strain 179","serovar":"","phylogroup":"A","MLST":46,"mash_cluster":22,"isolation_source":"blood culture, Ankara","isolation_country":"Turkey","geographic_location":"Turkey: Ankara","host_name":"Homo sapiens","host_health":"E coli sepsis","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5127133.0,"gc_content":51.148613,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4753.0,"refseq_cds":4183.0,"sequencing_platform":"IonTorrent","sequencing_depth":"20.0x","assembly_method":"Bowtie 2 v. 2.3.5","sequencing_centers":"Ankara Yildirim Beyazit University","completion_date":"2021-04-29T00:00:00Z","collection_date":"2018-05-12","bioproject_accession":"PRJNA666983","biosample_accession":"SAMN16339631","genbank_accessions":"CP062924,CP062925,CP062926","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Banu Sancak","comments":"This study was carried out to identify the molecular mechanisms that might be responsible for hereroresistance between E. coli and K. pneumoniae clinical isolates","n_reactions":2731,"n_metabolites":1931,"n_genes":1483,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"TUR","country":"Turkey"},{"gem_file":"562.45678.json.json","assembly_accession":"GCA_004295365.1","genome_id":"562.45678","genome_name":"Escherichia coli strain WCHEC025970","strain":"strain WCHEC025970","serovar":"","phylogroup":"A","MLST":167,"mash_cluster":21,"isolation_source":"","isolation_country":"China","geographic_location":"China: Chengdu, Sichuan","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5304202.0,"gc_content":50.582764,"contigs":9.0,"chromosomes":1.0,"plasmids":8.0,"patric_cds":5513.0,"refseq_cds":5164.0,"sequencing_platform":"Illumina HiSeq; Oxford Nanopore MiniION","sequencing_depth":"200.0x","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"West China Hospital, Sichuan University","completion_date":"2019-02-25T00:00:00Z","collection_date":"2017-10","bioproject_accession":"PRJNA418674","biosample_accession":"SAMN10956393","genbank_accessions":"CP036177,CP036180,CP036181,CP036182,CP036183,CP036184,CP036185,CP036178,CP036179","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Pure culture","comments":"The Genome sequencing and assembly of Escherichia spp.","n_reactions":2731,"n_metabolites":1940,"n_genes":1534,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.62718.json.json","assembly_accession":"GCA_013388275.1","genome_id":"562.62718","genome_name":"Escherichia coli strain 550","strain":"strain 550","serovar":"","phylogroup":"D","MLST":69,"mash_cluster":13,"isolation_source":"Rectal swab","isolation_country":"Italy","geographic_location":"Italy: Milan","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5225616.0,"gc_content":50.798374,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5195.0,"refseq_cds":4898.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"433.0x","assembly_method":"Microbial Assembly v. 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The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1935,"n_genes":1530,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_021166015.1.json.json","assembly_accession":"GCF_021166015.1","genome_id":"GCF_021166015.1","genome_name":"Escherichia coli","strain":"7386Nal","serovar":"","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN07666419","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1938,"n_genes":1476,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.66850.json.json","assembly_accession":"GCA_014605875.1","genome_id":"562.66850","genome_name":"Escherichia coli strain EC93","strain":"strain EC93","serovar":"","phylogroup":"B1","MLST":297,"mash_cluster":26,"isolation_source":"","isolation_country":"USA","geographic_location":"USA: Santa Barbara, UCSB animal house","host_name":"Rat, Rattus norvegicus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4953366.0,"gc_content":50.660824,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4776.0,"refseq_cds":4553.0,"sequencing_platform":"PacBio","sequencing_depth":"76.0x","assembly_method":"HGAP v. 3","sequencing_centers":"Uppsala University","completion_date":"2020-09-16T00:00:00Z","collection_date":"2005","bioproject_accession":"PRJNA658456","biosample_accession":"SAMN15871861","genbank_accessions":"CP061329,CP061330","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Single bacteria","comments":"Sequencing of Escherichia coli EC93 rat isolate. 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The plasmid-mediated qnrS1 gene is known to be situated on plasmids with different incompatibility (Inc) groups. In this study, the aim was to select QREC strains encoding qnrS1 situated on plasmids with different Inc-groups and to complete circular plasmid contigs. 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The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.61705.json.json","assembly_accession":"GCA_013372305.1","genome_id":"562.61705","genome_name":"Escherichia coli strain EcPF40","strain":"strain EcPF40","serovar":"","phylogroup":"B2","MLST":1193,"mash_cluster":6,"isolation_source":"urine","isolation_country":"USA","geographic_location":"USA: Dallas, Texas","host_name":"Human, Homo sapiens","host_health":"Chronic Cystitis","host_gender":"female","host_age":"","body_sample_site":"","disease":"","genome_length":5210779.0,"gc_content":50.643677,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5281.0,"refseq_cds":4966.0,"sequencing_platform":"Illumina NextSeq, ONT MinION","sequencing_depth":"64x, 315x","assembly_method":"Unicycler v. v.0.4.14","sequencing_centers":"University of Texas at Dallas","completion_date":"2020-06-24T00:00:00Z","collection_date":"Apr-2019","bioproject_accession":"PRJNA636382","biosample_accession":"SAMN15075998","genbank_accessions":"CP054214,CP054215,CP054216,CP054217,CP054218","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"UPEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"host_description:Postmenopausal","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:UT Southwestern Medical Center/ UT Dallas","comments":"Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.","n_reactions":2733,"n_metabolites":1947,"n_genes":1468,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_014169855.1.json.json","assembly_accession":"GCF_014169855.1","genome_id":"GCF_014169855.1","genome_name":"Escherichia coli","strain":"WP9-S17-ESBL-11","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMD00194670","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1936,"n_genes":1518,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.7257.json.json","assembly_accession":"GCF_001007915.1","genome_id":"562.7257","genome_name":"Escherichia coli strain CFSAN029787","strain":"strain CFSAN029787","serovar":"O96:H19","phylogroup":"B1","MLST":99,"mash_cluster":26,"isolation_source":"Stool sample","isolation_country":"Italy","geographic_location":"Italy:Milan","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5288947.0,"gc_content":50.53,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5537.0,"refseq_cds":5103.0,"sequencing_platform":"PacBio RS","sequencing_depth":"350X","assembly_method":"SMRT Portal HGAP v. 2.3.0","sequencing_centers":"FDA/CFSAN","completion_date":"2015-05-15T00:00:00Z","collection_date":"2012-04-15","bioproject_accession":"PRJNA243331","biosample_accession":"SAMN03612246","genbank_accessions":"CP011416,CP011417,CP011418","refseq_accessions":"NZ_CP011416.1,NZ_CP011417.1,NZ_CP011418.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Draft and complete genome sequences of foodborne bacterial pathogens collected for research purposes at the FDA's Center for Food Safety and Applied Nutrition.","n_reactions":2733,"n_metabolites":1937,"n_genes":1510,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"ITA","country":"Italy"},{"gem_file":"562.63041.json.json","assembly_accession":"GCA_013426095.1","genome_id":"562.63041","genome_name":"Escherichia coli strain WCHEC035125","strain":"strain WCHEC035125","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"sewage","isolation_country":"China","geographic_location":"China: Chengdu, Sichuan","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4944512.0,"gc_content":50.653534,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":4998.0,"refseq_cds":4684.0,"sequencing_platform":"Illumina HiSeq; 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The objective of this study is to characterize clonal, serial isolates that develop carbapenem resistance via non-carbapenemase mechanisms. Our hypothesis is that a proportion of recurrent bacteremia cases due to persistent carriage of the same clonal, re-infecting strains have the ability to develop resistance to carbapenems independent of carbapenemase acquisition within our cancer population. We believe this is occurring through a mobile genetic element amplification mechanism with concomitant outer membrane porin disruption.","n_reactions":2732,"n_metabolites":1943,"n_genes":1472,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83333.105.json.json","assembly_accession":"GCF_000974505.1","genome_id":"83333.105","genome_name":"Escherichia coli K-12 strain ER3476","strain":"K-12 strain ER3476","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4621164.0,"gc_content":50.79,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4664.0,"refseq_cds":4358.0,"sequencing_platform":"PacBio","sequencing_depth":"50-200","assembly_method":"SMRT Analysis v. 2.3","sequencing_centers":"New England Biolabs","completion_date":"2015-04-21T00:00:00Z","collection_date":"Jun-14","bioproject_accession":"PRJNA271807","biosample_accession":"SAMN03277619","genbank_accessions":"CP010440","refseq_accessions":"NZ_CP010440.1","genome_status":"Complete","taxon_id":83333.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"fhuA2::IS2 _(lacZ)4826 glnX44 trpE31 _(hisG)1 gyrA96 recA::cat(FRT) recD1014 rpsL104(StrR) xyl-7 mtlA2(Fs) metB1(FS) mrr::tetAR","substrain":"","additional_metadata":"identified_by:Anthony Kingston;sample_type:Cell Culture","comments":"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.","n_reactions":2733,"n_metabolites":1940,"n_genes":1561,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.471.json.json","assembly_accession":"GCA_017164815.1","genome_id":"83334.471","genome_name":"Escherichia coli O157:H7 strain Z1833","strain":"O157:H7 strain Z1833","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5649174.0,"gc_content":50.41967,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5911.0,"refseq_cds":5468.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"193.01500006903663x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327613","genbank_accessions":"CP062705,CP062706,CP062707","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:BECS Consortium","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"1248902.3.json.json","assembly_accession":"GCA_000520035.1","genome_id":"1248902.3","genome_name":"Escherichia coli O145:H28 str. RM13514","strain":"O145:H28 str. 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RM13514 was a clinical isolate and linked to the 2010 multi-state outbreak of E. coli O145 infection associated with consumption of shredded romaine lettuce in US.\"","n_reactions":2732,"n_metabolites":1941,"n_genes":1489,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.70510.json.json","assembly_accession":"GCA_016775945.1","genome_id":"562.70510","genome_name":"Escherichia coli strain RIVM_C029020","strain":"strain RIVM_C029020","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5251089.0,"gc_content":50.613846,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5197.0,"refseq_cds":4872.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"National Institute for Public Health and the Environment","completion_date":"2021-02-01T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA691727","biosample_accession":"SAMN17373188","genbank_accessions":"CP068812","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:chromosome","comments":"OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2732,"n_metabolites":1938,"n_genes":1517,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"562.58113.json.json","assembly_accession":"GCA_009951245.1","genome_id":"562.58113","genome_name":"Escherichia coli strain STEC313 strain not applicable","strain":"","serovar":"","phylogroup":"B1","MLST":1611,"mash_cluster":26,"isolation_source":"Raw beef","isolation_country":"China","geographic_location":"China: 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1485,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_003956365.1.json.json","assembly_accession":"GCF_003956365.1","genome_id":"GCF_003956365.1","genome_name":"Escherichia 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The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1936,"n_genes":1535,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.63088.json.json","assembly_accession":"GCA_902810325.1","genome_id":"562.63088","genome_name":"Escherichia coli strain SC423","strain":"strain SC423","serovar":"","phylogroup":"B1","MLST":2005,"mash_cluster":26,"isolation_source":"Sediment","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4716885.0,"gc_content":50.881237,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4521.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"MASSEY UNIVERSITY","completion_date":"2020-06-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB36951","biosample_accession":"SAMEA6595220","genbank_accessions":"LR778145","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Mike Sadowsky","comments":"Here we report the complete genomes of 47 Escherichia coli natural isolates, sampled from watersheds located at (46\u00b042\u203204\"N, 92\u00b012\u203226\"W) in Duluth, Minnesota. 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"1274814.3.json.json","assembly_accession":"GCA_000332755.1","genome_id":"1274814.3","genome_name":"Escherichia coli APEC O78","strain":"APEC O78","serovar":"","phylogroup":"C","MLST":23,"mash_cluster":25,"isolation_source":"the lung of a turkey clinically diagnosed with colibacillosis","isolation_country":"","geographic_location":"","host_name":"Turkey, Meleagris gallopavo","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Colibacillosis","genome_length":4798435.0,"gc_content":50.7,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4716.0,"refseq_cds":4589.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Iowa State University","completion_date":"2013-01-23T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA184588","biosample_accession":"SAMN02603426","genbank_accessions":"CP004009.1","refseq_accessions":"NC_020163.1","genome_status":"Complete","taxon_id":1274814.0,"organism_name":"Escherichia coli APEC O78","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from the lung of a turkey clinically diagnosed with colibacillosis","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting turkeys, layers, and broilers. Here we describe the sequence of APEC O78, an O78 strain isolated from the lung of a turkey clinically diagnosed with colibacillosis. Functional analysis of the genome should enhance the community\u00bf\u00bf\u00bf\u00bf\u00bf\u00bf\u00bfs knowledge of the pathogenesis of avian pathogenic E. coli.","n_reactions":2733,"n_metabolites":1938,"n_genes":1535,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1446707.3.json.json","assembly_accession":"GCA_002741175.1","genome_id":"1446707.3","genome_name":"Escherichia coli O25:NM strain 2014EL-1343-2","strain":"O25:NM strain 2014EL-1343-2","serovar":"O25:NM","phylogroup":"A","MLST":1312,"mash_cluster":22,"isolation_source":"","isolation_country":"United States","geographic_location":"United States","host_name":"","host_health":"","host_gender":"","host_age":"50-59","body_sample_site":"","disease":"","genome_length":5042926.0,"gc_content":50.71,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5050.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"91.0x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2017-11-02T00:00:00Z","collection_date":"Jul-2014","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN04578538","genbank_accessions":"CP024228,CP024229,CP024230,CP024231","refseq_accessions":"","genome_status":"Complete","taxon_id":1446707.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CDC","comments":"PulseNet STEC genome reference library","n_reactions":2733,"n_metabolites":1941,"n_genes":1536,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.76453.json.json","assembly_accession":"GCA_018884065.1","genome_id":"562.76453","genome_name":"Escherichia coli strain E2","strain":"strain E2","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"ascitic fluid","isolation_country":"Egypt","geographic_location":"Egypt:Giza","host_name":"Homo sapiens","host_health":"post-hepatitis cirrhosis","host_gender":"female","host_age":"52","body_sample_site":"","disease":"","genome_length":4998048.0,"gc_content":50.56514,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5008.0,"refseq_cds":4716.0,"sequencing_platform":"Oxford Nanopore MiniION; Illumina MiSeq","sequencing_depth":"70.0x","assembly_method":"Unicycler v. v0.4.7","sequencing_centers":"Hospital Universitari Vall d'Hebron","completion_date":"2021-06-15T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA577622","biosample_accession":"SAMN13031456","genbank_accessions":"CP048915,CP048917,CP048919,CP048916,CP048918","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"27048740","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Theodor Bilharz Research Institut","comments":"Escherichia coli clinical isolates ST410 co-producers of NDM-5 and OXA-181 collected from a traveler returning from Pakistan. 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Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. 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In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1488,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_016942475.1.json.json","assembly_accession":"GCF_016942475.1","genome_id":"GCF_016942475.1","genome_name":"Escherichia 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With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2752,"n_metabolites":2023,"n_genes":1729,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_021534945.1.json.json","assembly_accession":"GCF_021534945.1","genome_id":"GCF_021534945.1","genome_name":"Escherichia 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This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.29114.json.json","assembly_accession":"GCA_003018655.1","genome_id":"562.29114","genome_name":"Escherichia coli strain 2013C-3181","strain":"strain 2013C-3181","serovar":"E. coli O113:H21","phylogroup":"B1","MLST":3695,"mash_cluster":26,"isolation_source":"Stool","isolation_country":"United States","geographic_location":"United States","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"80-89","body_sample_site":"","disease":"","genome_length":5167951.0,"gc_content":50.78357,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5138.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"110.444x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Jan-2013","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN02991250","genbank_accessions":"CP027312","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CDC","comments":"PulseNet STEC genome reference library","n_reactions":2731,"n_metabolites":1936,"n_genes":1517,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"2605619.16.json.json","assembly_accession":"GCA_008124365.1","genome_id":"2605619.16","genome_name":"Escherichia coli O16:H48 strain PG20180052","strain":"O16:H48 strain PG20180052","serovar":"O16:H48","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"mouse gut","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4680348.0,"gc_content":50.64241,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4764.0,"refseq_cds":4474.0,"sequencing_platform":"Illumina MiSeq and Nanopore","sequencing_depth":"87x","assembly_method":"Unicycler v. 0.4.3","sequencing_centers":"National Microbiology Laboratory at Guelph","completion_date":"2019-08-29T00:00:00Z","collection_date":"18-May-2018","bioproject_accession":"PRJNA560883","biosample_accession":"SAMN12603258","genbank_accessions":"CP043209,CP043210","refseq_accessions":"","genome_status":"Complete","taxon_id":2605619.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Canadian Food Inspection Agency","comments":"Humans and farm animals commonly consume food- or waterborne bacteria that harbour antibiotic resistance genes. The fate and potential horizontal gene transfer of those genes into the host microbiome will have a crucial bearing on the eventual health risk of exposure to antibiotic resistance genes. In the present study, the effects of antibiotics on the in vivo transfer of \ud835\udefd-lactam resistance genes were evaluated in a mouse model by characterizing the microbiome in excreted feces. Mice were dosed with Escherichia coli, Salmonella enterica serovars Heidelberg or Bredeney referred to as donors. The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1936,"n_genes":1535,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"316407.41.json.json","assembly_accession":"GCF_001878695.1","genome_id":"316407.41","genome_name":"Escherichia coli str. K-12 substr. W3110","strain":"str. K-12 substr. 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Kaspar","comments":"Comparative genomic analysis of E. coli O157:H7 strains isolated from a Farm in Wisconsin","n_reactions":2731,"n_metabolites":1938,"n_genes":1481,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.67023.json.json","assembly_accession":"GCA_014863725.1","genome_id":"562.67023","genome_name":"Escherichia coli strain AML003_ev02","strain":"strain AML003_ev02","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"not applicable","isolation_country":"USA","geographic_location":"USA: Boston","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4631469.0,"gc_content":50.778664,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4508.0,"refseq_cds":"","sequencing_platform":"Illumina NextSeq","sequencing_depth":"50x","assembly_method":"breseq v. 0.35.1","sequencing_centers":"Boston University","completion_date":"2020-10-08T00:00:00Z","collection_date":"06-Dec-2019","bioproject_accession":"PRJNA666010","biosample_accession":"SAMN16090669","genbank_accessions":"CP062244","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolate from each separate evolution experiment and the parent strains are provided here","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"Cm resistance","substrain":"","additional_metadata":"sample_type:cell culture;biomaterial_provider:M.J. Dunlop, Boston University, 44 Cummington Mall, Boston, MA 02221;collected_by:A.M. Langevin;passage_history:72 h turbidostat with 5\ufffdg/mL Cm","comments":"In this work, we evolved strains of Escherichia coli with different genotypes related to the AcrAB-TolC efflux pump. Parent strains were either wild type, had the pump overexpressed, or had the pump knocked out. We evolved these three strains under different levels of chloramphenicol. Each parent strain was evolved in an evolution experiment using three biological replicates. The most resistant isolate from each separate evolution experiment and the parent strains are provided here. The goal of this work was to identify which chloramphenicol concentrations promote the evolution of antibiotic resistance and how the presence of the AcrAB-TolC pump impacts this evolution.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_900636005.1.json.json","assembly_accession":"GCF_900636005.1","genome_id":"GCF_900636005.1","genome_name":"Escherichia coli","strain":"NCTC11476","serovar":"","phylogroup":"B1","MLST":297,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMEA3368289","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1942,"n_genes":1518,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.29108.json.json","assembly_accession":"GCA_003018795.1","genome_id":"562.29108","genome_name":"Escherichia coli strain 2012C-4606","strain":"strain 2012C-4606","serovar":"E. coli O26:H11","phylogroup":"B1","MLST":21,"mash_cluster":23,"isolation_source":"Stool","isolation_country":"United States","geographic_location":"United States","host_name":"","host_health":"","host_gender":"","host_age":"30-39","body_sample_site":"","disease":"","genome_length":5725796.0,"gc_content":50.627666,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":6019.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"80.59x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Nov-2012","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN04498549","genbank_accessions":"CP027352,CP027353,CP027354","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CT","comments":"PulseNet STEC genome reference library","n_reactions":2731,"n_metabolites":1938,"n_genes":1521,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.50950.json.json","assembly_accession":"GCA_008632595.1","genome_id":"562.50950","genome_name":"Escherichia coli strain ST95-32","strain":"strain ST95-32","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"","isolation_country":"China","geographic_location":"China:Nanjing","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5517367.0,"gc_content":50.413776,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5721.0,"refseq_cds":5403.0,"sequencing_platform":"Illumina NovaSeq; 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Escherichia coli ED1a is an avirulent serogroup O81 strain and will be used for comparative analysis.","n_reactions":2733,"n_metabolites":1945,"n_genes":1445,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.76356.json.json","assembly_accession":"GCA_018734065.1","genome_id":"562.76356","genome_name":"Escherichia coli strain F11","strain":"strain F11","serovar":"","phylogroup":"B2","MLST":127,"mash_cluster":6,"isolation_source":"urine","isolation_country":"","geographic_location":"","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5162531.0,"gc_content":50.44849,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5056.0,"refseq_cds":4756.0,"sequencing_platform":"Illumina NextSeq; PacBio RSII","sequencing_depth":"65.0x","assembly_method":"Flye v. 2.8.1-b1676","sequencing_centers":"University of Queensland","completion_date":"2021-06-07T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA729869","biosample_accession":"SAMN19237597","genbank_accessions":"CP076123,CP076124","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Extra-intestinal pathogenic Escherichia coli (ExPEC) are members of a critical priority group of antibiotic resistant pathogens that cause severe human disease. ExPEC produce multiple virulence factors that contribute to host colonisation and infection, including adhesins from the chaperone-usher fimbriae class. ExPEC Ucl fimbriae mediate attachment to human exfoliated uroepithelial cells, biofilm formation and intestinal colonization. Here, we show that the ucl fimbrial genes are predominantly found in ExPEC strains from the B2 phylogeny. Genome editing of representative strains from two common sequence types, F11 (ST127) and UTI89 (ST95), identified a single nucleotide polymorphism in the ucl promoter region that increases Ucl fimbrial expression via activation by the global regulator OxyR, leading to enhanced colonisation of the mouse gut. We determined the glycan receptor repertoire and crystal structure of the UclD lectin domain, as well as the homologous UcaD fimbrial adhesin from Proteus mirabilis. Despite their conserved tertiary structure, glycan array analysis showed both adhesins recognise different oligosaccharides. Structural analyses of UcaD in complex with monosaccharides revealed a glycan binding pocket, providing a framework for the development of novel anti-adhesion drugs","n_reactions":2733,"n_metabolites":1946,"n_genes":1449,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.17710.json.json","assembly_accession":"GCA_002196475.1","genome_id":"562.17710","genome_name":"Escherichia coli strain EC974","strain":"strain EC974","serovar":"","phylogroup":"E","MLST":219,"mash_cluster":20,"isolation_source":"urine; urinary tract infection","isolation_country":"Taiwan","geographic_location":"Taiwan","host_name":"Human, Homo sapiens","host_health":"Urinary Tract 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It is frequently associated with antimicrobial resistance to several drug classes, including to fluoroquinolones, aminoglycosides and extended-spectrum cephalosporins. Resistance to extended-spectrum cephalosporins is often attributable to the presence of CTX-M genes encoding extended spectrum beta-lactamases. This study used whole genome sequencing to characterize the evolutionary history of the lineage as it has emerged and spread worldwide, and to explain the genetic context of the CTX-M genes. In order to do this, several DH10B E. coli isolates were transformed with extracted CTX-M plasmids, then sequenced, enabling an approximate reconstruction of the plasmid sequences by bioinformatically removing DH10B-associated reads and undertaking de novo assembly of the residual data.","n_reactions":2711,"n_metabolites":1877,"n_genes":1411,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.74672.json.json","assembly_accession":"GCA_017815815.1","genome_id":"562.74672","genome_name":"Escherichia coli strain SCU-101","strain":"strain SCU-101","serovar":"","phylogroup":"B2","MLST":1262,"mash_cluster":5,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5370586.0,"gc_content":50.453526,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5398.0,"refseq_cds":5070.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"91x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2021-04-07T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609767","genbank_accessions":"CP051849,CP051850,CP051851,CP051852","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"32759337","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. 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The goal of this work was to identify which chloramphenicol concentrations promote the evolution of antibiotic resistance and how the presence of the AcrAB-TolC pump impacts this evolution.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.79348.json.json","assembly_accession":"GCA_020091645.1","genome_id":"562.79348","genome_name":"Escherichia coli strain ECNB21-M121","strain":"strain ECNB21-M121","serovar":"","phylogroup":"E","MLST":1140,"mash_cluster":20,"isolation_source":"meat","isolation_country":"China","geographic_location":"China:Zhejiang","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5271753.0,"gc_content":50.518433,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5351.0,"refseq_cds":5029.0,"sequencing_platform":"Nanopore","sequencing_depth":"100.0x","assembly_method":"Unicycler v. 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Using long reads we completely resolved the structure of two tandemly inserted stx2-converting phage in 95NR1. Our analysis of the methylome of 95NR1 identified hemimethylation of a novel motif (5\u2019-CTGCm6AG-3\u2019) in more than 4000 sites in the genome. This study demonstrates the enormous potential of SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.","n_reactions":2731,"n_metabolites":1937,"n_genes":1510,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"1311757.3.json.json","assembly_accession":"GCF_001051135.1","genome_id":"1311757.3","genome_name":"Escherichia coli ACN001","strain":"ACN001","serovar":"","phylogroup":"C","MLST":23,"mash_cluster":25,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4936576.0,"gc_content":50.67,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4909.0,"refseq_cds":4794.0,"sequencing_platform":"454","sequencing_depth":"23.58x","assembly_method":"Newbler v. 2.3","sequencing_centers":"Huazhong Agricultural University","completion_date":"2015-07-09T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA194515","biosample_accession":"SAMN03852615","genbank_accessions":"CP007442","refseq_accessions":"NZ_CP007442.1","genome_status":"Complete","taxon_id":1311757.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Avian pathogenic E. coli strains represent potential zoonotic risk and should be worthy of attention. The whole genome sequencing of this avian pathogenic E. coli strain ACN001, including the sequencing of plasmids it contained could provide more information for better understanding the genome diversity and the virulence variation, and contribute to the control and prevention of the plasmid-mediated multidrug resistance.","n_reactions":2734,"n_metabolites":1938,"n_genes":1538,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_013374255.1.json.json","assembly_accession":"GCF_013374255.1","genome_id":"GCF_013374255.1","genome_name":"Escherichia coli","strain":"YJ1","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMD00157542","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1939,"n_genes":1528,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_021398935.1.json.json","assembly_accession":"GCF_021398935.1","genome_id":"GCF_021398935.1","genome_name":"Escherichia coli LF82","strain":"LF82","serovar":"","phylogroup":"B2","MLST":135,"mash_cluster":6,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN21159024","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":591946.0,"organism_name":"Escherichia coli LF82","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1946,"n_genes":1450,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.352.json.json","assembly_accession":"GCA_013167495.1","genome_id":"83334.352","genome_name":"Escherichia coli O157:H7 strain LSU61","strain":"O157:H7 strain LSU61","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:Louisiana","host_name":"Deer","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5669067.0,"gc_content":50.391827,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5956.0,"refseq_cds":5649.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"369x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11229493","genbank_accessions":"CP038336,CP038338,CP038337","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. 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This strain (CFT073\\; O6:K2:H1) is uropathogenic E. coli (UPEC) one of the most common causes of non-hospital-acquired urinary tract infections. There are numerous important differences between EHEC and UPEC, namely the loss of specific virulence factors such as the type III secretion system and plasmid- and phage-associated PAIs. UPEC has gained fimbrial operons, including genes for production of Pap pili, as well as other virulence factors that allow it to colonize the urinary tract.","n_reactions":2734,"n_metabolites":1945,"n_genes":1454,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.76478.json.json","assembly_accession":"GCA_018972265.1","genome_id":"562.76478","genome_name":"Escherichia coli strain S103EC","strain":"strain S103EC","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"Australia","geographic_location":"Australia:Brisbane","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5337095.0,"gc_content":50.71227,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5442.0,"refseq_cds":5134.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"149x","assembly_method":"flye v. 2.5","sequencing_centers":"University of Queensland","completion_date":"2021-06-21T00:00:00Z","collection_date":"2010-01","bioproject_accession":"PRJNA737575","biosample_accession":"SAMN19700014","genbank_accessions":"CP076693,CP076694,CP076696,CP076695","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"In this project, we described the diversity and prevalence of afa/dr fimbria genes in ST131, revealing the dominance of a new afaE-IX allelic variant. We additionally showed how different IS elements can alter the regulation of afa transcription and provide evidence for a more widespread impact of IS1 on ST131 genome evolution.The genomes in this BioProject are 4 ST131 representative strains with different IS elements located in the promoter region of afa operon. These genomes are assembled using Nanopore long reads and polished with Illumina short reads.","n_reactions":2732,"n_metabolites":1943,"n_genes":1474,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"562.48255.json.json","assembly_accession":"GCA_900699165.1","genome_id":"562.48255","genome_name":"Escherichia coli strain NCTC86","strain":"strain NCTC86","serovar":"O(Rough):H10","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"not available: not collected","isolation_country":"","geographic_location":"","host_name":"not available: not collected","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5102517.0,"gc_content":50.690197,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5042.0,"refseq_cds":4708.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"SC","completion_date":"2019-03-01T00:00:00Z","collection_date":"1885","bioproject_accession":"PRJEB6403","biosample_accession":"SAMEA3446340","genbank_accessions":"LR217818","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"NCTC:86","publication":"","isolation_comments":"","other_clinical":"host_health_state:not available: not collected","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/","n_reactions":2731,"n_metabolites":1937,"n_genes":1547,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.353.json.json","assembly_accession":"GCA_013167475.1","genome_id":"83334.353","genome_name":"Escherichia coli O157:H7 strain N8B7-2","strain":"O157:H7 strain N8B7-2","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle feces","isolation_country":"USA","geographic_location":"USA:Nebraska","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5658182.0,"gc_content":50.44494,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":6010.0,"refseq_cds":5711.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"178x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN05360221","genbank_accessions":"CP038333,CP038335,CP038334","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. 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JANUARY-2020","sequencing_centers":"Shandong Agricultural University","completion_date":"2021-04-27T00:00:00Z","collection_date":"2017-12-26","bioproject_accession":"PRJNA638999","biosample_accession":"SAMN15214392","genbank_accessions":"CP056073,CP056074,CP056075","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:faeces","comments":"The objective of this study was to investigate the prevalence of FosA3-producing Escherichia coli isolates in ducks","n_reactions":2711,"n_metabolites":1877,"n_genes":1482,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"83334.354.json.json","assembly_accession":"GCA_013167515.1","genome_id":"83334.354","genome_name":"Escherichia coli O157:H7 strain H6437","strain":"O157:H7 strain H6437","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5626776.0,"gc_content":50.361576,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5937.0,"refseq_cds":5618.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"259x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11229492","genbank_accessions":"CP038339,CP038341,CP038340","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.63782.json.json","assembly_accession":"GCA_014075475.1","genome_id":"562.63782","genome_name":"Escherichia coli strain 74-2","strain":"strain 74-2","serovar":"","phylogroup":"A","MLST":7187,"mash_cluster":22,"isolation_source":"","isolation_country":"China","geographic_location":"China:Sichuan","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4900056.0,"gc_content":50.68293,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4851.0,"refseq_cds":4580.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"100x","assembly_method":"Unicycler v. v0.3.4","sequencing_centers":"China Agricutual University","completion_date":"2020-08-05T00:00:00Z","collection_date":"2019-05-14","bioproject_accession":"PRJNA610125","biosample_accession":"SAMN14278031","genbank_accessions":"CP050044,CP050045,CP050046","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"tet(X4) RESEARCH","n_reactions":2732,"n_metabolites":1939,"n_genes":1514,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.50511.json.json","assembly_accession":"GCA_007108305.1","genome_id":"562.50511","genome_name":"Escherichia coli strain 963","strain":"strain 963","serovar":"","phylogroup":"D","MLST":963,"mash_cluster":15,"isolation_source":"blood","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"Bloodstream infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5253812.0,"gc_content":50.697525,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5296.0,"refseq_cds":5013.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"100x","assembly_method":"HGAP v. 4","sequencing_centers":"Duke University","completion_date":"2019-07-18T00:00:00Z","collection_date":"2012","bioproject_accession":"PRJNA551684","biosample_accession":"SAMN12163100","genbank_accessions":"CP041532,CP041533,CP041534","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Vance G. Fowler Jr.","comments":"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2751,"n_metabolites":2025,"n_genes":1690,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_004405205.2.json.json","assembly_accession":"GCF_004405205.2","genome_id":"GCF_004405205.2","genome_name":"Escherichia coli","strain":"GZ04-0086","serovar":"","phylogroup":"A","MLST":44,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN11174938","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1937,"n_genes":1514,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13759.json.json","assembly_accession":"GCF_001900775.1","genome_id":"562.13759","genome_name":"Escherichia coli strain H1","strain":"strain H1","serovar":"","phylogroup":"A","MLST":193,"mash_cluster":22,"isolation_source":"river water","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4826576.0,"gc_content":50.89,"contigs":3.0,"chromosomes":3.0,"plasmids":"","patric_cds":4864.0,"refseq_cds":4550.0,"sequencing_platform":"Illumina Miseq; Roche 454 GS Junior","sequencing_depth":"30-80x","assembly_method":"Newbler v. 2.7","sequencing_centers":"Nanjing Agricultural University","completion_date":"2016-12-12T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA269191","biosample_accession":"SAMN03252429","genbank_accessions":"CP010160,CP010161,CP010162","refseq_accessions":"NZ_CP010160.1,NZ_CP010161.1,NZ_CP010162.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"env_biome:water","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments","n_reactions":2734,"n_metabolites":1944,"n_genes":1521,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.60270.json.json","assembly_accession":"GCA_012934615.1","genome_id":"562.60270","genome_name":"Escherichia coli strain SCU-123","strain":"strain SCU-123","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5260004.0,"gc_content":50.631367,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5325.0,"refseq_cds":5009.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"44x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-04-30T00:00:00Z","collection_date":"2016","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609783","genbank_accessions":"CP051711,CP051712,CP051713","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2732,"n_metabolites":1944,"n_genes":1458,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"511145.879.json.json","assembly_accession":"GCA_904425475.1","genome_id":"511145.879","genome_name":"Escherichia coli str. K-12 substr. MG1655","strain":"str. K-12 substr. 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In E. coli, most functional genomic studies have been limited to the laboratory-evolved model strain K12 which is not representative of the broad diversity of the E. coli species. Indeed, E. coli is characterized by an open pangenome with high rates of recombination and horizontal gene transfer. While gene essentiality is known to be evolutionary conserved, it remains to be investigated to what extent this holds true in a species with such a genetic diversity. Here, we used CRISPRi screening to evaluate how the genetic background affects gene essentiality in E. coli. We designed a sgRNA library targeting ~3,300 conserved genes and used it in 18 E. coli isolates to evaluate the fitness of each knockdown in 3 different growth conditions. As expected, most gene essentiality was conserved across all tested strains but the screens highlighted strain-specific effects showing that gene essentiality can vary at the strain level. In particular, these differences involve some highly-studied genes such as the sigma factor E and the Lon and ClpXP proteases. We further showed that mobile genetic elements can modify the essentiality of conserved genes and that a significant part of the core genome is susceptible to become essential under certain genetic backgrounds.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_021398975.1.json.json","assembly_accession":"GCF_021398975.1","genome_id":"GCF_021398975.1","genome_name":"Escherichia coli O99:H6","strain":"O99:H6","serovar":"","phylogroup":"B2","MLST":1859,"mash_cluster":6,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN21159022","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":2874051.0,"organism_name":"Escherichia coli O99:H6","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1946,"n_genes":1451,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"511145.180.json.json","assembly_accession":"GCA_000269645.1","genome_id":"511145.180","genome_name":"Escherichia coli str. 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Escherichia coli MG1655 was one of these five microbial genomes. At least two libraries (short fragment and jumping) were generated and sequenced using Illumina. Likewise in particular for E. coli, libraries were also generated and run for 454 sequencing. Genomic DNA from Erica Sodergren. Two different genome assemblies are part of this project. The assembly in AKBV00000000 is the complete chromosome assembled from Illumina reads. The assembly in AKVX00000000 is the complete chromosome assembled from reads used to assemble U000096 plus reads from a different isolate of the strain.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.48225.json.json","assembly_accession":"GCA_900520365.1","genome_id":"562.48225","genome_name":"Escherichia coli strain Escherichia coli str. TO217","strain":"strain Escherichia coli str. 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Dunlop, Boston University, 44 Cummington Mall, Boston, MA 02217;collected_by:A.M. Langevin;passage_history:72 h turbidostat with 2\ufffdg/mL Cm","comments":"In this work, we evolved strains of Escherichia coli with different genotypes related to the AcrAB-TolC efflux pump. Parent strains were either wild type, had the pump overexpressed, or had the pump knocked out. We evolved these three strains under different levels of chloramphenicol. Each parent strain was evolved in an evolution experiment using three biological replicates. The most resistant isolate from each separate evolution experiment and the parent strains are provided here. The goal of this work was to identify which chloramphenicol concentrations promote the evolution of antibiotic resistance and how the presence of the AcrAB-TolC pump impacts this evolution.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.366.json.json","assembly_accession":"GCA_013167775.1","genome_id":"83334.366","genome_name":"Escherichia coli O157:H7 strain F6294","strain":"O157:H7 strain F6294","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"beef","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5685865.0,"gc_content":50.50577,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":6027.0,"refseq_cds":5718.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"212x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11229489","genbank_accessions":"CP038372,CP038373","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.20516.json.json","assembly_accession":"GCA_002393365.1","genome_id":"562.20516","genome_name":"Escherichia coli strain FDAARGOS_403","strain":"FDAARGOS_403","serovar":"O104:H4","phylogroup":"B1","MLST":678,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5475414.0,"gc_content":50.63,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5827.0,"refseq_cds":5684.0,"sequencing_platform":"PacBio; Illumina","sequencing_depth":"24.86x","assembly_method":"SMRT v. 2.3.0, HGAP v. 3","sequencing_centers":"US Food and Drug Administration","completion_date":"2017-09-28T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN07312447","genbank_accessions":"CP023535,CP023534,CP023533,CP023532","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_403","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USAMRIID < Columbia University","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: \u2022Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. \u2022Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). \u2022Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2711,"n_metabolites":1877,"n_genes":1466,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13742.json.json","assembly_accession":"GCF_001900415.1","genome_id":"562.13742","genome_name":"Escherichia coli strain H5","strain":"strain H5","serovar":"","phylogroup":"A","MLST":197,"mash_cluster":22,"isolation_source":"river water","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4833228.0,"gc_content":50.75,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4817.0,"refseq_cds":4535.0,"sequencing_platform":"Illumina Miseq; Roche 454 GS Junior","sequencing_depth":"30-80x","assembly_method":"Newbler v. 2.7","sequencing_centers":"Nanjing Agricultural University","completion_date":"2016-12-12T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA269191","biosample_accession":"SAMN03252432","genbank_accessions":"CP010169","refseq_accessions":"NZ_CP010169.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"env_biome:water","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments","n_reactions":2731,"n_metabolites":1937,"n_genes":1513,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1078032.3.json.json","assembly_accession":"GCA_005037845.2","genome_id":"1078032.3","genome_name":"Escherichia coli O45:H2 strain FWSEC0003","strain":"O45:H2 strain FWSEC0003","serovar":"O45:H2","phylogroup":"B1","MLST":17,"mash_cluster":26,"isolation_source":"Clinical: Human (Homo sapiens)","isolation_country":"Canada","geographic_location":"Canada:Nova Scotia,Halifax","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5680623.0,"gc_content":50.60373,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":6253.0,"refseq_cds":6018.0,"sequencing_platform":"Illumina MiSeq;Oxford Nanopore MinION","sequencing_depth":"100.74x;244.02x","assembly_method":"Unicycler;Canu v. 0.4.4.0;1.7","sequencing_centers":"National Microbiology Laboratory","completion_date":"2019-05-03T00:00:00Z","collection_date":"2005","bioproject_accession":"PRJNA287560","biosample_accession":"SAMN08768104","genbank_accessions":"NJGS01000000","refseq_accessions":"","genome_status":"Complete","taxon_id":1078032.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"is from Environmental, animal husbandry, food samples, and medical isolates","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"Mesophilic","optimal_temperature":"37 C","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"collected_by:National Microbiology Laboratory: Public Health Agency of Canada","comments":"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.","n_reactions":2732,"n_metabolites":1939,"n_genes":1526,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.7235.json.json","assembly_accession":"GCF_000971615.1","genome_id":"562.7235","genome_name":"Escherichia coli strain CI5","strain":"strain CI5","serovar":"","phylogroup":"B1","MLST":5082,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5092643.0,"gc_content":50.66,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5163.0,"refseq_cds":4879.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"National University of Singapore and Genome Institute of Singapore","completion_date":"2015-06-10T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA277394","biosample_accession":"SAMN03390066","genbank_accessions":"CP011018,CP011019","refseq_accessions":"NZ_CP011018.1,NZ_CP011019.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"26021932","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Bacterial isolate","comments":"Sequencing of E. coli CI5","n_reactions":2752,"n_metabolites":2025,"n_genes":1659,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.53932.json.json","assembly_accession":"GCA_009664455.1","genome_id":"562.53932","genome_name":"Escherichia coli strain AUSMDU00002545","strain":"strain AUSMDU00002545","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"Australia","geographic_location":"Australia","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5647778.0,"gc_content":50.47716,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5895.0,"refseq_cds":5464.0,"sequencing_platform":"PacBio RSII, Illumina NextSeq","sequencing_depth":"68x","assembly_method":"HGAP v. 3","sequencing_centers":"Microbiological Diagnostic Unit","completion_date":"2019-11-17T00:00:00Z","collection_date":"2013","bioproject_accession":"PRJNA556438","biosample_accession":"SAMN13191633","genbank_accessions":"CP045975,CP045976","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.","n_reactions":2731,"n_metabolites":1939,"n_genes":1489,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"562.45686.json.json","assembly_accession":"GCA_004328685.1","genome_id":"562.45686","genome_name":"Escherichia coli strain D72","strain":"strain D72","serovar":"","phylogroup":"A","MLST":1114,"mash_cluster":22,"isolation_source":"","isolation_country":"China","geographic_location":"China: Henan","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4851057.0,"gc_content":50.826694,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":4929.0,"refseq_cds":4656.0,"sequencing_platform":"Illumina; Oxford Nanopore MiniION","sequencing_depth":"60.0x","assembly_method":"unicycler v. 0.4.4","sequencing_centers":"Henan Agricultural University","completion_date":"2019-03-06T00:00:00Z","collection_date":"2017-10-01","bioproject_accession":"PRJNA515800","biosample_accession":"SAMN10768946","genbank_accessions":"CP035312,CP035314,CP035316,CP035315,CP035313","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:faecal sample","comments":"genome of an MCR-1-producing E. coli strain","n_reactions":2731,"n_metabolites":1930,"n_genes":1496,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.7386.json.json","assembly_accession":"GCF_001183645.1","genome_id":"562.7386","genome_name":"Escherichia coli strain DH1Ec095","strain":"strain DH1Ec095","serovar":"","phylogroup":"A","MLST":1060,"mash_cluster":21,"isolation_source":"","isolation_country":"USA","geographic_location":"USA: Walnut Creek","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4614223.0,"gc_content":50.83,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4607.0,"refseq_cds":4352.0,"sequencing_platform":"Illumina","sequencing_depth":">200x","assembly_method":"Geneious v. 8.1.2","sequencing_centers":"Joint Genome Institute","completion_date":"2015-07-21T00:00:00Z","collection_date":"01-Dec-2013","bioproject_accession":"PRJNA290012","biosample_accession":"SAMN03861948","genbank_accessions":"CP012125","refseq_accessions":"NZ_CP012125.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"C","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Whole genome sequencing to detect off-target changes (if any) after CRISPR-Cas9 editings","n_reactions":2732,"n_metabolites":1940,"n_genes":1559,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.47708.json.json","assembly_accession":"GCA_005886035.1","genome_id":"562.47708","genome_name":"Escherichia coli strain A1_136","strain":"strain A1_136","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"feces","isolation_country":"USA","geographic_location":"USA: Alaska, Kasilof River","host_name":"Larus sp. (gull)","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5305706.0,"gc_content":50.626213,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5386.0,"refseq_cds":5125.0,"sequencing_platform":"Illumina HiSeq; PacBio Sequel","sequencing_depth":"123.0x","assembly_method":"Unicycler v. NOV-2018","sequencing_centers":"USGS","completion_date":"2019-05-29T00:00:00Z","collection_date":"20-Jun-2016","bioproject_accession":"PRJNA521419","biosample_accession":"SAMN10887812","genbank_accessions":"CP040390","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:pure culture","comments":"Gull feces were sampled at seven locations in Alaska and cultured for carbapenem resistant E. coli. Seven isolates harbored plasmid-encoded blaKPC-2 or chromosomally-encoded blaOXA-48, and genes associated with antimicrobial resistance towards up to eight antibiotic classes.","n_reactions":2731,"n_metabolites":1936,"n_genes":1518,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_014904435.2.json.json","assembly_accession":"GCF_014904435.2","genome_id":"GCF_014904435.2","genome_name":"Escherichia coli","strain":"NT1F10","serovar":"","phylogroup":"A","MLST":761,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN16120638","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1934,"n_genes":1528,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.67257.json.json","assembly_accession":"GCA_015033265.1","genome_id":"562.67257","genome_name":"Escherichia coli strain ERP001","strain":"strain ERP001","serovar":"","phylogroup":"B2","MLST":1946,"mash_cluster":6,"isolation_source":"kidney","isolation_country":"China","geographic_location":"China: Chengdu","host_name":"Red panda","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4990420.0,"gc_content":50.503063,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4866.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"200.42x","assembly_method":"Celera Assembler v. 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The genomes were assembled using a combination of Nanopore R9.4 and Illumina sequencing data.","n_reactions":2733,"n_metabolites":1943,"n_genes":1532,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.10883.json.json","assembly_accession":"GCF_001660565.1","genome_id":"562.10883","genome_name":"Escherichia coli strain S51","strain":"strain S51","serovar":"","phylogroup":"B1","MLST":7060,"mash_cluster":26,"isolation_source":"poultry meat","isolation_country":"Switzerland","geographic_location":"Switzerland","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5186163.0,"gc_content":50.67,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5332.0,"refseq_cds":5087.0,"sequencing_platform":"PacBio","sequencing_depth":"209.0x","assembly_method":"PacBio SMRT Analysis v. 2.3.0","sequencing_centers":"University of Zurich","completion_date":"2016-06-09T00:00:00Z","collection_date":"17-Aug-15","bioproject_accession":"PRJNA323827","biosample_accession":"SAMN05190012","genbank_accessions":"CP015995,CP015996,CP015997","refseq_accessions":"NZ_CP015995.1,NZ_CP015996.1,NZ_CP015997.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Identification of the mcr-1 location","n_reactions":2731,"n_metabolites":1939,"n_genes":1535,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHE","country":"Switzerland"},{"gem_file":"562.46748.json.json","assembly_accession":"GCA_005222385.1","genome_id":"562.46748","genome_name":"Escherichia coli strain 113","strain":"strain 113","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5551313.0,"gc_content":50.498974,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5962.0,"refseq_cds":5797.0,"sequencing_platform":"PacBio","sequencing_depth":"133x","assembly_method":"HGAP v. 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This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_016403975.2.json.json","assembly_accession":"GCF_016403975.2","genome_id":"GCF_016403975.2","genome_name":"Escherichia coli","strain":"STEC17-190","serovar":"","phylogroup":"B1","MLST":641,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN16993369","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1938,"n_genes":1519,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_021398955.1.json.json","assembly_accession":"GCF_021398955.1","genome_id":"GCF_021398955.1","genome_name":"Escherichia coli O16:H6","strain":"O16:H6","serovar":"","phylogroup":"B2","MLST":144,"mash_cluster":6,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN21159021","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":2874052.0,"organism_name":"Escherichia coli O16:H6","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1941,"n_genes":1456,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.374.json.json","assembly_accession":"GCA_013168015.1","genome_id":"83334.374","genome_name":"Escherichia coli O157:H7 strain DEC5A","strain":"O157:H7 strain DEC5A","serovar":"O157:H7","phylogroup":"E","MLST":7444,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:New York","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5380215.0,"gc_content":50.40468,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5517.0,"refseq_cds":5242.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"275x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"1950","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11229483","genbank_accessions":"CP038394,CP038395,CP038396,CP038397","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2732,"n_metabolites":1937,"n_genes":1497,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.46732.json.json","assembly_accession":"GCA_005221905.1","genome_id":"562.46732","genome_name":"Escherichia coli strain 142","strain":"strain 142","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5680026.0,"gc_content":50.52454,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":6133.0,"refseq_cds":5976.0,"sequencing_platform":"PacBio","sequencing_depth":"200x","assembly_method":"HGAP v. 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These SNPs are in the core genome and don't reflect the diversity of the complete genome. This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13738.json.json","assembly_accession":"GCF_001900335.1","genome_id":"562.13738","genome_name":"Escherichia coli strain C10","strain":"strain C10","serovar":"","phylogroup":"B1","MLST":109,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5021692.0,"gc_content":50.81,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5023.0,"refseq_cds":4709.0,"sequencing_platform":"Illumina Miseq; Roche 454 GS Junior","sequencing_depth":"30-80x","assembly_method":"Newbler v. 2.7","sequencing_centers":"Nanjing Agricultural University","completion_date":"2016-12-12T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA269191","biosample_accession":"SAMN03252417","genbank_accessions":"CP010132","refseq_accessions":"NZ_CP010132.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"env_biome:faeces","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments","n_reactions":2733,"n_metabolites":1937,"n_genes":1523,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.500.json.json","assembly_accession":"GCA_017165215.1","genome_id":"83334.500","genome_name":"Escherichia coli O157:H7 strain Z1615","strain":"O157:H7 strain Z1615","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5611694.0,"gc_content":50.489548,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5817.0,"refseq_cds":5431.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"248.7599878040392x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327595","genbank_accessions":"CP062744,CP062745","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Roslin Institute","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.17357.json.json","assembly_accession":"GCA_002156825.1","genome_id":"562.17357","genome_name":"Escherichia coli strain 95JB1","strain":"strain 95JB1","serovar":"O111:H-","phylogroup":"B1","MLST":294,"mash_cluster":23,"isolation_source":"fecal sample","isolation_country":"Australia","geographic_location":"Australia: Adelaide","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5517971.0,"gc_content":50.55,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5712.0,"refseq_cds":5319.0,"sequencing_platform":"PacBio","sequencing_depth":"200.0x","assembly_method":"HGAP v. 2","sequencing_centers":"University of Queensland","completion_date":"2017-05-23T00:00:00Z","collection_date":"1995","bioproject_accession":"PRJNA383943","biosample_accession":"SAMN06924970","genbank_accessions":"CP021335,CP021336,CP021337","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"In this study we have used Pacific Bioscience single molecule real-time (SMRT) long read sequencing to characterise the complete epigenome (genome and methylome) of 95JB1. Our analysis of the methylome of 95JB1 and a second isolate, 95NR1, identified hemimethylation of a novel motif (5\u2019-CTGCm6AG-3\u2019) in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethalyted in the 95JB1, including at least 180 potential promoter regions that could explain regulatory differences between the strains. We identified a Type IIG methyltransferase encoded in both genomes in association with three additional genes in an operon-like arrangement. IS1203 mediated disruption of this operon in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the enormous potential of SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.","n_reactions":2731,"n_metabolites":1941,"n_genes":1511,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"83334.487.json.json","assembly_accession":"GCA_017165075.1","genome_id":"83334.487","genome_name":"Escherichia coli O157:H7 strain Z1768","strain":"O157:H7 strain Z1768","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5609264.0,"gc_content":50.486946,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5823.0,"refseq_cds":5426.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"205.15533267822659x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327600","genbank_accessions":"CP062731,CP062732","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Roslin Institute","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.79207.json.json","assembly_accession":"GCA_019971055.1","genome_id":"562.79207","genome_name":"Escherichia coli strain CX07","strain":"strain CX07","serovar":"","phylogroup":"A","MLST":635,"mash_cluster":22,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada: Alberta","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5197714.0,"gc_content":50.877136,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5308.0,"refseq_cds":4981.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"82x","assembly_method":"flye v. 2.8.2","sequencing_centers":"Agriculture & Agri-Food Canada","completion_date":"2021-09-14T00:00:00Z","collection_date":"2014/2015","bioproject_accession":"PRJNA716667","biosample_accession":"SAMN18446041","genbank_accessions":"CP081724,CP081725,CP081726,CP081727,CP081728","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The presence of locus of heat resistance is a common way of screening heat resistance in E.coli, however harboring LHR does not always confer extreme heat resistance suggesting other genetic components may play a role in heat resistance. WGS was performed to determine genetic determinants in E.coli for different levels of heat resistance and determine the evolution regarding the emergence of heat resistant strains of E.coli in a meat plant setting.","n_reactions":2735,"n_metabolites":1949,"n_genes":1523,"n_exchange":331,"n_with_gpr":2289,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"GCF_020683045.1.json.json","assembly_accession":"GCF_020683045.1","genome_id":"GCF_020683045.1","genome_name":"Escherichia coli","strain":"EC32","serovar":"","phylogroup":"B2","MLST":-1,"mash_cluster":3,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN22488132","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1941,"n_genes":1485,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.16328.json.json","assembly_accession":"GCA_002057245.1","genome_id":"562.16328","genome_name":"Escherichia coli strain 13E0780","strain":"strain 13E0780","serovar":"O156:H25","phylogroup":"B1","MLST":300,"mash_cluster":24,"isolation_source":"cattle","isolation_country":"Germany","geographic_location":"Germany","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5371291.0,"gc_content":50.62,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5825.0,"refseq_cds":5654.0,"sequencing_platform":"PacBio","sequencing_depth":"200.0x","assembly_method":"HGAP3 v. DEC-2014","sequencing_centers":"Friedrich-Loeffler-Institut","completion_date":"2017-03-21T00:00:00Z","collection_date":"06-Jul-1998","bioproject_accession":"PRJNA378906","biosample_accession":"SAMN06563569","genbank_accessions":"CP020106","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:FLI","comments":"STEC","n_reactions":2732,"n_metabolites":1942,"n_genes":1513,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"562.60269.json.json","assembly_accession":"GCA_012934635.1","genome_id":"562.60269","genome_name":"Escherichia coli strain SCU-124","strain":"strain SCU-124","serovar":"","phylogroup":"B2","MLST":357,"mash_cluster":3,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4954354.0,"gc_content":50.56611,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5006.0,"refseq_cds":4702.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"36x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-04-30T00:00:00Z","collection_date":"2016","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609784","genbank_accessions":"CP051706,CP051707,CP051708,CP051709,CP051710","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2731,"n_metabolites":1945,"n_genes":1452,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.76465.json.json","assembly_accession":"GCA_018884565.1","genome_id":"562.76465","genome_name":"Escherichia coli strain WS0115A","strain":"strain WS0115A","serovar":"","phylogroup":"A","MLST":2368,"mash_cluster":22,"isolation_source":"feces","isolation_country":"Egypt","geographic_location":"Egypt","host_name":"Homo sapiens","host_health":"diarrhea","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5015532.0,"gc_content":50.83706,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4961.0,"refseq_cds":"","sequencing_platform":"PacBio RSII","sequencing_depth":"27.53x","assembly_method":"Canu v. v.1.2","sequencing_centers":"University of Maryland, School of Medicine","completion_date":"2021-06-15T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA521509","biosample_accession":"SAMN10904668","genbank_accessions":"CP035882,CP035883","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates","n_reactions":2752,"n_metabolites":2027,"n_genes":1751,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"EGY","country":"Egypt"},{"gem_file":"562.76274.json.json","assembly_accession":"GCA_018628815.1","genome_id":"562.76274","genome_name":"Escherichia coli strain Stbl4","strain":"strain Stbl4","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:California, Palo Alto","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4502782.0,"gc_content":50.69486,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4500.0,"refseq_cds":4234.0,"sequencing_platform":"PacBio Sequel; Illumina NovaSeq","sequencing_depth":"431.0x","assembly_method":"HGAP v. MARCH-2021","sequencing_centers":"University of Tuebingen","completion_date":"2021-06-02T00:00:00Z","collection_date":"1922","bioproject_accession":"PRJNA674993","biosample_accession":"SAMN16686196","genbank_accessions":"CP076043,CP076044","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture;collected_by:Blair","comments":"The strain Stbl4 is frequently used as a tool for heterologous expression of biosynthetic gene clusters encoding secondary metabolites. However, no information was available about its own metabolic profile. In order to gain insight into the full capacity of Stbl4 to produce natural products we sequenced the whole genome.","n_reactions":2731,"n_metabolites":1933,"n_genes":1503,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.55129.json.json","assembly_accession":"GCA_009867035.1","genome_id":"562.55129","genome_name":"Escherichia coli strain 1896","strain":"strain 1896","serovar":"","phylogroup":"B1","MLST":58,"mash_cluster":26,"isolation_source":"Bovine adult","isolation_country":"France","geographic_location":"France","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5235376.0,"gc_content":50.831936,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5451.0,"refseq_cds":5372.0,"sequencing_platform":"PacBio","sequencing_depth":"30.0x","assembly_method":"CANU v. 1.6","sequencing_centers":"University College Dublin","completion_date":"2020-01-14T00:00:00Z","collection_date":"20-Jan-2010","bioproject_accession":"PRJNA433820","biosample_accession":"SAMN08522770","genbank_accessions":"CP026939,CP026940,CP026941,CP026942","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Cell Culture","comments":"Genetic diversity of E. coli isolated from diseased animals","n_reactions":2733,"n_metabolites":1942,"n_genes":1526,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"FRA","country":"France"},{"gem_file":"GCF_020423205.1.json.json","assembly_accession":"GCF_020423205.1","genome_id":"GCF_020423205.1","genome_name":"Escherichia coli O157:H7","strain":"O157:H7","serovar":"","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN17295280","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"Escherichia coli O157:H7","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1938,"n_genes":1468,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.55235.json.json","assembly_accession":"GCA_009905115.1","genome_id":"562.55235","genome_name":"Escherichia coli strain 2EC1","strain":"strain 2EC1","serovar":"","phylogroup":"A","MLST":4977,"mash_cluster":22,"isolation_source":"feces","isolation_country":"Singapore","geographic_location":"Singapore","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4868589.0,"gc_content":50.89801,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":4929.0,"refseq_cds":4616.0,"sequencing_platform":"Oxford Nanopore MiniION; Illumina NovaSeq","sequencing_depth":"421.0x","assembly_method":"Unicycler v. v0.4.8","sequencing_centers":"Temasek Life Sciences Laboratory Limited","completion_date":"2020-01-19T00:00:00Z","collection_date":"2019-01","bioproject_accession":"PRJNA599529","biosample_accession":"SAMN13756204","genbank_accessions":"CP047571,CP047572,CP047573,CP047574,CP047575","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Bacterial pure culture","comments":"In this project, we isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore. Their genomes were sequenced and analysed to identify resistance mechanisms, plasmids and mode of antibiotic resistance gene acquisition.","n_reactions":2732,"n_metabolites":1935,"n_genes":1489,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"SGP","country":"Singapore"},{"gem_file":"562.19205.json.json","assembly_accession":"GCA_002310615.1","genome_id":"562.19205","genome_name":"Escherichia coli strain 1190","strain":"strain 1190","serovar":"","phylogroup":"D","MLST":349,"mash_cluster":18,"isolation_source":"urinary tract infections","isolation_country":"United Kingdom","geographic_location":"United Kingdom: Scotland, Edinburgh","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":4987038.0,"gc_content":50.83,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5043.0,"refseq_cds":4994.0,"sequencing_platform":"PacBio","sequencing_depth":"20x","assembly_method":"De-novo v. Celera Assembler 8.2","sequencing_centers":"The Roslin Institute","completion_date":"2017-09-18T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA402083","biosample_accession":"SAMN07618121","genbank_accessions":"CP023386,CP023387","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from urinary tract infections in dogs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.","n_reactions":2732,"n_metabolites":1942,"n_genes":1512,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.63879.json.json","assembly_accession":"GCA_014216715.1","genome_id":"562.63879","genome_name":"Escherichia coli strain RH-045-MS","strain":"strain RH-045-MS","serovar":"","phylogroup":"A","MLST":226,"mash_cluster":22,"isolation_source":"Human feces","isolation_country":"Bangladesh","geographic_location":"Bangladesh: Hajiganj","host_name":"Human, Homo sapiens","host_health":"Healthy Individual","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":6042336.0,"gc_content":50.736427,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5636.0,"refseq_cds":"","sequencing_platform":"Illumina NextSeq","sequencing_depth":"196x","assembly_method":"ABySS v. 4.1","sequencing_centers":"icddr,b","completion_date":"2020-08-17T00:00:00Z","collection_date":"2017","bioproject_accession":"PRJNA607650","biosample_accession":"SAMN14342442","genbank_accessions":"CP050203","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Laboratory of Food Safety and One Health","comments":"E. coli whole genome sequence comparison","n_reactions":2732,"n_metabolites":1935,"n_genes":1510,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BGD","country":"Bangladesh"},{"gem_file":"GCF_003697165.2.json.json","assembly_accession":"GCF_003697165.2","genome_id":"GCF_003697165.2","genome_name":"Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775","strain":"DSM 30083 = JCM 1649 = ATCC 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FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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University","completion_date":"2020-10-30T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA646837","biosample_accession":"SAMEA3357527","genbank_accessions":"LR890606,LR890607,LR890608,LR890609,LR890610,LR890611,LR890612,LR890613,LR890614,LR890615","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU","n_reactions":2731,"n_metabolites":1935,"n_genes":1532,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.50524.json.json","assembly_accession":"GCA_007109465.1","genome_id":"562.50524","genome_name":"Escherichia coli strain 131","strain":"strain 131","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5364246.0,"gc_content":50.754456,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5613.0,"refseq_cds":5324.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"78x","assembly_method":"HGAP v. 4","sequencing_centers":"Duke University","completion_date":"2019-07-18T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA551684","biosample_accession":"SAMN12163086","genbank_accessions":"CP041581,CP041582,CP041583","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Deverick Anderson","comments":"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2732,"n_metabolites":1943,"n_genes":1471,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"2605620.3.json.json","assembly_accession":"GCA_008124005.1","genome_id":"2605620.3","genome_name":"Escherichia coli O80:H26 strain EC-107","strain":"O80:H26 strain EC-107","serovar":"O80:H26","phylogroup":"A","MLST":-1,"mash_cluster":22,"isolation_source":"chicken","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5338095.0,"gc_content":50.678547,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5572.0,"refseq_cds":5262.0,"sequencing_platform":"Illumina MiSeq and PacBio","sequencing_depth":"379x","assembly_method":"HGAP v. 3.1","sequencing_centers":"National Microbiology Laboratory at Guelph","completion_date":"2019-08-29T00:00:00Z","collection_date":"19-Dec-2016","bioproject_accession":"PRJNA560883","biosample_accession":"SAMN12603254","genbank_accessions":"CP043217,CP043218,CP043219,CP043220,CP043221","refseq_accessions":"","genome_status":"Complete","taxon_id":2605620.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Public Health Agency of Canada","comments":"Humans and farm animals commonly consume food- or waterborne bacteria that harbour antibiotic resistance genes. The fate and potential horizontal gene transfer of those genes into the host microbiome will have a crucial bearing on the eventual health risk of exposure to antibiotic resistance genes. In the present study, the effects of antibiotics on the in vivo transfer of \ud835\udefd-lactam resistance genes were evaluated in a mouse model by characterizing the microbiome in excreted feces. Mice were dosed with Escherichia coli, Salmonella enterica serovars Heidelberg or Bredeney referred to as donors. The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2733,"n_metabolites":1939,"n_genes":1527,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.77320.json.json","assembly_accession":"GCA_019265445.1","genome_id":"562.77320","genome_name":"Escherichia coli strain Colony374","strain":"strain Colony374","serovar":"","phylogroup":"A","MLST":3594,"mash_cluster":26,"isolation_source":"food","isolation_country":"Thailand","geographic_location":"Thailand: Loei","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4733683.0,"gc_content":51.24731,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4268.0,"refseq_cds":"","sequencing_platform":"Illumina HiSeq","sequencing_depth":"87.54x","assembly_method":"idba_ud v. V1.1.3","sequencing_centers":"Ministry of Public Health-Thailand","completion_date":"2021-07-18T00:00:00Z","collection_date":"Not collected","bioproject_accession":"PRJNA668870","biosample_accession":"SAMN17910922","genbank_accessions":"CP078555","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Department of Disease Control, Ministry of Public Health","comments":"Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand","n_reactions":2751,"n_metabolites":2023,"n_genes":1660,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"THA","country":"Thailand"},{"gem_file":"562.29027.json.json","assembly_accession":"GCA_003044015.1","genome_id":"562.29027","genome_name":"Escherichia coli strain RM14715","strain":"strain RM14715","serovar":"","phylogroup":"B2","MLST":1877,"mash_cluster":6,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4825089.0,"gc_content":50.63799,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5237.0,"refseq_cds":4947.0,"sequencing_platform":"PacBio","sequencing_depth":"130.51x","assembly_method":"Hgap v. 3","sequencing_centers":"USDA","completion_date":"2018-04-06T00:00:00Z","collection_date":"08-Jun-2011","bioproject_accession":"PRJNA341281","biosample_accession":"SAMN08581174","genbank_accessions":"CP027104","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:feces","comments":"Comparative genomics of shiga toxin producing Enterobacter Cloacae with Shiga toxin producing Escherichia coli;many frameshifted proteins","n_reactions":2732,"n_metabolites":1942,"n_genes":1437,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.60266.json.json","assembly_accession":"GCA_012934535.1","genome_id":"562.60266","genome_name":"Escherichia coli strain SCU-112","strain":"strain SCU-112","serovar":"","phylogroup":"B2","MLST":73,"mash_cluster":5,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5198425.0,"gc_content":50.531303,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5154.0,"refseq_cds":4846.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"25x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-04-30T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609776","genbank_accessions":"CP051725,CP051726","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2733,"n_metabolites":1946,"n_genes":1450,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83333.108.json.json","assembly_accession":"GCF_000974825.1","genome_id":"83333.108","genome_name":"Escherichia coli K-12 strain ER3446","strain":"K-12 strain ER3446","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4606859.0,"gc_content":50.81,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4612.0,"refseq_cds":4361.0,"sequencing_platform":"PacBio","sequencing_depth":"50-200","assembly_method":"SMRT Analysis v. 2.3","sequencing_centers":"New England Biolabs","completion_date":"2015-04-21T00:00:00Z","collection_date":"Jun-14","bioproject_accession":"PRJNA271807","biosample_accession":"SAMN03277615","genbank_accessions":"CP010443","refseq_accessions":"NZ_CP010443.1","genome_status":"Complete","taxon_id":83333.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"supQ80? _(hisG)1 e14- (McrA-) gyrA96 recA::cat(FRT)(CmR)  recD1014 rpsL104(StrR) xyl-7 mtlA2(Fs) metB1(FS) mrr::tetAR","substrain":"","additional_metadata":"identified_by:Anthony Kingston;sample_type:Cell Culture","comments":"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.","n_reactions":2732,"n_metabolites":1937,"n_genes":1560,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"316407.9.json.json","assembly_accession":"GCA_000010245.1","genome_id":"316407.9","genome_name":"Escherichia coli str. K-12 substr. W3110","strain":"str. K-12 substr. W3110","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4646332.0,"gc_content":50.8,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4454.0,"refseq_cds":4226.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Nara Institute of Science and Technology","completion_date":"2006-01-23T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA16351","biosample_accession":"","genbank_accessions":"AP009048","refseq_accessions":"AC_000091","genome_status":"Complete","taxon_id":316407.0,"organism_name":"Escherichia coli str. K-12 substr. 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It is considered a more wild-type strain than MG1655, although it has also been cured of the lambda prophage and lacks the fertility factor (F+ plasmid) of the original E. coli K-12 (EMG2).Comparison of the two genomes revealed that they are not identical with strain-specific differences reflecting their distinct lineages.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.63049.json.json","assembly_accession":"GCA_013459015.1","genome_id":"562.63049","genome_name":"Escherichia coli strain CE1803A","strain":"strain CE1803A","serovar":"","phylogroup":"F","MLST":457,"mash_cluster":11,"isolation_source":"silver gulls","isolation_country":"Australia","geographic_location":"Australia: Five Islands","host_name":"Chroicocephalus novaehollandiae","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4878730.0,"gc_content":50.519623,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4713.0,"refseq_cds":4473.0,"sequencing_platform":"PacBio","sequencing_depth":"30x","assembly_method":"HGAP v. v.6","sequencing_centers":"The ithree institute","completion_date":"2020-07-22T00:00:00Z","collection_date":"2012-10","bioproject_accession":"PRJNA630096","biosample_accession":"SAMN14966948","genbank_accessions":"CP053851","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from silver gulls in three colonies in New South Wales, Australia, carrying antimicrobial resistance genes conferring resistance to critically important antimicrobials used for effective treatment of human infection, including carbapenems, 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3","sequencing_centers":"FDA/CFSAN","completion_date":"2019-08-20T00:00:00Z","collection_date":"2016","bioproject_accession":"PRJNA230969","biosample_accession":"SAMN06909729","genbank_accessions":"NIYB01000000","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Laboratory of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City","comments":"Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.","n_reactions":2752,"n_metabolites":2025,"n_genes":1738,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"EGY","country":"Egypt"},{"gem_file":"511145.181.json.json","assembly_accession":"GCF_000273425.1","genome_id":"511145.181","genome_name":"Escherichia coli str. 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Escherichia coli MG1655 was one of these five microbial genomes. At least two libraries (short fragment and jumping) were generated and sequenced using Illumina. Likewise in particular for E. coli, libraries were also generated and run for 454 sequencing. Genomic DNA from Erica Sodergren. Two different genome assemblies are part of this project. The assembly in AKBV00000000 is the complete chromosome assembled from Illumina reads. The assembly in AKVX00000000 is the complete chromosome assembled from reads used to assemble U000096 plus reads from a different isolate of the strain.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1055545.3.json.json","assembly_accession":"GCA_002716885.1","genome_id":"1055545.3","genome_name":"Escherichia coli O91 str. RM7190","strain":"O91 str. 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The major serovars of STEC associated with illness have been O26, O111, O103, O121, O45, and O145, accounting for 25-50% of human illness caused by STECs and, in some cases, severe illness comparable to illness caused by E. coli O157:H7. 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The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2731,"n_metabolites":1937,"n_genes":1486,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.66857.json.json","assembly_accession":"GCA_014705965.1","genome_id":"562.66857","genome_name":"Escherichia coli strain WEM25","strain":"strain WEM25","serovar":"","phylogroup":"A","MLST":2491,"mash_cluster":22,"isolation_source":"Beach water","isolation_country":"China","geographic_location":"China: Hong Kong island","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4875160.0,"gc_content":50.76543,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":4962.0,"refseq_cds":4631.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore MiniION","sequencing_depth":"30.0x","assembly_method":"SPAdes v. 3.12.0","sequencing_centers":"The Independent Schools Foundation Academy","completion_date":"2020-09-23T00:00:00Z","collection_date":"Jun-2018","bioproject_accession":"PRJNA655572","biosample_accession":"SAMN15743069","genbank_accessions":"CP061530,CP061531,CP061532,CP061533,CP061534","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from a beach front water sample in Hong Kong","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:water sample;biomaterial_provider:SY-EnvMicrobes-WEM25;collected_by:Evelyn Moore;passage_history:10","comments":"A strain of E coli isolated from a beach front water sample in Hong Kong.","n_reactions":2733,"n_metabolites":1935,"n_genes":1531,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"GCF_900636215.1.json.json","assembly_accession":"GCF_900636215.1","genome_id":"GCF_900636215.1","genome_name":"Escherichia coli","strain":"NCTC9022","serovar":"","phylogroup":"B2","MLST":73,"mash_cluster":5,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMEA3446350","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1946,"n_genes":1455,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.63863.json.json","assembly_accession":"GCA_014170945.1","genome_id":"562.63863","genome_name":"Escherichia coli strain 101.3","strain":"strain 101.3","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"Turkey's","isolation_country":"Canada","geographic_location":"Canada","host_name":"Turkey","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4861548.0,"gc_content":50.658432,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5147.0,"refseq_cds":4619.0,"sequencing_platform":"Oxford Nanopore MinION","sequencing_depth":"34.5x","assembly_method":"Flye v. 2.6","sequencing_centers":"University of Guelph","completion_date":"2020-08-12T00:00:00Z","collection_date":"2016/2017","bioproject_accession":"PRJNA596173","biosample_accession":"SAMN13613890","genbank_accessions":"CP059944,CP059945,CP059946","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from Turkey's in Canada","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:fecal","comments":"Chromosomes and plasmids were assembled from E. coli isolated from Turkey's in Canada. 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The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.46179.json.json","assembly_accession":"GCA_004801575.1","genome_id":"562.46179","genome_name":"Escherichia coli strain PigCaeca_1","strain":"strain PigCaeca_1","serovar":"","phylogroup":"A","MLST":48,"mash_cluster":22,"isolation_source":"feces","isolation_country":"United Kingdom","geographic_location":"United Kingdom: Yorkshire and the Humber","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4898477.0,"gc_content":50.77819,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5006.0,"refseq_cds":4745.0,"sequencing_platform":"Hybrid assembly: Illumina HiSeq 4000 and","sequencing_depth":"30x","assembly_method":"Unicycler v. v0.4.0","sequencing_centers":"University of Oxford","completion_date":"2019-04-21T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA529503","biosample_accession":"SAMN11268909","genbank_accessions":"CP039298,CP039299,CP039300,CP039301,CP039302","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Single colony culture","comments":"In this pilot study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to help establish optimum protocols and approaches for sample processing. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced these samples with shotgun metagenomics at high depth (~200 million reads per sample). Alongside this, we cultured multiple single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data.","n_reactions":2732,"n_metabolites":1937,"n_genes":1517,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_002863885.1.json.json","assembly_accession":"GCF_002863885.1","genome_id":"GCF_002863885.1","genome_name":"Escherichia coli","strain":"SMN013SH2","serovar":"","phylogroup":"A","MLST":659,"mash_cluster":24,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN07716515","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1941,"n_genes":1513,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.16499.json.json","assembly_accession":"GCA_900174625.1","genome_id":"562.16499","genome_name":"Escherichia coli strain WI1 isolate","strain":"strain WI1 isolate","serovar":"","phylogroup":"A","MLST":1288,"mash_cluster":21,"isolation_source":"clinical isolate","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5008891.0,"gc_content":50.79,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5019.0,"refseq_cds":4862.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"CHU Clermont-ferrand","completion_date":"2017-04-20T00:00:00Z","collection_date":"2016","bioproject_accession":"PRJEB18462","biosample_accession":"SAMEA19195168","genbank_accessions":"LT838196,LT838197,LT838198,LT838199","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"host_health_state:diseased","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The spread of mcr-1-encoding plasmids into carbapenem-resistant Enterobacteriaceae raises concern about the emergence of untreatable bacteria. We report the acquisition of mcr-1 in a carbapenem resistant E. coli after a 3-week course of colistin in a patient repatriated to France from Portugal.","n_reactions":2733,"n_metabolites":1939,"n_genes":1531,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.70768.json.json","assembly_accession":"GCA_016904055.1","genome_id":"562.70768","genome_name":"Escherichia coli strain FDAARGOS_1293 strain Not applicable","strain":"","serovar":"","phylogroup":"B2","MLST":73,"mash_cluster":5,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5140750.0,"gc_content":50.585926,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5116.0,"refseq_cds":4813.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"1284.19x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357435","genbank_accessions":"CP070041,CP070042,CP070043","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1293","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2732,"n_metabolites":1944,"n_genes":1453,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.28183.json.json","assembly_accession":"GCA_002887715.1","genome_id":"562.28183","genome_name":"Escherichia coli strain BH100L","strain":"strain BH100L","serovar":"","phylogroup":"B2","MLST":127,"mash_cluster":6,"isolation_source":"urine","isolation_country":"Brazil","geographic_location":"Brazil: Belo Horizonte","host_name":"Human, Homo sapiens","host_health":"Urinary tract infection","host_gender":"female","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":5033214.0,"gc_content":50.53016,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5014.0,"refseq_cds":4824.0,"sequencing_platform":"Illumina HiSeq","sequencing_depth":"888.0x","assembly_method":"SPAdes v. 2.9","sequencing_centers":"UFMG","completion_date":"2018-01-17T00:00:00Z","collection_date":"1974","bioproject_accession":"PRJNA389912","biosample_accession":"SAMN08118424","genbank_accessions":"CP025716","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"UPEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from a patient with urinary tract infection in Belo Horizonte, Brazil","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Edmar Chartone Souza","comments":"Escherichia coli BH100 was isolated from a patient with urinary tract infection in Belo Horizonte, Brazil.","n_reactions":2733,"n_metabolites":1947,"n_genes":1387,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BRA","country":"Brazil"},{"gem_file":"83334.496.json.json","assembly_accession":"GCA_017165375.1","genome_id":"83334.496","genome_name":"Escherichia coli O157:H7 strain Z866","strain":"O157:H7 strain Z866","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5656808.0,"gc_content":50.497208,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5909.0,"refseq_cds":5485.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"257.91779007065x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327586","genbank_accessions":"CP062766,CP062767,CP062768","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:IPRAVE Consortium","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.46726.json.json","assembly_accession":"GCA_005221785.1","genome_id":"562.46726","genome_name":"Escherichia coli strain 123","strain":"strain 123","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5551589.0,"gc_content":50.46521,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5948.0,"refseq_cds":5783.0,"sequencing_platform":"PacBio","sequencing_depth":"183x","assembly_method":"HGAP v. 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This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.473.json.json","assembly_accession":"GCA_017164895.1","genome_id":"83334.473","genome_name":"Escherichia coli O157:H7 strain Z1826","strain":"O157:H7 strain Z1826","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5619058.0,"gc_content":50.51523,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5838.0,"refseq_cds":5438.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"174.0238305068216x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327609","genbank_accessions":"CP062715,CP062716","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:BECS Consortium","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.77338.json.json","assembly_accession":"GCA_019269355.1","genome_id":"562.77338","genome_name":"Escherichia coli strain Colony317","strain":"strain Colony317","serovar":"","phylogroup":"A","MLST":5891,"mash_cluster":26,"isolation_source":"Rectal Swab","isolation_country":"Thailand","geographic_location":"Thailand: Chiang Mai","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4733682.0,"gc_content":51.277546,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4326.0,"refseq_cds":"","sequencing_platform":"Illumina HiSeq","sequencing_depth":"88.244x","assembly_method":"idba_ud v. 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Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2731,"n_metabolites":1930,"n_genes":1504,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.70765.json.json","assembly_accession":"GCA_016903915.1","genome_id":"562.70765","genome_name":"Escherichia coli strain FDAARGOS_1300 strain Not applicable","strain":"","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5457554.0,"gc_content":50.662567,"contigs":11.0,"chromosomes":1.0,"plasmids":10.0,"patric_cds":5637.0,"refseq_cds":5258.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"1255.12x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357442","genbank_accessions":"CP069996,CP069997,CP070006,CP069998,CP069999,CP070000,CP070001,CP070002,CP070003,CP070004,CP070005","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1300","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2733,"n_metabolites":1946,"n_genes":1457,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.13549.json.json","assembly_accession":"GCF_001886935.1","genome_id":"562.13549","genome_name":"Escherichia coli strain FORC_041","strain":"strain FORC_041","serovar":"","phylogroup":"B1","MLST":679,"mash_cluster":26,"isolation_source":"Bulgogi","isolation_country":"South Korea","geographic_location":"South Korea: 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Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2732,"n_metabolites":1940,"n_genes":1485,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.6963.json.json","assembly_accession":"GCF_000599705.1","genome_id":"562.6963","genome_name":"Escherichia coli strain ST2747","strain":"strain ST2747","serovar":"","phylogroup":"D","MLST":6131,"mash_cluster":17,"isolation_source":"water","isolation_country":"Belgium","geographic_location":"Belgium","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5090442.0,"gc_content":50.78,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5136.0,"refseq_cds":4572.0,"sequencing_platform":"PacBio","sequencing_depth":"25x","assembly_method":"HGAP, SMRT Analysis Portal v. 2.0.1","sequencing_centers":"University of Antwerpen","completion_date":"2014-04-16T00:00:00Z","collection_date":"2012-04-18","bioproject_accession":"PRJNA238952","biosample_accession":"SAMN02666698","genbank_accessions":"CP007394","refseq_accessions":"NZ_CP007394.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"24723707","isolation_comments":"","other_clinical":"","other_environmental":"env_biome:air","cell_shape":"Bacilli","motility":"Yes","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"To study Nitrofurantoin resistant mechanism","n_reactions":2733,"n_metabolites":1944,"n_genes":1521,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BEL","country":"Belgium"},{"gem_file":"562.58373.json.json","assembly_accession":"GCA_011045455.1","genome_id":"562.58373","genome_name":"Escherichia coli strain IVRI Kol CP4","strain":"strain IVRI Kol CP4","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"Mastitis Milk","isolation_country":"India","geographic_location":"India","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4863292.0,"gc_content":50.576565,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5204.0,"refseq_cds":4788.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"61.26x","assembly_method":"HGAP v. 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With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: \u2022Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. \u2022Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). \u2022Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2711,"n_metabolites":1877,"n_genes":1465,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GEO","country":"Georgia"},{"gem_file":"GCF_000010485.1.json.json","assembly_accession":"GCF_000010485.1","genome_id":"GCF_000010485.1","genome_name":"Escherichia coli SE15","strain":"SE15","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMD00060923","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":431946.0,"organism_name":"Escherichia coli SE15","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1941,"n_genes":1487,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.11470.json.json","assembly_accession":"GCF_001679985.1","genome_id":"562.11470","genome_name":"Escherichia coli strain 210205630","strain":"strain 210205630","serovar":"","phylogroup":"B1","MLST":7051,"mash_cluster":26,"isolation_source":"swine cecum","isolation_country":"United States","geographic_location":"United States","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5424193.0,"gc_content":50.59,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5566.0,"refseq_cds":5311.0,"sequencing_platform":"Illumina; PacBio","sequencing_depth":"91x","assembly_method":"CANU v. 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Miller","comments":"Submission of consensus genome assemblies from a critically ill patient with polymicrobial infections due to multi-drug resistant Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa who had traveled to India and was also colonized by Candida auris. A precision medicine approach using whole genome sequencing revealed a multiplicity of mobile elements associated with NDM-1, NDM-5, and OXA-181. This case illustrates the rapidly evolving landscape of resistance and its challenges to clinicians.","n_reactions":2732,"n_metabolites":1946,"n_genes":1547,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.502.json.json","assembly_accession":"GCA_017165455.1","genome_id":"83334.502","genome_name":"Escherichia coli O157:H7 strain Z563","strain":"O157:H7 strain Z563","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5633885.0,"gc_content":50.424015,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5853.0,"refseq_cds":5454.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"208.59433776286156x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327583","genbank_accessions":"CP062774,CP062775,CP062776,CP062777","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:IPRAVE Consortium","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.79192.json.json","assembly_accession":"GCA_019969525.1","genome_id":"562.79192","genome_name":"Escherichia coli strain 0H23","strain":"strain 0H23","serovar":"","phylogroup":"A","MLST":399,"mash_cluster":22,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada: Alberta","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5457970.0,"gc_content":50.582726,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5646.0,"refseq_cds":5256.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"95x","assembly_method":"flye v. 2.8.2","sequencing_centers":"Agriculture & Agri-Food Canada","completion_date":"2021-09-14T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA716667","biosample_accession":"SAMN18446029","genbank_accessions":"CP081684,CP081685,CP081686,CP081687,CP081688,CP081689","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The presence of locus of heat resistance is a common way of screening heat resistance in E.coli, however harboring LHR does not always confer extreme heat resistance suggesting other genetic components may play a role in heat resistance. WGS was performed to determine genetic determinants in E.coli for different levels of heat resistance and determine the evolution regarding the emergence of heat resistant strains of E.coli in a meat plant setting.","n_reactions":2733,"n_metabolites":1948,"n_genes":1526,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.46717.json.json","assembly_accession":"GCA_005221605.1","genome_id":"562.46717","genome_name":"Escherichia coli strain 141","strain":"strain 141","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5555563.0,"gc_content":50.50095,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5962.0,"refseq_cds":5801.0,"sequencing_platform":"PacBio","sequencing_depth":"121x","assembly_method":"HGAP v. 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This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.70515.json.json","assembly_accession":"GCA_016776085.1","genome_id":"562.70515","genome_name":"Escherichia coli strain RIVM_C028613","strain":"strain RIVM_C028613","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5385668.0,"gc_content":50.565964,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5404.0,"refseq_cds":5052.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"National Institute for Public Health and the Environment","completion_date":"2021-02-01T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA691727","biosample_accession":"SAMN17373190","genbank_accessions":"CP068814","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:chromosome","comments":"OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. 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The objectives of the current study are\\; 1) to identify potential virulence factors encoded in peritonitis causing E. coli strain using whole genome sequencing, 2) ascertain genotypic homology among avian pathogenic E. coli (APEC) and human extraintestinal pathogenic E. coli (ExPEC) by comparative genomics and 3) to identify potential vaccine targets through antigenome approach","n_reactions":2732,"n_metabolites":1943,"n_genes":1431,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.70526.json.json","assembly_accession":"GCA_016776025.1","genome_id":"562.70526","genome_name":"Escherichia coli strain RIVM_C030197","strain":"strain RIVM_C030197","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5256191.0,"gc_content":50.527405,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5210.0,"refseq_cds":4920.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"National Institute for Public Health and the Environment","completion_date":"2021-02-01T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA691727","biosample_accession":"SAMN17373200","genbank_accessions":"CP068824","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:chromosome","comments":"OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2732,"n_metabolites":1941,"n_genes":1519,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"562.9857.json.json","assembly_accession":"GCF_001612475.1","genome_id":"562.9857","genome_name":"Escherichia coli strain 28RC1","strain":"strain 28RC1","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine carcass","isolation_country":"USA","geographic_location":"USA:midwest","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5643099.0,"gc_content":50.55,"contigs":2.0,"chromosomes":"","plasmids":1.0,"patric_cds":5946.0,"refseq_cds":5641.0,"sequencing_platform":"PacBio; IonTorrent","sequencing_depth":"107.5X","assembly_method":"SMRT Analysis v. 2.3.0","sequencing_centers":"USDA","completion_date":"2016-04-06T00:00:00Z","collection_date":"Aug-1999","bioproject_accession":"PRJNA299666","biosample_accession":"SAMN04202540","genbank_accessions":"CP015020,CP015021","refseq_accessions":"NZ_CP015020.1,NZ_CP015021.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"C","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Genevieve A. Barkocy-Gallagher et al.","comments":"The current BioProject aims to assemble a complete genome sequence of the organism Escherichia coli O157:H7 strain 28RC1. The obtained sequence will use for genomic and transcriptomic comparison between Escherichia coli O157:H7 strains with different levels of acid resistance.","n_reactions":2731,"n_metabolites":1940,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.67027.json.json","assembly_accession":"GCA_014863825.1","genome_id":"562.67027","genome_name":"Escherichia coli strain AML002_ev01","strain":"strain AML002_ev01","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"not applicable","isolation_country":"USA","geographic_location":"USA: Boston","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4632668.0,"gc_content":50.779312,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4512.0,"refseq_cds":"","sequencing_platform":"Illumina NextSeq","sequencing_depth":"50x","assembly_method":"breseq v. 0.35.1","sequencing_centers":"Boston University","completion_date":"2020-10-08T00:00:00Z","collection_date":"11-Oct-2019","bioproject_accession":"PRJNA666010","biosample_accession":"SAMN16090664","genbank_accessions":"CP062249","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolate from each separate evolution experiment and the parent strains are provided here","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"Cm resistance","substrain":"","additional_metadata":"sample_type:cell culture;biomaterial_provider:M.J. Dunlop, Boston University, 44 Cummington Mall, Boston, MA 02216;collected_by:A.M. Langevin;passage_history:72 h turbidostat with 2\ufffdg/mL Cm","comments":"In this work, we evolved strains of Escherichia coli with different genotypes related to the AcrAB-TolC efflux pump. Parent strains were either wild type, had the pump overexpressed, or had the pump knocked out. We evolved these three strains under different levels of chloramphenicol. Each parent strain was evolved in an evolution experiment using three biological replicates. The most resistant isolate from each separate evolution experiment and the parent strains are provided here. The goal of this work was to identify which chloramphenicol concentrations promote the evolution of antibiotic resistance and how the presence of the AcrAB-TolC pump impacts this evolution.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.68711.json.json","assembly_accession":"GCA_016126995.1","genome_id":"562.68711","genome_name":"Escherichia coli strain FDAARGOS_1058 strain Not applicable","strain":"","serovar":"","phylogroup":"C","MLST":1807,"mash_cluster":25,"isolation_source":"","isolation_country":"Germany","geographic_location":"Germany: Braunschweig","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5400968.0,"gc_content":50.652718,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5445.0,"refseq_cds":5068.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"685.4x","assembly_method":"SMRT v. 7.1.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2020-12-20T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357227","genbank_accessions":"CP065970,CP065968,CP065969,CP065971","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"DSM:8695","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:DSMZ","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2711,"n_metabolites":1877,"n_genes":1482,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"444450.8.json.json","assembly_accession":"GCA_000021125.1","genome_id":"444450.8","genome_name":"Escherichia coli O157:H7 str. EC4115","strain":"O157:H7 str. 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A type III secretion system, the locus of enterocyte effacement, numerous toxins and adhesins, as well as fimbrial gene clusters and iron uptake systems are found in these PAIs. Pathogenicity genes are also found on the plasmid pO157.Escherichia coli O157:H7 str. EC4115. This strain will be used for comparative analysis.","n_reactions":2711,"n_metabolites":1877,"n_genes":1423,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1045010.60.json.json","assembly_accession":"GCA_008462425.1","genome_id":"1045010.60","genome_name":"Escherichia coli O157 strain Al Ain","strain":"O157 strain Al Ain","serovar":"O157","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"fecal samples","isolation_country":"United Arab Emirates","geographic_location":"United Arab Emirates: Abu Dhabi","host_name":"camel","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5444610.0,"gc_content":50.53159,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5749.0,"refseq_cds":5399.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"20.0x","assembly_method":"HGAP v. 3","sequencing_centers":"United Arab Emirates University","completion_date":"2019-09-17T00:00:00Z","collection_date":"2018-04-10","bioproject_accession":"PRJNA563225","biosample_accession":"SAMN12670427","genbank_accessions":"CP043539","refseq_accessions":"","genome_status":"Complete","taxon_id":1045010.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Dawood Al Ajmi and Shafeeq Rahman","comments":"E.coli O157 was isolated from camel feces from slaughterhouse in Al Ain, United Arab Emirates","n_reactions":2732,"n_metabolites":1938,"n_genes":1488,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"ARE","country":"United Arab Emirates"},{"gem_file":"562.70448.json.json","assembly_accession":"GCA_016772495.1","genome_id":"562.70448","genome_name":"Escherichia coli strain EF7-18-58","strain":"strain EF7-18-58","serovar":"","phylogroup":"B1","MLST":155,"mash_cluster":26,"isolation_source":"chicken stool","isolation_country":"Laos","geographic_location":"Laos","host_name":"Gallus gallus","host_health":"not applicable","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5015610.0,"gc_content":50.677864,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5029.0,"refseq_cds":4700.0,"sequencing_platform":"Illumina HiSeq","sequencing_depth":"246.0x","assembly_method":"Flye v. v.2.7.1; Pilon v. v.1.22","sequencing_centers":"University of Bern","completion_date":"2021-01-30T00:00:00Z","collection_date":"2018","bioproject_accession":"PRJNA670073","biosample_accession":"SAMN16387487","genbank_accessions":"CP068591,CP068594,CP068592,CP068593","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Institute for Infectious Diseases Bern","comments":"Complete genome and plasmid sequences of MDR Escherichia coli from local people and environmental sources in Laos","n_reactions":2732,"n_metabolites":1939,"n_genes":1506,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"LAO","country":"Laos"},{"gem_file":"1055541.4.json.json","assembly_accession":"GCA_003112205.1","genome_id":"1055541.4","genome_name":"Escherichia coli O103 str. 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The major serovars of STEC associated with illness have been O26, O111, O103, O121, O45, and O145, accounting for 25-50% of human illness caused by STECs and, in some cases, severe illness comparable to illness caused by E. coli O157:H7. Sequencing of STECs from the agriculturally important region of the California central coast will address the diversity of genomic content and physiology of STECs compared to E. coli O157.","n_reactions":2711,"n_metabolites":1877,"n_genes":1467,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.28414.json.json","assembly_accession":"GCA_002953895.1","genome_id":"562.28414","genome_name":"Escherichia coli strain 1A","strain":"1A","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4651857.0,"gc_content":50.805,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4543.0,"refseq_cds":"","sequencing_platform":"illumina","sequencing_depth":"100x","assembly_method":"unknown v. not applicable","sequencing_centers":"University of Texas at Austin","completion_date":"2018-02-01T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA430697","biosample_accession":"SAMN08380000","genbank_accessions":"CP026361","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:not applicable","comments":"We have carried out directed evolution experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine across from amber codons, creating a 21 amino acid genetic code in which the amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.10009.json.json","assembly_accession":"GCF_001618365.1","genome_id":"562.10009","genome_name":"Escherichia coli strain Ecol_448","strain":"strain Ecol_448","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"Argentina","geographic_location":"Argentina: Buenos Aires","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5212298.0,"gc_content":50.78,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5366.0,"refseq_cds":5101.0,"sequencing_platform":"PacBio","sequencing_depth":"1x","assembly_method":"HGAP v. 2.2.0","sequencing_centers":"University of Oxford","completion_date":"2016-04-11T00:00:00Z","collection_date":"2011","bioproject_accession":"PRJNA316786","biosample_accession":"SAMN04590097","genbank_accessions":"CP015076,CP015077,CP015078","refseq_accessions":"NZ_CP015076.1,NZ_CP015077.1,NZ_CP015078.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART)","comments":"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.","n_reactions":2733,"n_metabolites":1941,"n_genes":1489,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"ARG","country":"Argentina"},{"gem_file":"562.13760.json.json","assembly_accession":"GCF_001900795.1","genome_id":"562.13760","genome_name":"Escherichia coli strain H2","strain":"strain H2","serovar":"","phylogroup":"A","MLST":46,"mash_cluster":22,"isolation_source":"river water","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4577859.0,"gc_content":50.8,"contigs":4.0,"chromosomes":4.0,"plasmids":"","patric_cds":4689.0,"refseq_cds":4326.0,"sequencing_platform":"Illumina Miseq; Roche 454 GS 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. 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For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/","n_reactions":2732,"n_metabolites":1943,"n_genes":1471,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.9018.json.json","assembly_accession":"GCF_000953515.1","genome_id":"562.9018","genome_name":"Escherichia coli strain K-12 substr. HMS174","strain":"strain K-12 substr. 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Whole genome sequencing for genome assembly and comparative genomics.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.50521.json.json","assembly_accession":"GCA_007109385.1","genome_id":"562.50521","genome_name":"Escherichia coli strain 131","strain":"strain 131","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5353799.0,"gc_content":50.71572,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5593.0,"refseq_cds":5298.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"50x","assembly_method":"HGAP v. 4","sequencing_centers":"Duke University","completion_date":"2019-07-18T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA551684","biosample_accession":"SAMN12163089","genbank_accessions":"CP041572,CP041573,CP041574,CP041575,CP041576,CP041577","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Deverick Anderson","comments":"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2732,"n_metabolites":1943,"n_genes":1471,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.58215.json.json","assembly_accession":"GCA_010669005.1","genome_id":"562.58215","genome_name":"Escherichia coli strain PapRG-06-3","strain":"strain PapRG-06-3","serovar":"","phylogroup":"B1","MLST":-1,"mash_cluster":26,"isolation_source":"feces","isolation_country":"Gambia","geographic_location":"Gambia","host_name":"Papio papio","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4703889.0,"gc_content":50.74161,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4580.0,"refseq_cds":4357.0,"sequencing_platform":"Oxford Nanopore 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Nanopore","sequencing_depth":"192.0x","assembly_method":"SPAdes v. 3.8.0","sequencing_centers":"University Medical Center Hamburg-Eppendorf","completion_date":"2016-06-20T00:00:00Z","collection_date":"5/1/15","bioproject_accession":"PRJNA321990","biosample_accession":"SAMN04963292","genbank_accessions":"CP016034,CP016035,CP016036,CP016037,CP016038,CP016039,CP016040,CP016041,CP016042","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"We report the first E. coli strain co-producing the two carbapenemases blaNDM-1 and blaOXA-232. While endemic in Greece and India, double-carbapenemase producing enterobacteria are still rare in Germany. The dissemination of these pathogens is worrisome as it potentially further narrows the therapeutic options. Carbapenemase positive strains often display only moderately elevated MICs for at least one carbapenem and high-dose carbapenem therapy with prolonged infusion may be used for treatment in those instances. Double-carbapenemase production likely compromises this therapeutic option. Furthermore, newly developed beta-lactamase inhibitors with activity towards carbapenemases have recently been approved by several drug agencies and hold great promise for currently difficult or even untreatable infections. The presence of diverse beta-lactamases from different molecular groups in one pathogen may result in only partial inhibition and consequently in therapeutic failure. The isolation of nearly identical blaOXA-232 carrying plasmids from geographically and temporally unrelated cases not only from K. pneumoniae but now also from E. coli suggests high mobility of the plasmid, which may be more widespread than currently appreciated. Taken together, we characterized the first blaNDM-1/blaOXA-232 double-carbapenemase producing E. coli, highlighting the constant emergence of novel, highly drug resistant pathogens in central Europe and the necessity to control their spread.","n_reactions":2731,"n_metabolites":1935,"n_genes":1518,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"562.66885.json.json","assembly_accession":"GCA_014854675.1","genome_id":"562.66885","genome_name":"Escherichia coli strain K_EC180","strain":"strain K_EC180","serovar":"","phylogroup":"D","MLST":1,"mash_cluster":18,"isolation_source":"feces","isolation_country":"South Korea","geographic_location":"South Korea","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5017281.0,"gc_content":50.42773,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5126.0,"refseq_cds":4752.0,"sequencing_platform":"PacBio RSII; Illumina NextSeq","sequencing_depth":"100.0x","assembly_method":"HGAP v. 2.3","sequencing_centers":"DANKOOK UNIVERSITY","completion_date":"2020-10-06T00:00:00Z","collection_date":"2019-07-17","bioproject_accession":"PRJNA666028","biosample_accession":"SAMN16277032","genbank_accessions":"CP062203","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from a swine feces that was collected to livestock farm","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Cell culture","comments":"The Escherichia coli K_EC180 was isolated from a swine feces that was collected to livestock farm.","n_reactions":2732,"n_metabolites":1945,"n_genes":1516,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"KOR","country":"South Korea"},{"gem_file":"562.70783.json.json","assembly_accession":"GCA_016904695.1","genome_id":"562.70783","genome_name":"Escherichia coli strain 10R","strain":"strain 10R","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"anal swab","isolation_country":"China","geographic_location":"China:Henan","host_name":"turkey","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4678626.0,"gc_content":50.848648,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4611.0,"refseq_cds":4339.0,"sequencing_platform":"Illumina; Oxford Nanopore","sequencing_depth":"214.49x","assembly_method":"Recyrrent NeuralNetwork v. 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DECEMBER-2019","sequencing_centers":"Texas A&M","completion_date":"2021-03-15T00:00:00Z","collection_date":"2005","bioproject_accession":"PRJNA669526","biosample_accession":"SAMN16454192","genbank_accessions":"CP063970,CP063971,CP063972,CP063973,CP063974","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from cattle isolates at Iowa State University","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"This is a non-pathogenic/toxigenic E. coli strain that has been recommended by the USDA for use as a surrogate indicator organism to measure changes in microbial counts. This isolate was originally isolated from cattle isolates at Iowa State University. It has been verified to lack by the E. coli Reference Center of Pennsylvania State University, as well as has been reported by the depositor to express no cytotoxicity when cultured with African green monkey kidney (Vero) cells. Further analysis incorporating whole genome sequencing by the current submitter also demonstrates a lack of virulence. This isolate was purchased from the American Type Culture Collection (ATCC), and the current sequence data was generated by both the Illumina MiSeq and Oxford Nanopore MinION platforms.For further information please see the following:https://www.atcc.org/products/all/BAA-1430.aspx#generalinformationhttps://doi.org/10.4315/0362-028x-68.12.2580","n_reactions":2731,"n_metabolites":1938,"n_genes":1509,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.7564.json.json","assembly_accession":"GCF_001276585.1","genome_id":"562.7564","genome_name":"Escherichia coli strain RR1","strain":"strain RR1","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4587291.0,"gc_content":50.82,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4585.0,"refseq_cds":4344.0,"sequencing_platform":"Illumina HiSeq","sequencing_depth":"1000.0x","assembly_method":"CLC Genomics Workbench v. 6.5","sequencing_centers":"KRIBB","completion_date":"2015-08-31T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA272568","biosample_accession":"SAMN03384316","genbank_accessions":"CP011113","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"KCTC:2134","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"To trace genetic makeup of a common laboratory strain\\; comparative genomic research purpose","n_reactions":2752,"n_metabolites":2027,"n_genes":1721,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.29092.json.json","assembly_accession":"GCA_003019175.1","genome_id":"562.29092","genome_name":"Escherichia coli strain 2013C-4187","strain":"strain 2013C-4187","serovar":"O71:H11","phylogroup":"B1","MLST":21,"mash_cluster":23,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5605298.0,"gc_content":50.652134,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5802.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"69.884x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Jul-2013","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08579590","genbank_accessions":"CP027546,CP027547","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2731,"n_metabolites":1939,"n_genes":1521,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.74747.json.json","assembly_accession":"GCA_018075285.1","genome_id":"562.74747","genome_name":"Escherichia coli strain EC2341","strain":"strain EC2341","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"pus","isolation_country":"China","geographic_location":"China: Zhejiang","host_name":"Homo sapiens","host_health":"infenction","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5098723.0,"gc_content":50.64115,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5185.0,"refseq_cds":4829.0,"sequencing_platform":"PacBio","sequencing_depth":"200X","assembly_method":"CLC NGS Cell v. 10.0","sequencing_centers":"Zhejiang Provincial People's Hospital","completion_date":"2021-04-19T00:00:00Z","collection_date":"2017-10-21","bioproject_accession":"PRJNA720492","biosample_accession":"SAMN18652119","genbank_accessions":"CP072976,CP072977,CP072978,CP072979","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Xi Li","comments":"this is the first report of E. coli strains carrying blaKPC-2 gene on IncU plasmids. Emergence of IncU type blaKPC-2-positve plasmid highlights further dissemination of blaKPC-2 in Enterobacteriaceae. Therefore, it is imperative that effective measures are taken immediately to control the spread of these blaKPC-2-positive plasmids.","n_reactions":2733,"n_metabolites":1942,"n_genes":1532,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.5745.json.json","assembly_accession":"GCA_000830035.1","genome_id":"562.5745","genome_name":"Escherichia coli C41(DE3)","strain":"C41(DE3)","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"BL21(DE3) for its improved ability to produce recombinant proteins (see: J Mol Biol","isolation_country":"Sweden","geographic_location":"Sweden","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4557511.0,"gc_content":50.83,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4342.0,"refseq_cds":4299.0,"sequencing_platform":"454; Sanger","sequencing_depth":"43x (454)","assembly_method":"Newbler v. 2009","sequencing_centers":"Stockholm University","completion_date":"2015-01-29T00:00:00Z","collection_date":"2009","bioproject_accession":"PRJNA273434","biosample_accession":"SAMN03292179","genbank_accessions":"CP010585.1","refseq_accessions":"NZ_CP010585.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"derived from BL21(DE3) for its improved ability to produce recombinant proteins (see: J Mol Biol","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The Escherichia coli strain C41(DE3) was derived from BL21(DE3) for its improved ability to produce recombinant proteins (see: J Mol Biol. 1996 Jul 19\\;260(3):289-98). This study aims at identifying and understanding the genetic adaptations that have occurred during the isolation of C41(DE3). 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Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli\u2019s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a \u2018trade-up\u2019 is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic\\; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.","n_reactions":2732,"n_metabolites":1935,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.76479.json.json","assembly_accession":"GCA_018988345.1","genome_id":"562.76479","genome_name":"Escherichia coli strain XJW9B263","strain":"strain XJW9B263","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"feces","isolation_country":"China","geographic_location":"China: Xinjiang","host_name":"Bovine","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5051738.0,"gc_content":50.758472,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5107.0,"refseq_cds":4779.0,"sequencing_platform":"Illumina MiniSeq; Oxford Nanopore's","sequencing_depth":"200.0x","assembly_method":"Unicycler v. v0.4.7; SPAdes v. v3.8.7","sequencing_centers":"South China Agricultural University","completion_date":"2021-06-23T00:00:00Z","collection_date":"2018-05-06","bioproject_accession":"PRJNA690212","biosample_accession":"SAMN17246086","genbank_accessions":"CP067399,CP067400,CP067401","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"34156173","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"fosA3-positive Escherichia coli of bovine origin","n_reactions":2733,"n_metabolites":1939,"n_genes":1520,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.79354.json.json","assembly_accession":"GCA_020105395.1","genome_id":"562.79354","genome_name":"Escherichia coli strain CX11","strain":"strain CX11","serovar":"","phylogroup":"A","MLST":635,"mash_cluster":22,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada: Alberta","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5347167.0,"gc_content":50.87939,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5496.0,"refseq_cds":5156.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"303x","assembly_method":"flye v. 2.8.2","sequencing_centers":"Agriculture & Agri-Food Canada","completion_date":"2021-09-14T00:00:00Z","collection_date":"2014/2015","bioproject_accession":"PRJNA716667","biosample_accession":"SAMN18446043","genbank_accessions":"CP081729,CP081732,CP081733,CP081730,CP081731,CP081734,CP081735","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The presence of locus of heat resistance is a common way of screening heat resistance in E.coli, however harboring LHR does not always confer extreme heat resistance suggesting other genetic components may play a role in heat resistance. WGS was performed to determine genetic determinants in E.coli for different levels of heat resistance and determine the evolution regarding the emergence of heat resistant strains of E.coli in a meat plant setting.","n_reactions":2736,"n_metabolites":1951,"n_genes":1528,"n_exchange":331,"n_with_gpr":2290,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"331112.6.json.json","assembly_accession":"GCA_000017765.1","genome_id":"331112.6","genome_name":"Escherichia coli HS","strain":"HS","serovar":"serovar O9","phylogroup":"A","MLST":46,"mash_cluster":22,"isolation_source":"laboratory scientist at Walter Reed Army Institute of Research","isolation_country":"United States","geographic_location":"Walter Reed Army Institute","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4643538.0,"gc_content":50.8,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4520.0,"refseq_cds":4378.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"TIGR","completion_date":"2007-09-10T00:00:00Z","collection_date":"1978","bioproject_accession":"PRJNA13959","biosample_accession":"SAMN02604037","genbank_accessions":"CP000802","refseq_accessions":"NC_009800","genome_status":"Complete","taxon_id":331112.0,"organism_name":"Escherichia coli HS","pathovar":"Nonpathogenic","antimicrobial_resistance":"","culture_collection":"","publication":"18676672","isolation_comments":"isolated from a laboratory scientist at Walter Reed Army Institute of Research in 1978 (Levine, 1978)","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"Yes","temperature_range":"Mesophilic","optimal_temperature":"37","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"Escherichia coli strain HS. This strain (HS\\; serotype O9) is a human commensal that was originally isolated from a laboratory scientist at Walter Reed Army Institute of Research in 1978 (Levine, 1978). It was obtained from Drs. Kaper and Nataro at the School of Medicine at the University of Maryland. Strain HS colonizes the human gastrointestinal tract in challenge experiments, but no overt signs of disease occur. Thus, this strain represents a genomic baseline for human gastrointestinal tract colonization. It is competent and amenable to genetic manipulation.","n_reactions":2732,"n_metabolites":1939,"n_genes":1507,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.60287.json.json","assembly_accession":"GCA_012974525.1","genome_id":"562.60287","genome_name":"Escherichia coli strain C21","strain":"strain C21","serovar":"","phylogroup":"B1","MLST":156,"mash_cluster":26,"isolation_source":"","isolation_country":"China","geographic_location":"China: Chengdu","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5066017.0,"gc_content":50.616825,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5038.0,"refseq_cds":4757.0,"sequencing_platform":"PacBio RSII; Illumina NovaSeq","sequencing_depth":"99.7x","assembly_method":"HGAP v. 2.3.0","sequencing_centers":"Henan Agricultural University","completion_date":"2020-05-05T00:00:00Z","collection_date":"sep-2009","bioproject_accession":"PRJNA628170","biosample_accession":"SAMN14732738","genbank_accessions":"CP052877,CP052878,CP052879,CP052880,CP052881","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"IS1294 reorganizes plasmids in a multidrug-resistant Escherichia coli strain by replicative transposition","n_reactions":2731,"n_metabolites":1939,"n_genes":1523,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.63040.json.json","assembly_accession":"GCA_013426075.1","genome_id":"562.63040","genome_name":"Escherichia coli strain WCHEC035123","strain":"strain WCHEC035123","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"Sewage","isolation_country":"China","geographic_location":"China: Chengdu, Sichuan","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4972571.0,"gc_content":50.62347,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5028.0,"refseq_cds":4714.0,"sequencing_platform":"Illumina HiSeq; 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Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2711,"n_metabolites":1877,"n_genes":1438,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"562.70530.json.json","assembly_accession":"GCA_016776325.1","genome_id":"562.70530","genome_name":"Escherichia coli strain RIVM_C018583","strain":"strain RIVM_C018583","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5419042.0,"gc_content":50.551296,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5455.0,"refseq_cds":5103.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"National Institute for Public Health and the Environment","completion_date":"2021-02-01T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA691727","biosample_accession":"SAMN17373183","genbank_accessions":"CP068807","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:chromosome","comments":"OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2732,"n_metabolites":1938,"n_genes":1520,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"511693.14.json.json","assembly_accession":"GCA_013166975.1","genome_id":"511693.14","genome_name":"Escherichia coli 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University","completion_date":"2021-04-19T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA681611","biosample_accession":"SAMN16963731","genbank_accessions":"CP072986,CP072987","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:pure culture","comments":"A beta-lactam sensitive gfp-labelled E. coli was inoculated directly into the manure enriched overnight with buffered peptone containing 4 mg/ml cefotaxime as a recipient strain to capture plasmids carrying extended beta-lactamase genes.","n_reactions":2732,"n_metabolites":1936,"n_genes":1547,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"1055538.9.json.json","assembly_accession":"GCA_014622965.1","genome_id":"1055538.9","genome_name":"Escherichia coli O145 strain RM12275-C1","strain":"O145 strain RM12275-C1","serovar":"","phylogroup":"D","MLST":32,"mash_cluster":20,"isolation_source":"","isolation_country":"USA","geographic_location":"USA: CA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5497342.0,"gc_content":50.70883,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5825.0,"refseq_cds":5435.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"135.18x","assembly_method":"HGAP v. RS_HGAP Assembly.3","sequencing_centers":"USDA, ARS, WRRC","completion_date":"2020-09-16T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA483500","biosample_accession":"SAMN09742416","genbank_accessions":"CP031341,CP031340","refseq_accessions":"","genome_status":"Complete","taxon_id":1055538.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Complete Genomes of Environmental Shiga Toxin- Producing Escherichia coli O145","n_reactions":2711,"n_metabolites":1877,"n_genes":1425,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"585055.56.json.json","assembly_accession":"GCA_003028695.1","genome_id":"585055.56","genome_name":"Escherichia coli 55989","strain":"55989","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"urine","isolation_country":"Pakistan","geographic_location":"Pakistan: Sheikh Zaid Hospital, Lahore","host_name":"Human, Homo sapiens","host_health":"Urinary tract infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4989876.0,"gc_content":50.786613,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4966.0,"refseq_cds":"","sequencing_platform":"Illumina MiSeq","sequencing_depth":"30X","assembly_method":"SPAdes v. 3.10.1","sequencing_centers":"Rehman Medical Institute","completion_date":"2018-04-02T00:00:00Z","collection_date":"06-Dec-2016","bioproject_accession":"PRJNA389368","biosample_accession":"SAMN07196158","genbank_accessions":"CP028304","refseq_accessions":"","genome_status":"Complete","taxon_id":585055.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Asma Manzoor, Nabila Ishaq","comments":"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","n_reactions":2732,"n_metabolites":1943,"n_genes":1464,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"PAK","country":"Pakistan"},{"gem_file":"562.67508.json.json","assembly_accession":"GCA_015571555.1","genome_id":"562.67508","genome_name":"Escherichia coli strain Res13-Sevr-PER06-05-b-A","strain":"strain Res13-Sevr-PER06-05-b-A","serovar":"O-untypeable:H4","phylogroup":"A","MLST":761,"mash_cluster":22,"isolation_source":"feces","isolation_country":"Canada","geographic_location":"Canada: Quebec","host_name":"Pig, Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5113439.0,"gc_content":50.62405,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5194.0,"refseq_cds":4855.0,"sequencing_platform":"Oxford Nanopore MinION and Illumina MiSeq","sequencing_depth":"1.00x","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Government of Canada","completion_date":"2020-11-18T00:00:00Z","collection_date":"11-Apr-2017","bioproject_accession":"PRJNA662792","biosample_accession":"SAMN16304267","genbank_accessions":"CP062815,CP062816,CP062817,CP062818,CP062819,CP062820","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Agriculture and Agri-Food Canada","comments":"The majority of antibiotics sold are administered to livestock, presumably promoting the development and spread of antibiotic resistance genes in food-borne pathogens such as Enterobacteriaceae producing extended spectrum beta-lactamases (ESBL). Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. The major goal of the study was to characterize cefotaxime-resistant bacteria isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2732,"n_metabolites":1940,"n_genes":1526,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.58141.json.json","assembly_accession":"GCA_010365345.1","genome_id":"562.58141","genome_name":"Escherichia coli strain 32-4","strain":"strain 32-4","serovar":"","phylogroup":"A","MLST":1284,"mash_cluster":21,"isolation_source":"environment","isolation_country":"Switzerland","geographic_location":"Switzerland","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5173218.0,"gc_content":50.741375,"contigs":12.0,"chromosomes":1.0,"plasmids":11.0,"patric_cds":5306.0,"refseq_cds":4898.0,"sequencing_platform":"Oxford Nanopore/illumina 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sequenced.","n_reactions":2733,"n_metabolites":1940,"n_genes":1527,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHE","country":"Switzerland"},{"gem_file":"199310.237.json.json","assembly_accession":"GCA_014262945.1","genome_id":"199310.237","genome_name":"Escherichia coli CFT073","strain":"CFT073","serovar":"","phylogroup":"B2","MLST":73,"mash_cluster":5,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:California","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5242376.0,"gc_content":50.4827,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5126.0,"refseq_cds":"","sequencing_platform":"Illumina","sequencing_depth":"114.0x","assembly_method":"SPAdes v. 3.9.0","sequencing_centers":"Genentech","completion_date":"2020-08-21T00:00:00Z","collection_date":"02-Nov-2016","bioproject_accession":"PRJNA624646","biosample_accession":"SAMN14575425","genbank_accessions":"CP051263","refseq_accessions":"","genome_status":"Complete","taxon_id":199310.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"32788728","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"De novo assembly of modified E coli strain CFT073.","n_reactions":2733,"n_metabolites":1943,"n_genes":1450,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_002246595.2.json.json","assembly_accession":"GCF_002246595.2","genome_id":"GCF_002246595.2","genome_name":"Escherichia coli","strain":"ECCTRSRTH03","serovar":"","phylogroup":"A","MLST":34,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN07450616","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia 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familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":5309743.0,"gc_content":50.51,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5513.0,"refseq_cds":5399.0,"sequencing_platform":"PacBio","sequencing_depth":"20x","assembly_method":"De-novo v. Celera Assembler 8.6","sequencing_centers":"The Roslin Institute","completion_date":"2017-09-18T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA402083","biosample_accession":"SAMN07618125","genbank_accessions":"CP023366,CP023367,CP023368,CP023369,CP023370","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from urinary tract infections in dogs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.","n_reactions":2733,"n_metabolites":1944,"n_genes":1527,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_900635175.1.json.json","assembly_accession":"GCF_900635175.1","genome_id":"GCF_900635175.1","genome_name":"Escherichia coli","strain":"NCTC9084","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMEA3403037","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2734,"n_metabolites":1941,"n_genes":1527,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.50948.json.json","assembly_accession":"GCA_008632555.1","genome_id":"562.50948","genome_name":"Escherichia coli strain AR202.2","strain":"strain AR202.2","serovar":"O:H9","phylogroup":"A","MLST":167,"mash_cluster":21,"isolation_source":"Rectal swab","isolation_country":"Switzerland","geographic_location":"Switzerland:Zurich","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5129890.0,"gc_content":50.85023,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5241.0,"refseq_cds":4947.0,"sequencing_platform":"Illumina HiSeq, Oxford Nanopore MinION","sequencing_depth":"300x","assembly_method":"Canu, Racon, Pilon(3x) v. Canu v1.7","sequencing_centers":"University of Bern","completion_date":"2019-09-23T00:00:00Z","collection_date":"20-Jun-2018","bioproject_accession":"PRJNA565187","biosample_accession":"SAMN12736389","genbank_accessions":"CP043946,CP043949,CP043948,CP043947","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"ST167","substrain":"","additional_metadata":"sample_type:Pure culture","comments":"The study aimed at the carriage of carbapenem-resistant Enterobacteriaceae in hospitalized pets in a companion animal clinic in Switzerland.","n_reactions":2753,"n_metabolites":2029,"n_genes":1758,"n_exchange":331,"n_with_gpr":2307,"dataset":"EcopanGEM","organism":"Escherichia 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We additionally showed how different IS elements can alter the regulation of afa transcription and provide evidence for a more widespread impact of IS1 on ST131 genome evolution.The genomes in this BioProject are 4 ST131 representative strains with different IS elements located in the promoter region of afa operon. These genomes are assembled using Nanopore long reads and polished with Illumina short reads.","n_reactions":2751,"n_metabolites":2021,"n_genes":1736,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_905332355.1.json.json","assembly_accession":"GCF_905332355.1","genome_id":"GCF_905332355.1","genome_name":"Escherichia 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Escherichia coli 0127:H6 E2348/69 is an enteropathogenic E. coli strain to be used for comparative studies with related Escherichia and Shigella species. ","n_reactions":2731,"n_metabolites":1940,"n_genes":1441,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.29119.json.json","assembly_accession":"GCA_003018515.1","genome_id":"562.29119","genome_name":"Escherichia coli strain 2013C-3996","strain":"strain 2013C-3996","serovar":"O26:H11","phylogroup":"B1","MLST":21,"mash_cluster":23,"isolation_source":"Stool","isolation_country":"United States","geographic_location":"United States","host_name":"","host_health":"","host_gender":"","host_age":"10-19","body_sample_site":"","disease":"","genome_length":5955903.0,"gc_content":50.65573,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":6323.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"91.841x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"May-2013","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN04504054","genbank_accessions":"CP027572,CP027571","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CDC","comments":"PulseNet STEC genome reference library","n_reactions":2711,"n_metabolites":1877,"n_genes":1465,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.13758.json.json","assembly_accession":"GCF_001900735.1","genome_id":"562.13758","genome_name":"Escherichia coli strain D10","strain":"strain D10","serovar":"","phylogroup":"G","MLST":117,"mash_cluster":2,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5247683.0,"gc_content":50.73,"contigs":3.0,"chromosomes":3.0,"plasmids":"","patric_cds":5310.0,"refseq_cds":4946.0,"sequencing_platform":"Illumina Miseq; Roche 454 GS Junior","sequencing_depth":"30-80x","assembly_method":"Newbler v. 2.7","sequencing_centers":"Nanjing Agricultural University","completion_date":"2016-12-12T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA269191","biosample_accession":"SAMN03252428","genbank_accessions":"CP010157,CP010158,CP010159","refseq_accessions":"NZ_CP010157.1,NZ_CP010158.1,NZ_CP010159.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"env_biome:faeces","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments","n_reactions":2732,"n_metabolites":1944,"n_genes":1494,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.77332.json.json","assembly_accession":"GCA_019269415.1","genome_id":"562.77332","genome_name":"Escherichia coli strain Colony156","strain":"strain Colony156","serovar":"","phylogroup":"Unknown","MLST":131,"mash_cluster":3,"isolation_source":"Rectal swab","isolation_country":"Thailand","geographic_location":"Thailand","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4733683.0,"gc_content":51.362385,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4390.0,"refseq_cds":"","sequencing_platform":"Illumina HiSeq","sequencing_depth":"84.739x","assembly_method":"idba_ud v. 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In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_020526745.1.json.json","assembly_accession":"GCF_020526745.1","genome_id":"GCF_020526745.1","genome_name":"Escherichia 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Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. The major goal of the study was to characterize cefotaxime-resistant bacteria isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2732,"n_metabolites":1942,"n_genes":1501,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.47721.json.json","assembly_accession":"GCA_005954725.1","genome_id":"562.47721","genome_name":"Escherichia coli strain S17-1","strain":"strain S17-1","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4772290.0,"gc_content":50.926033,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4803.0,"refseq_cds":4546.0,"sequencing_platform":"Illumina MiSeq","sequencing_depth":"188.0x","assembly_method":"CLC Genomics workbench v. 11.0.1","sequencing_centers":"University of Nottingham","completion_date":"2019-06-04T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA544747","biosample_accession":"SAMN11854565","genbank_accessions":"CP040667","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"RP4-2(Km::Tn7,Tc::Mu-1)","substrain":"","additional_metadata":"","comments":"Escherichia coli S17-1 draft genome sequence","n_reactions":2732,"n_metabolites":1940,"n_genes":1560,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_020883515.1.json.json","assembly_accession":"GCF_020883515.1","genome_id":"GCF_020883515.1","genome_name":"Escherichia coli","strain":"E2","serovar":"","phylogroup":"B1","MLST":224,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN23015264","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1935,"n_genes":1511,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.380.json.json","assembly_accession":"GCA_013168175.1","genome_id":"83334.380","genome_name":"Escherichia coli O157:H7 strain 2-6-2","strain":"O157:H7 strain 2-6-2","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle feces","isolation_country":"USA","geographic_location":"USA:Nebraska","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5650829.0,"gc_content":50.479336,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5984.0,"refseq_cds":5687.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"232x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"1999","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN05360202","genbank_accessions":"CP038419,CP038420","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. 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This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.48215.json.json","assembly_accession":"GCA_900497095.1","genome_id":"562.48215","genome_name":"Escherichia coli strain EC-TO75","strain":"strain EC-TO75","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4899425.0,"gc_content":50.675724,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":4868.0,"refseq_cds":4611.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Leibniz-Institut DSMZ-Deutsche Sammlung von Mikro","completion_date":"2019-01-29T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB27479","biosample_accession":"SAMEA4785258","genbank_accessions":"LS998785,LS998786,LS998787,LS998788","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Genome sequencing of Escherichia coli strain TO75","n_reactions":2733,"n_metabolites":1940,"n_genes":1533,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83333.1302.json.json","assembly_accession":"GCA_015534975.1","genome_id":"83333.1302","genome_name":"Escherichia coli K-12 strain CETR1G40 strain not applicable","strain":"","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada: Manitoba","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4631467.0,"gc_content":50.77877,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4591.0,"refseq_cds":4341.0,"sequencing_platform":"Illumina","sequencing_depth":"30X","assembly_method":"Geneious v. 11.1.5","sequencing_centers":"University of Manitoba","completion_date":"2020-11-17T00:00:00Z","collection_date":"2018","bioproject_accession":"PRJNA646979","biosample_accession":"SAMN15572258","genbank_accessions":"CP064680","refseq_accessions":"","genome_status":"Complete","taxon_id":83333.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:pure culture","comments":"These isolates were created by gradually adapting an Escherichia coli K-12 BW25113 strain over 40 generations to one of two quaternary ammonium compounds, benzakonium (BZK) or cetrimide (CET). Three replicates were created for each compound, generating BZKR1, BZKR2, BZKR3, CETR1, CETR2, and CETR3, as well as an unadapted wild-type. At the end of the experiment, the BZK-adapted bacteria were tolerant to 72-144 ug/ml of BZK, and the CET-adapted bacteria were tolerant to 240 ug/ml of CET.;Cetrimide adapted E.coli bioreplicate 1 derived from BW25113","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.46724.json.json","assembly_accession":"GCA_005221745.1","genome_id":"562.46724","genome_name":"Escherichia coli strain 130","strain":"strain 130","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5553251.0,"gc_content":50.49966,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5967.0,"refseq_cds":5800.0,"sequencing_platform":"PacBio","sequencing_depth":"252x","assembly_method":"HGAP v. 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With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. 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The fate and potential horizontal gene transfer of those genes into the host microbiome will have a crucial bearing on the eventual health risk of exposure to antibiotic resistance genes. In the present study, the effects of antibiotics on the in vivo transfer of \ud835\udefd-lactam resistance genes were evaluated in a mouse model by characterizing the microbiome in excreted feces. Mice were dosed with Escherichia coli, Salmonella enterica serovars Heidelberg or Bredeney referred to as donors. The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1936,"n_genes":1547,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.78039.json.json","assembly_accession":"GCA_019431185.1","genome_id":"562.78039","genome_name":"Escherichia coli strain 135","strain":"strain 135","serovar":"","phylogroup":"E","MLST":1158,"mash_cluster":12,"isolation_source":"Chicken fecal","isolation_country":"China","geographic_location":"China:Guangdong province","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5897998.0,"gc_content":50.655018,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":6116.0,"refseq_cds":5650.0,"sequencing_platform":"Oxford Nanopore GridION","sequencing_depth":"418.0x","assembly_method":"Canu v. 1.7.11","sequencing_centers":"South China Agricultural University","completion_date":"2021-08-01T00:00:00Z","collection_date":"2017","bioproject_accession":"PRJNA749258","biosample_accession":"SAMN20360180","genbank_accessions":"CP080260,CP080261,CP080262,CP080263,CP080264,CP080265","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Sun-Yinhuan","comments":"blaCMY-2-positive Escherichia coli Genome sequencing and assembly","n_reactions":2731,"n_metabolites":1939,"n_genes":1504,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"1055533.4.json.json","assembly_accession":"GCA_003112185.1","genome_id":"1055533.4","genome_name":"Escherichia coli O26 str. 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Sequencing of STECs isolated from the agriculturally important region of the California Central Coast will address the diversity of genomic content and physiology of STECs compared to E. coli O157.","n_reactions":2711,"n_metabolites":1877,"n_genes":1465,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"1411691.4.json.json","assembly_accession":"GCF_001020945.1","genome_id":"1411691.4","genome_name":"Escherichia coli K-12 GM4792","strain":"K-12 GM4792","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4622332.0,"gc_content":50.81,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4504.0,"refseq_cds":3552.0,"sequencing_platform":"Illumina 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.63818.json.json","assembly_accession":"GCA_014157395.1","genome_id":"562.63818","genome_name":"Escherichia coli strain WP2-W18-ESBL-10","strain":"strain WP2-W18-ESBL-10","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"wastewater treatment plant effluent","isolation_country":"Japan","geographic_location":"Japan:Tokyo","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4993983.0,"gc_content":50.677746,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4776.0,"refseq_cds":4543.0,"sequencing_platform":"Sequel; 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coli","country_iso":"BGD","country":"Bangladesh"},{"gem_file":"562.58371.json.json","assembly_accession":"GCA_011045295.1","genome_id":"562.58371","genome_name":"Escherichia coli strain E686","strain":"strain E686","serovar":"","phylogroup":"D","MLST":405,"mash_cluster":16,"isolation_source":"","isolation_country":"South Korea","geographic_location":"South Korea","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5162306.0,"gc_content":50.58528,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5064.0,"refseq_cds":"","sequencing_platform":"PacBio RSII","sequencing_depth":"183.0x","assembly_method":"SMRT v. 3.0","sequencing_centers":"Yonsei University College of Medicine","completion_date":"2020-03-02T00:00:00Z","collection_date":"10-Feb-2019","bioproject_accession":"PRJNA607818","biosample_accession":"SAMN14149127","genbank_accessions":"CP049198","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:fece","comments":"WGS of chromosome in CMY-2-producing E. coli","n_reactions":2734,"n_metabolites":1945,"n_genes":1514,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"KOR","country":"South Korea"},{"gem_file":"562.63862.json.json","assembly_accession":"GCA_014170915.1","genome_id":"562.63862","genome_name":"Escherichia coli strain 154AHL.1","strain":"strain 154AHL.1","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":21,"isolation_source":"Turkey's","isolation_country":"Canada","geographic_location":"Canada","host_name":"Turkey","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4964007.0,"gc_content":50.59815,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5911.0,"refseq_cds":4732.0,"sequencing_platform":"Oxford Nanopore MinION","sequencing_depth":"11.6x","assembly_method":"Flye v. 2.6","sequencing_centers":"University of Guelph","completion_date":"2020-08-12T00:00:00Z","collection_date":"2016/2017","bioproject_accession":"PRJNA596173","biosample_accession":"SAMN13613892","genbank_accessions":"CP059988,CP059989,CP059990","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from Turkey's in Canada","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:fecal","comments":"Chromosomes and plasmids were assembled from E. coli isolated from Turkey's in Canada. Both long reads (Oxford Nanopore) and short reads (Illumina) were used.","n_reactions":2739,"n_metabolites":1954,"n_genes":1557,"n_exchange":331,"n_with_gpr":2293,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.60463.json.json","assembly_accession":"GCA_013166955.1","genome_id":"562.60463","genome_name":"Escherichia coli strain Nico21(DE3) strain Nico21(DE3) strain Nico21(DE3)","strain":"strain Nico21(DE3) strain Nico21(DE3) strain Nico21(DE3)","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4560909.0,"gc_content":50.833485,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4524.0,"refseq_cds":4286.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"209x","assembly_method":"HGAP v. 3","sequencing_centers":"New England Biolabs","completion_date":"2020-05-26T00:00:00Z","collection_date":"2010-01-01","bioproject_accession":"PRJNA341475","biosample_accession":"SAMN14933841","genbank_accessions":"CP053600","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"21602383","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Closed and finished genome of NEB 5-alpha, an immediate fhuA derivative of (E. coli K-12) DH5alpha.","n_reactions":2733,"n_metabolites":1935,"n_genes":1512,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.46723.json.json","assembly_accession":"GCA_005221725.1","genome_id":"562.46723","genome_name":"Escherichia coli strain 132","strain":"strain 132","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5553163.0,"gc_content":50.4996,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5965.0,"refseq_cds":5797.0,"sequencing_platform":"PacBio","sequencing_depth":"233x","assembly_method":"HGAP v. RS_HGAP_Assembly.3","sequencing_centers":"United State Department of Agriculture","completion_date":"2019-05-07T00:00:00Z","collection_date":"2006","bioproject_accession":"PRJNA445267","biosample_accession":"SAMN08773039","genbank_accessions":"CP028641,CP028643,CP028642","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The aim of this project is to compare complete closed genomes with whole genome sequencing (WGS) using short reads. SNPs from WGS is used in many studies to determine relatedness of strains. These SNPs are in the core genome and don't reflect the diversity of the complete genome. This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"2605619.11.json.json","assembly_accession":"GCA_008124265.1","genome_id":"2605619.11","genome_name":"Escherichia coli O16:H48 strain PG20180059","strain":"O16:H48 strain PG20180059","serovar":"O16:H48","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"mouse gut","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4721143.0,"gc_content":50.65839,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4788.0,"refseq_cds":4505.0,"sequencing_platform":"Illumina MiSeq and Nanopore","sequencing_depth":"89x","assembly_method":"Unicycler v. 0.4.3","sequencing_centers":"National Microbiology Laboratory at Guelph","completion_date":"2019-08-29T00:00:00Z","collection_date":"18-May-2018","bioproject_accession":"PRJNA560883","biosample_accession":"SAMN12603262","genbank_accessions":"CP043201,CP043202","refseq_accessions":"","genome_status":"Complete","taxon_id":2605619.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Canadian Food Inspection Agency","comments":"Humans and farm animals commonly consume food- or waterborne bacteria that harbour antibiotic resistance genes. The fate and potential horizontal gene transfer of those genes into the host microbiome will have a crucial bearing on the eventual health risk of exposure to antibiotic resistance genes. In the present study, the effects of antibiotics on the in vivo transfer of \ud835\udefd-lactam resistance genes were evaluated in a mouse model by characterizing the microbiome in excreted feces. Mice were dosed with Escherichia coli, Salmonella enterica serovars Heidelberg or Bredeney referred to as donors. The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1936,"n_genes":1547,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.69717.json.json","assembly_accession":"GCA_016757655.1","genome_id":"562.69717","genome_name":"Escherichia coli strain M-17","strain":"strain M-17","serovar":"","phylogroup":"B2","MLST":141,"mash_cluster":6,"isolation_source":"medicine \"BIOFLOR\"","isolation_country":"Belarus","geographic_location":"Belarus:Minsk","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5028010.0,"gc_content":50.811356,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4935.0,"refseq_cds":4705.0,"sequencing_platform":"Oxford Nanopore MinION; Illumina MiSeq","sequencing_depth":"410.0x","assembly_method":"Barapost v. 2020-12-28 edition; Flye v.","sequencing_centers":"Institute of Microbiology, National Academy of Sciences of Belarus","completion_date":"2021-01-27T00:00:00Z","collection_date":"2019-11","bioproject_accession":"PRJNA692547","biosample_accession":"SAMN17348805","genbank_accessions":"CP068394","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"VKPM:B-8208","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Genome analysis of soviet probiotic strain of E.coli","n_reactions":2732,"n_metabolites":1943,"n_genes":1448,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BLR","country":"Belarus"},{"gem_file":"562.60623.json.json","assembly_accession":"GCA_902825195.1","genome_id":"562.60623","genome_name":"Escherichia coli strain SC468","strain":"strain SC468","serovar":"","phylogroup":"Unknown","MLST":1164,"mash_cluster":6,"isolation_source":"Soil","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4426017.0,"gc_content":50.947227,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4502.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"MASSEY UNIVERSITY","completion_date":"2020-03-11T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB36951","biosample_accession":"SAMEA6595239","genbank_accessions":"LR782233","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Mike Sadowsky","comments":"Here we report the complete genomes of 47 Escherichia coli natural isolates, sampled from watersheds located at (46\u00b042\u203204\"N, 92\u00b012\u203226\"W) in Duluth, Minnesota. The genomes were assembled using a combination of Nanopore R9.4 and Illumina sequencing data.","n_reactions":2731,"n_metabolites":1933,"n_genes":1450,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_014168595.1.json.json","assembly_accession":"GCF_014168595.1","genome_id":"GCF_014168595.1","genome_name":"Escherichia coli","strain":"WP2-W18-CRE-03","serovar":"","phylogroup":"B1","MLST":602,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMD00194346","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1940,"n_genes":1506,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"2592065.4.json.json","assembly_accession":"GCA_006777045.1","genome_id":"2592065.4","genome_name":"Escherichia coli O1:H42 strain CLSC36","strain":"O1:H42 strain CLSC36","serovar":"O1:H42","phylogroup":"F","MLST":648,"mash_cluster":9,"isolation_source":"urine from healthy adult with cystitis","isolation_country":"Canada","geographic_location":"Canada: Montreal","host_name":"Human, Homo sapiens","host_health":"cystitis","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5278774.0,"gc_content":50.42186,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5293.0,"refseq_cds":4992.0,"sequencing_platform":"PacBio","sequencing_depth":"138.0x","assembly_method":"HGAP v. May-2015; Celera Assembler v.","sequencing_centers":"McGill University","completion_date":"2019-07-09T00:00:00Z","collection_date":"2005-09-26","bioproject_accession":"PRJNA551561","biosample_accession":"SAMN12158196","genbank_accessions":"CP041300,CP041299","refseq_accessions":"","genome_status":"Complete","taxon_id":2592065.0,"organism_name":"","pathovar":"UPEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Student health services McGill University","comments":"This strain was sequenced as part of a study that investigated the activity of the outer membrane protease OmpT among uropathogenic Escherichia coli clinical isolates. Healthy adult with cystitis","n_reactions":2711,"n_metabolites":1877,"n_genes":1452,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.66874.json.json","assembly_accession":"GCA_014825845.1","genome_id":"562.66874","genome_name":"Escherichia coli strain 20R2R","strain":"strain 20R2R","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"culture mutant","isolation_country":"USA","geographic_location":"USA:Pennsylvania","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5603401.0,"gc_content":50.47624,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5841.0,"refseq_cds":5409.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"256.0x","assembly_method":"HGAP v. 3","sequencing_centers":"USDA/ARS/Eastern Regional Research Center","completion_date":"2020-09-30T00:00:00Z","collection_date":"2009","bioproject_accession":"PRJNA294158","biosample_accession":"SAMN16202109","genbank_accessions":"CP062160,CP062161","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"C","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:bacteria","comments":"The project goals are to study DNA sequence, transcriptomic, and phenotypic variations among strains of Shiga toxin producing Escherichia coli in reference to biofilm formation and surface adhesion.","n_reactions":2731,"n_metabolites":1940,"n_genes":1488,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"511145.876.json.json","assembly_accession":"GCA_015291845.1","genome_id":"511145.876","genome_name":"Escherichia coli str. K-12 substr. MG1655","strain":"str. K-12 substr. MG1655","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"not applicable","isolation_country":"Brazil","geographic_location":"Brazil:Sao Paulo","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4631543.0,"gc_content":50.7823,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4641.0,"refseq_cds":4442.0,"sequencing_platform":"Illumina MiSeq","sequencing_depth":"65.0x","assembly_method":"SPAdes v. 3.6","sequencing_centers":"Instituto de Ciencias Biomedicas","completion_date":"2020-11-09T00:00:00Z","collection_date":"2015-06","bioproject_accession":"PRJNA493825","biosample_accession":"SAMN10144109","genbank_accessions":"CP032679","refseq_accessions":"","genome_status":"Complete","taxon_id":511145.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":" MG1655","additional_metadata":"sample_type:Bacterial culture","comments":"Characterization of phosphonate transporter coded by the phnCDE genes as a inorganic phosphate transporter. The reversion of the 8 bp insertion with the ORF of phnE of E. coli K12 MG1655 rendered the transporter fully functional and allowed the bactria to grow in phosphonate and in phosphate as the only P source.","n_reactions":2732,"n_metabolites":1936,"n_genes":1552,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BRA","country":"Brazil"},{"gem_file":"562.19207.json.json","assembly_accession":"GCA_002310655.1","genome_id":"562.19207","genome_name":"Escherichia coli strain 746","strain":"strain 746","serovar":"","phylogroup":"D","MLST":963,"mash_cluster":15,"isolation_source":"urinary tract infections","isolation_country":"United Kingdom","geographic_location":"United Kingdom: Scotland, Edinburgh","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":5319278.0,"gc_content":50.69,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5538.0,"refseq_cds":5388.0,"sequencing_platform":"PacBio","sequencing_depth":"20x","assembly_method":"De-novo v. Celera Assembler 8.10","sequencing_centers":"The Roslin Institute","completion_date":"2017-09-18T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA402083","biosample_accession":"SAMN07618129","genbank_accessions":"CP023353,CP023354,CP023355,CP023356","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from urinary tract infections in dogs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.","n_reactions":2733,"n_metabolites":1940,"n_genes":1521,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.29036.json.json","assembly_accession":"GCA_003028815.1","genome_id":"562.29036","genome_name":"Escherichia coli strain APEC 01","strain":"strain APEC 01","serovar":"","phylogroup":"A","MLST":167,"mash_cluster":21,"isolation_source":"urine","isolation_country":"Pakistan","geographic_location":"Pakistan: Sheikh Zaid Hospital, Lahore","host_name":"Human, Homo sapiens","host_health":"Urinary tract infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4609982.0,"gc_content":50.83303,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4500.0,"refseq_cds":"","sequencing_platform":"Illumina MiSeq","sequencing_depth":"30X","assembly_method":"SPAdes v. 3.10.1","sequencing_centers":"Rehman Medical Institute","completion_date":"2018-04-02T00:00:00Z","collection_date":"06-Dec-2016","bioproject_accession":"PRJNA389368","biosample_accession":"SAMN07196152","genbank_accessions":"CP028310","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Asma Manzoor, Nabila Ishaq","comments":"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","n_reactions":2732,"n_metabolites":1938,"n_genes":1523,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"PAK","country":"Pakistan"},{"gem_file":"562.48250.json.json","assembly_accession":"GCA_900622665.1","genome_id":"562.48250","genome_name":"Escherichia coli strain MS14386","strain":"strain MS14386","serovar":"","phylogroup":"B1","MLST":224,"mash_cluster":26,"isolation_source":"blood","isolation_country":"Australia","geographic_location":"Australia","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5058016.0,"gc_content":50.880287,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4954.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Bioplatforms Australia","completion_date":"2019-01-10T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB29930","biosample_accession":"SAMEA5128443","genbank_accessions":"LR130552,LR130553,LR130554","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"102.100.100.25768","publication":"","isolation_comments":"","other_clinical":"host_health_state:diseased","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Escherichia coli.","n_reactions":2731,"n_metabolites":1939,"n_genes":1512,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"83334.489.json.json","assembly_accession":"GCA_017165235.1","genome_id":"83334.489","genome_name":"Escherichia coli O157:H7 strain Z1504","strain":"O157:H7 strain Z1504","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5600699.0,"gc_content":50.487896,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5811.0,"refseq_cds":5415.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"221.2448311204877x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327594","genbank_accessions":"CP062746,CP062747,CP062748","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:IPRAVE Consortium","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.61709.json.json","assembly_accession":"GCA_013372385.1","genome_id":"562.61709","genome_name":"Escherichia coli strain EcPF14","strain":"strain EcPF14","serovar":"","phylogroup":"B2","MLST":73,"mash_cluster":5,"isolation_source":"urine","isolation_country":"USA","geographic_location":"USA: Dallas, Texas","host_name":"Human, Homo sapiens","host_health":"Chronic Cystitis","host_gender":"female","host_age":"","body_sample_site":"","disease":"","genome_length":5137006.0,"gc_content":50.505352,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5103.0,"refseq_cds":4800.0,"sequencing_platform":"Illumina NextSeq, ONT MinION","sequencing_depth":"83x, 338x","assembly_method":"Unicycler v. v.0.4.10","sequencing_centers":"University of Texas at Dallas","completion_date":"2020-06-24T00:00:00Z","collection_date":"June-2018","bioproject_accession":"PRJNA636382","biosample_accession":"SAMN15075994","genbank_accessions":"CP054230,CP054231","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"UPEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"host_description:Postmenopausal","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:UT Southwestern Medical Center/ UT Dallas","comments":"Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.","n_reactions":2733,"n_metabolites":1946,"n_genes":1458,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.60263.json.json","assembly_accession":"GCA_012934475.1","genome_id":"562.60263","genome_name":"Escherichia coli strain SCU-108","strain":"strain SCU-108","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5239110.0,"gc_content":50.594395,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5315.0,"refseq_cds":4999.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"37x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-04-30T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609773","genbank_accessions":"CP051735,CP051736,CP051737","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2732,"n_metabolites":1944,"n_genes":1458,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_014169455.1.json.json","assembly_accession":"GCF_014169455.1","genome_id":"GCF_014169455.1","genome_name":"Escherichia coli","strain":"WP7-S17-ESBL-01","serovar":"","phylogroup":"D","MLST":69,"mash_cluster":13,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMD00194553","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1940,"n_genes":1499,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.372.json.json","assembly_accession":"GCA_013167995.1","genome_id":"83334.372","genome_name":"Escherichia coli O157:H7 strain DEC5B","strain":"O157:H7 strain DEC5B","serovar":"O157:H7","phylogroup":"E","MLST":335,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:Florida","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5484204.0,"gc_content":50.461163,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5724.0,"refseq_cds":5398.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"120x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"1979","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11229484","genbank_accessions":"CP038389,CP038390,CP038391,CP038392,CP038393","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1935,"n_genes":1490,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.74755.json.json","assembly_accession":"GCA_018128405.1","genome_id":"562.74755","genome_name":"Escherichia coli strain 3347558","strain":"strain 3347558","serovar":"","phylogroup":"D","MLST":69,"mash_cluster":13,"isolation_source":"rectal swab","isolation_country":"Switzerland","geographic_location":"Switzerland","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5631387.0,"gc_content":50.76673,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5750.0,"refseq_cds":5409.0,"sequencing_platform":"Illumina NovaSeq; Oxford Nanopore MiniION","sequencing_depth":"144x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"","completion_date":"2021-04-22T00:00:00Z","collection_date":"2020","bioproject_accession":"PRJNA698767","biosample_accession":"SAMN17736024","genbank_accessions":"CP071073,CP071074,CP071075,CP071076,CP071077,CP071078,CP071079","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Institute for Infectious Diseases Bern","comments":"","n_reactions":2711,"n_metabolites":1877,"n_genes":1441,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHE","country":"Switzerland"},{"gem_file":"585056.7.json.json","assembly_accession":"GCA_000026325.1","genome_id":"585056.7","genome_name":"Escherichia coli UMN026","strain":"UMN026","serovar":"serovar O7","phylogroup":"D","MLST":597,"mash_cluster":13,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":5358200.0,"gc_content":50.7,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5198.0,"refseq_cds":5017.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Genoscope","completion_date":"2008-12-18T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA33415","biosample_accession":"SAMEA3138233","genbank_accessions":"CU928163,CU928148,CU928149","refseq_accessions":"NC_011751,NC_011749,NC_011739","genome_status":"Complete","taxon_id":585056.0,"organism_name":"Escherichia coli UMN026","pathovar":"UPEC","antimicrobial_resistance":"","culture_collection":"","publication":"19165319","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"Yes","temperature_range":"Mesophilic","optimal_temperature":"-","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"Escherichia coli UMN026. Escherichia coli UMN026 is a serotype O7:K1 clinical isolate. This strain is drug resistant and will be used for comparative analysis.","n_reactions":2711,"n_metabolites":1877,"n_genes":1445,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.66884.json.json","assembly_accession":"GCA_014854635.1","genome_id":"562.66884","genome_name":"Escherichia coli strain L3Cip3","strain":"strain L3Cip3","serovar":"","phylogroup":"B1","MLST":101,"mash_cluster":26,"isolation_source":"river water","isolation_country":"New Zealand","geographic_location":"New Zealand: Christchurch","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5331255.0,"gc_content":50.49462,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5466.0,"refseq_cds":5123.0,"sequencing_platform":"Oxford Nanopore; Illumina HiSeq","sequencing_depth":"150.0x","assembly_method":"unicycler v. 2020-04-01","sequencing_centers":"Massey University","completion_date":"2020-10-06T00:00:00Z","collection_date":"2020-01-28","bioproject_accession":"PRJNA665137","biosample_accession":"SAMN16242922","genbank_accessions":"CP062211,CP062212,CP062213,CP062214,CP062215,CP062216,CP062217","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Complete genome sequence of Escherichia coli L3Cip3 isolated from the Avon River in Christchurch, New Zealand","n_reactions":2734,"n_metabolites":1941,"n_genes":1507,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NZL","country":"New Zealand"},{"gem_file":"562.63864.json.json","assembly_accession":"GCA_014170975.1","genome_id":"562.63864","genome_name":"Escherichia coli strain 268.2","strain":"strain 268.2","serovar":"","phylogroup":"B1","MLST":58,"mash_cluster":26,"isolation_source":"Turkey's","isolation_country":"Canada","geographic_location":"Canada","host_name":"Turkey","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5073447.0,"gc_content":50.76379,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5081.0,"refseq_cds":4782.0,"sequencing_platform":"Oxford Nanopore MinION","sequencing_depth":"22.7x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"University of Guelph","completion_date":"2020-08-12T00:00:00Z","collection_date":"2016/2017","bioproject_accession":"PRJNA596173","biosample_accession":"SAMN13613889","genbank_accessions":"CP059947,CP059948,CP059949,CP059950,CP059951,CP059952","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from Turkey's in Canada","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:fecal","comments":"Chromosomes and plasmids were assembled from E. coli isolated from Turkey's in Canada. Both long reads (Oxford Nanopore) and short reads (Illumina) were used.","n_reactions":2732,"n_metabolites":1942,"n_genes":1526,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.79201.json.json","assembly_accession":"GCA_019970895.1","genome_id":"562.79201","genome_name":"Escherichia coli strain CX08","strain":"strain CX08","serovar":"","phylogroup":"A","MLST":3202,"mash_cluster":22,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada: Alberta","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4866875.0,"gc_content":51.074642,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4973.0,"refseq_cds":4680.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"71x","assembly_method":"flye v. 2.8.2","sequencing_centers":"Agriculture & Agri-Food Canada","completion_date":"2021-09-14T00:00:00Z","collection_date":"2014/2015","bioproject_accession":"PRJNA716667","biosample_accession":"SAMN18446042","genbank_accessions":"CP073718","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The presence of locus of heat resistance is a common way of screening heat resistance in E.coli, however harboring LHR does not always confer extreme heat resistance suggesting other genetic components may play a role in heat resistance. WGS was performed to determine genetic determinants in E.coli for different levels of heat resistance and determine the evolution regarding the emergence of heat resistant strains of E.coli in a meat plant setting.","n_reactions":2733,"n_metabolites":1941,"n_genes":1505,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.29121.json.json","assembly_accession":"GCA_003018475.1","genome_id":"562.29121","genome_name":"Escherichia coli strain 2015C-4136CT1","strain":"strain 2015C-4136CT1","serovar":"O145:H34","phylogroup":"B2","MLST":722,"mash_cluster":6,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4999728.0,"gc_content":50.590492,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5098.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"78.081x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Jul-2015","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08579593","genbank_accessions":"CP027550,CP027551","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2732,"n_metabolites":1942,"n_genes":1433,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.46721.json.json","assembly_accession":"GCA_005221685.1","genome_id":"562.46721","genome_name":"Escherichia coli strain 134","strain":"strain 134","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5553158.0,"gc_content":50.499573,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5968.0,"refseq_cds":5798.0,"sequencing_platform":"PacBio","sequencing_depth":"158x","assembly_method":"HGAP v. 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This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_016403625.2.json.json","assembly_accession":"GCF_016403625.2","genome_id":"GCF_016403625.2","genome_name":"Escherichia coli","strain":"STEC2018-607","serovar":"","phylogroup":"B1","MLST":33,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN16993387","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1945,"n_genes":1522,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.67794.json.json","assembly_accession":"GCA_904831825.1","genome_id":"562.67794","genome_name":"Escherichia coli strain L3_E36_ETEC","strain":"strain L3_E36_ETEC","serovar":"","phylogroup":"B1","MLST":173,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5632468.0,"gc_content":50.66484,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5782.0,"refseq_cds":5279.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Quadram Institute Bioscience","completion_date":"2020-10-30T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB40413","biosample_accession":"SAMEA7368284","genbank_accessions":"LR882997,LR882998,LR882999","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time","n_reactions":2732,"n_metabolites":1937,"n_genes":1524,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.55236.json.json","assembly_accession":"GCA_009905135.1","genome_id":"562.55236","genome_name":"Escherichia coli strain 94EC","strain":"strain 94EC","serovar":"","phylogroup":"B1","MLST":156,"mash_cluster":26,"isolation_source":"feces","isolation_country":"Singapore","geographic_location":"Singapore","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5240704.0,"gc_content":50.546913,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5269.0,"refseq_cds":4971.0,"sequencing_platform":"Oxford Nanopore MiniION; Illumina NovaSeq","sequencing_depth":"433.0x","assembly_method":"Unicycler v. v0.4.8","sequencing_centers":"Temasek Life Sciences Laboratory Limited","completion_date":"2020-01-19T00:00:00Z","collection_date":"2019-02","bioproject_accession":"PRJNA599529","biosample_accession":"SAMN13756518","genbank_accessions":"CP047576,CP047577,CP047578,CP047579,CP047580,CP047581,CP047582","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Bacterial pure culture","comments":"In this project, we isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore. 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In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.70725.json.json","assembly_accession":"GCA_016888925.1","genome_id":"562.70725","genome_name":"Escherichia coli strain FDAARGOS_1260 strain Not applicable","strain":"","serovar":"","phylogroup":"B2","MLST":12,"mash_cluster":6,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5180264.0,"gc_content":50.5775,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5244.0,"refseq_cds":4931.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"833.14x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-15T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357402","genbank_accessions":"CP069438,CP069439","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1260","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2732,"n_metabolites":1946,"n_genes":1446,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.201.json.json","assembly_accession":"GCF_001753525.1","genome_id":"83334.201","genome_name":"Escherichia coli O157:H7 strain 9234","strain":"O157:H7 strain 9234","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Cattle Hide","isolation_country":"USA","geographic_location":"USA:Texas","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5503176.0,"gc_content":50.47,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5785.0,"refseq_cds":5486.0,"sequencing_platform":"PacBio","sequencing_depth":"244X","assembly_method":"RS_HGAP_Assembly v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2016-10-06T00:00:00Z","collection_date":"2003-10","bioproject_accession":"PRJNA291880","biosample_accession":"SAMN04447632","genbank_accessions":"CP017446,CP017447","refseq_accessions":"NZ_CP017446.1,NZ_CP017447.1","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"Mesophilic","optimal_temperature":"37 C","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"collected_by:T. M. Arthur","comments":"Whole genome sequencing of STEC O157:H7 strains.","n_reactions":2731,"n_metabolites":1939,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.79228.json.json","assembly_accession":"GCA_020034595.1","genome_id":"562.79228","genome_name":"Escherichia coli strain Rosetta2-DE3","strain":"strain Rosetta2-DE3","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"Not Applicable","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4493178.0,"gc_content":50.797543,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4484.0,"refseq_cds":4277.0,"sequencing_platform":"Illumina MiniSeq","sequencing_depth":"104X","assembly_method":"SPAdes v. 3.9.0","sequencing_centers":"Gennova Biopharmaceuticals Ltd","completion_date":"2021-09-18T00:00:00Z","collection_date":"2021","bioproject_accession":"PRJNA749934","biosample_accession":"SAMN20826664","genbank_accessions":"CP083274","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Whole Genome Sequencing of Competent cells","n_reactions":2733,"n_metabolites":1935,"n_genes":1514,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.67698.json.json","assembly_accession":"GCA_904711265.1","genome_id":"562.67698","genome_name":"Escherichia coli strain 2014-01-7375","strain":"strain 2014-01-7375","serovar":"","phylogroup":"B1","MLST":453,"mash_cluster":26,"isolation_source":"Broiler","isolation_country":"Norway","geographic_location":"Norway","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5270466.0,"gc_content":50.640644,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5298.0,"refseq_cds":5005.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"NORWEGIAN VETERINARY INSTITUTE","completion_date":"2020-09-28T00:00:00Z","collection_date":"2014-12-01","bioproject_accession":"PRJEB40078","biosample_accession":"SAMEA7287982","genbank_accessions":"LR882057,LR882058,LR882059,LR882060,LR882061","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"Norwegian Veterinary Institute","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The presence of quinolone resistant Escherichia coli (QREC) in the animal reservoir might be of public health concern especially related to acquired quinolone resistance genes encoded on plasmids as they might spread to more pathogenic and disease-causing bacteria. The plasmid-mediated qnrS1 gene is known to be situated on plasmids with different incompatibility (Inc) groups. In this study, the aim was to select QREC strains encoding qnrS1 situated on plasmids with different Inc-groups and to complete circular plasmid contigs. We created hybrid assemblies using data from Illumina and minION sequencing.","n_reactions":2732,"n_metabolites":1938,"n_genes":1513,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NOR","country":"Norway"},{"gem_file":"GCF_020716665.1.json.json","assembly_accession":"GCF_020716665.1","genome_id":"GCF_020716665.1","genome_name":"Escherichia coli","strain":"B95. delta A","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN22566690","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1935,"n_genes":1512,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13737.json.json","assembly_accession":"GCF_001900315.1","genome_id":"562.13737","genome_name":"Escherichia coli strain C4","strain":"strain C4","serovar":"","phylogroup":"D","MLST":7063,"mash_cluster":12,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4990476.0,"gc_content":50.56,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4889.0,"refseq_cds":4681.0,"sequencing_platform":"Illumina Miseq; 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V0.4.4","sequencing_centers":"Yangzhou University","completion_date":"2020-01-21T00:00:00Z","collection_date":"Aug-2018","bioproject_accession":"PRJNA600679","biosample_accession":"SAMN13829575","genbank_accessions":"CP047665,CP047667,CP047666","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Xiaoyu Lu","comments":"Prevalence of plasmid Mediated Colistin Resistance Gene mcr-1 in E.coli from Deer in China","n_reactions":2732,"n_metabolites":1937,"n_genes":1518,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.66917.json.json","assembly_accession":"GCA_014858525.1","genome_id":"562.66917","genome_name":"Escherichia coli strain UTI89","strain":"strain UTI89","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"urine pellicle","isolation_country":"India","geographic_location":"India: Thanjavur","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5065741.0,"gc_content":50.604263,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5033.0,"refseq_cds":4748.0,"sequencing_platform":"Illumina MiSeq","sequencing_depth":"10.0x","assembly_method":"ABySS v. 2.3","sequencing_centers":"SASTRA University","completion_date":"2020-10-07T00:00:00Z","collection_date":"20-Sep-2018","bioproject_accession":"PRJNA664911","biosample_accession":"SAMN16237063","genbank_accessions":"CP062228","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Bacterial culture;biomaterial_provider:Dr. CS Srinandan;collected_by:Sandeep miryala","comments":"Uropathogenic e.coli will cause urinary tract infection which one major nosocomial infection. In our observation UTI89 strain shown heterogen colonies regarding the biofilm formation. If we can understand the interaction between these variants will give some insight to the treatment.","n_reactions":2733,"n_metabolites":1946,"n_genes":1454,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"IND","country":"India"},{"gem_file":"GCF_020149645.1.json.json","assembly_accession":"GCF_020149645.1","genome_id":"GCF_020149645.1","genome_name":"Escherichia coli","strain":"NDM1","serovar":"","phylogroup":"C","MLST":90,"mash_cluster":25,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN21398202","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1937,"n_genes":1539,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1045010.61.json.json","assembly_accession":"GCA_008727135.1","genome_id":"1045010.61","genome_name":"Escherichia coli O157 strain AR-0430","strain":"O157 strain AR-0430","serovar":"","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5764004.0,"gc_content":50.427204,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":6076.0,"refseq_cds":"","sequencing_platform":"PacBio RSII","sequencing_depth":"131.331x","assembly_method":"Canu v. 1.6","sequencing_centers":"Centers for Disease Control and Prevention","completion_date":"2019-09-29T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA562719","biosample_accession":"SAMN12648980","genbank_accessions":"CP044140,CP044137,CP044138,CP044139,CP044141","refseq_accessions":"","genome_status":"Complete","taxon_id":1045010.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"Resistant;Not defined;Susceptible","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"This panel of pathogens includes isolates of Salmonella spp, Shigella spp., Campylobacter spp., and Escherichia coli O157. The isolates included demonstrate varied susceptibility patterns to antibiotics. These susceptibility patterns are representative of the diversity of susceptibility identified in surveillance isolates collected in the United States.","n_reactions":2711,"n_metabolites":1877,"n_genes":1426,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.347.json.json","assembly_accession":"GCA_013167375.1","genome_id":"83334.347","genome_name":"Escherichia coli O157:H7 strain NE92","strain":"O157:H7 strain NE92","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:Nebraska","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5538109.0,"gc_content":50.399677,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5811.0,"refseq_cds":5479.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"278x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11229494","genbank_accessions":"CP038316,CP038318,CP038317","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1939,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.78005.json.json","assembly_accession":"GCA_019378855.1","genome_id":"562.78005","genome_name":"Escherichia coli strain Colony157","strain":"strain Colony157","serovar":"","phylogroup":"A","MLST":40,"mash_cluster":26,"isolation_source":"Rectal swab","isolation_country":"Thailand","geographic_location":"Thailand","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4733683.0,"gc_content":51.297504,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4345.0,"refseq_cds":"","sequencing_platform":"Illumina HiSeq","sequencing_depth":"88.465x","assembly_method":"idba_ud v. 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RS_HGAP_Assembly.3","sequencing_centers":"United State Department of Agriculture","completion_date":"2019-05-07T00:00:00Z","collection_date":"2003","bioproject_accession":"PRJNA445267","biosample_accession":"SAMN08773020","genbank_accessions":"CP028693,CP028694","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The aim of this project is to compare complete closed genomes with whole genome sequencing (WGS) using short reads. SNPs from WGS is used in many studies to determine relatedness of strains. These SNPs are in the core genome and don't reflect the diversity of the complete genome. This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.50517.json.json","assembly_accession":"GCA_007109305.1","genome_id":"562.50517","genome_name":"Escherichia coli strain 144","strain":"strain 144","serovar":"","phylogroup":"B2","MLST":144,"mash_cluster":6,"isolation_source":"blood","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"Bloodstream infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5368883.0,"gc_content":50.54842,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5636.0,"refseq_cds":5356.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"100x","assembly_method":"HGAP v. 4","sequencing_centers":"Duke University","completion_date":"2019-07-18T00:00:00Z","collection_date":"2003","bioproject_accession":"PRJNA551684","biosample_accession":"SAMN12163093","genbank_accessions":"CP041550,CP041551,CP041552,CP041553,CP041554,CP041555","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Vance G. Fowler Jr.","comments":"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2751,"n_metabolites":2021,"n_genes":1680,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.6959.json.json","assembly_accession":"GCF_000599625.1","genome_id":"562.6959","genome_name":"Escherichia coli strain ST540","strain":"strain ST540","serovar":"","phylogroup":"A","MLST":540,"mash_cluster":22,"isolation_source":"water","isolation_country":"Belgium","geographic_location":"Belgium","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4807977.0,"gc_content":51.04,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4901.0,"refseq_cds":4562.0,"sequencing_platform":"PacBio","sequencing_depth":"25x","assembly_method":"HGAP, SMRT Analysis Portal v. 2.0.1","sequencing_centers":"University of Antwerpen","completion_date":"2014-04-16T00:00:00Z","collection_date":"2012-04-12","bioproject_accession":"PRJNA238952","biosample_accession":"SAMN02666434","genbank_accessions":"CP007390","refseq_accessions":"NZ_CP007390.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"24723707","isolation_comments":"","other_clinical":"","other_environmental":"env_biome:air","cell_shape":"Bacilli","motility":"Yes","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"To study Nitrofurantoin resistant mechanism","n_reactions":2733,"n_metabolites":1940,"n_genes":1523,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BEL","country":"Belgium"},{"gem_file":"562.45584.json.json","assembly_accession":"GCA_004193755.1","genome_id":"562.45584","genome_name":"Escherichia coli strain U15A","strain":"strain U15A","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"urine","isolation_country":"USA","geographic_location":"USA:Utah","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5128015.0,"gc_content":50.851276,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5141.0,"refseq_cds":4830.0,"sequencing_platform":"PacBio RSII; Illumina NextSeq","sequencing_depth":"108.0x","assembly_method":"HGAP v. 2.3.0","sequencing_centers":"The University of Queensland","completion_date":"2019-02-13T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA516749","biosample_accession":"SAMN10837069","genbank_accessions":"CP035720,CP035721,CP035722,CP035723,CP035724,CP035725,CP035726","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated over a 5-year period (2012-2016) from the urine and feces of a single individual","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Recurrent urinary tract infections (rUTI) are extremely common, with ~25% of all women who suffer an initial UTI experiencing a recurrence within one year of the original infection. rUTI often occurs when bacteria from the initial infection persist after treatment. Escherichia coli ST131 is a major contributor to hospital and community acquired UTI and is strongly associated with limited treatment options and high rates of recurrence. Here, using a combination of both short and long read sequencing technologies we examined the dynamics of an E. coli ST131 population isolated over a 5-year period (2012-2016) from the urine and feces of a single individual. This longitudinal study provides the first comprehensive, in vivo, genomic analysis of a clonal lineage within a single individual and serves as a valuable resource for understanding how plasmid dynamics contribute to pathogen evolution in a chronic long-term infection.","n_reactions":2732,"n_metabolites":1943,"n_genes":1462,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.61473.json.json","assembly_accession":"GCA_013282355.1","genome_id":"562.61473","genome_name":"Escherichia coli strain NMBU-W10C18","strain":"strain NMBU-W10C18","serovar":"O102:H6","phylogroup":"D","MLST":405,"mash_cluster":16,"isolation_source":"surface 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This strain also contains at least 5 large plasmids.","n_reactions":2732,"n_metabolites":1938,"n_genes":1532,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.79034.json.json","assembly_accession":"GCA_019844035.1","genome_id":"562.79034","genome_name":"Escherichia coli strain NDM_11.16372","strain":"strain NDM_11.16372","serovar":"","phylogroup":"A","MLST":167,"mash_cluster":21,"isolation_source":"rectal swab from HIV infected patient","isolation_country":"Tanzania","geographic_location":"Tanzania:Dar es Salaam","host_name":"Homo sapiens","host_health":"Gut colonization","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5032831.0,"gc_content":50.81651,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5066.0,"refseq_cds":4745.0,"sequencing_platform":"Oxford Nanopore","sequencing_depth":"76.3x","assembly_method":"Unicyler v. v0.4.8.0","sequencing_centers":"University of Bergen","completion_date":"2021-09-01T00:00:00Z","collection_date":"2018-02-03","bioproject_accession":"PRJNA756169","biosample_accession":"SAMN20857180","genbank_accessions":"CP082129,CP082130,CP082131,CP082132","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Joel Manyahi","comments":"NDM-5 gut colonization","n_reactions":2731,"n_metabolites":1940,"n_genes":1539,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"TZA","country":"Tanzania"},{"gem_file":"562.68397.json.json","assembly_accession":"GCA_014930915.1","genome_id":"562.68397","genome_name":"Escherichia coli strain KC-Dl-1","strain":"strain KC-Dl-1","serovar":"","phylogroup":"B2","MLST":12,"mash_cluster":6,"isolation_source":"","isolation_country":"South Korea","geographic_location":"South Korea: Yeosu","host_name":"Delphinapterus leucas (Beluga whale)","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5305214.0,"gc_content":50.382698,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5358.0,"refseq_cds":5011.0,"sequencing_platform":"PacBio RSII; Illumina HiSeq","sequencing_depth":"195.0x","assembly_method":"HGAP v. 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This longitudinal study provides the first comprehensive, in vivo, genomic analysis of a clonal lineage within a single individual and serves as a valuable resource for understanding how plasmid dynamics contribute to pathogen evolution in a chronic long-term infection.","n_reactions":2732,"n_metabolites":1943,"n_genes":1472,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.60467.json.json","assembly_accession":"GCA_013167055.1","genome_id":"562.60467","genome_name":"Escherichia coli strain NEB_Turbo","strain":"strain NEB_Turbo","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4758579.0,"gc_content":50.745716,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4746.0,"refseq_cds":4470.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"279x","assembly_method":"HGAP v. 3","sequencing_centers":"New England Biolabs","completion_date":"2020-05-26T00:00:00Z","collection_date":"2010-01-01","bioproject_accession":"PRJNA341475","biosample_accession":"SAMN14933836","genbank_accessions":"CP053605,CP053606","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Closed and finished genome of NEB 5-alpha, an immediate fhuA derivative of (E. coli K-12) DH5alpha.","n_reactions":2731,"n_metabolites":1934,"n_genes":1562,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.191.json.json","assembly_accession":"GCF_001651945.1","genome_id":"83334.191","genome_name":"Escherichia coli O157:H7 strain FRIK2533","strain":"O157:H7 strain FRIK2533","serovar":"","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"feces","isolation_country":"USA","geographic_location":"USA: FL","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5645219.0,"gc_content":50.55,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5984.0,"refseq_cds":5678.0,"sequencing_platform":"PacBio","sequencing_depth":"25x","assembly_method":"HGAP v. 3","sequencing_centers":"University of Florida","completion_date":"2016-05-25T00:00:00Z","collection_date":"20-Jul-11","bioproject_accession":"PRJNA322195","biosample_accession":"SAMN04191553","genbank_accessions":"CP015842","refseq_accessions":"NZ_CP015842.1","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:FLUFL","comments":"Comparative genomics using PacBio sequencing","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.58458.json.json","assembly_accession":"GCA_011492885.1","genome_id":"562.58458","genome_name":"Escherichia coli strain T28R","strain":"strain T28R","serovar":"","phylogroup":"A","MLST":7366,"mash_cluster":22,"isolation_source":"","isolation_country":"China","geographic_location":"China: Henan","host_name":"pet dog","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5025884.0,"gc_content":50.59896,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5104.0,"refseq_cds":4781.0,"sequencing_platform":"Illumina; 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Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.","n_reactions":2733,"n_metabolites":1934,"n_genes":1532,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"GCF_021513335.1.json.json","assembly_accession":"GCF_021513335.1","genome_id":"GCF_021513335.1","genome_name":"Escherichia coli","strain":"NCCP12480","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN17319586","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2730,"n_metabolites":1929,"n_genes":1476,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.67021.json.json","assembly_accession":"GCA_014863685.1","genome_id":"562.67021","genome_name":"Escherichia coli strain AML001_par","strain":"strain AML001_par","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"not applicable","isolation_country":"USA","geographic_location":"USA: Boston","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4631469.0,"gc_content":50.778664,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4507.0,"refseq_cds":"","sequencing_platform":"Illumina NextSeq","sequencing_depth":"50x","assembly_method":"breseq v. 0.35.1","sequencing_centers":"Boston University","completion_date":"2020-10-08T00:00:00Z","collection_date":"02-Sep-2015","bioproject_accession":"PRJNA666010","biosample_accession":"SAMN16090671","genbank_accessions":"CP062242","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolate from each separate evolution experiment and the parent strains are provided here","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture;biomaterial_provider:M.J. 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The goal of this work was to identify which chloramphenicol concentrations promote the evolution of antibiotic resistance and how the presence of the AcrAB-TolC pump impacts this evolution.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.28386.json.json","assembly_accession":"GCA_002944935.1","genome_id":"562.28386","genome_name":"Escherichia coli strain FDAARGOS_144","strain":"FDAARGOS_144","serovar":"","phylogroup":"B2","MLST":538,"mash_cluster":3,"isolation_source":"urine","isolation_country":"USA","geographic_location":"USA:DC","host_name":"Human, Homo sapiens","host_health":"Urinary tract infection","host_gender":"female","host_age":"21Y","body_sample_site":"","disease":"","genome_length":5022152.0,"gc_content":50.671803,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5164.0,"refseq_cds":5098.0,"sequencing_platform":"PacBio; Illumina","sequencing_depth":"19.454x","assembly_method":"HGAP3 v. 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FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2752,"n_metabolites":2023,"n_genes":1748,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.68399.json.json","assembly_accession":"GCA_015649805.1","genome_id":"562.68399","genome_name":"Escherichia coli strain 20","strain":"strain 20","serovar":"O11:H25","phylogroup":"F","MLST":1722,"mash_cluster":11,"isolation_source":"wastewater","isolation_country":"Hong Kong","geographic_location":"Hong Kong","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5301345.0,"gc_content":50.557602,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5266.0,"refseq_cds":5010.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"60.0x","assembly_method":"FALCON v. NA","sequencing_centers":"The Hong Kong University of Science and Technology","completion_date":"2020-11-23T00:00:00Z","collection_date":"Jun-2018","bioproject_accession":"PRJNA670589","biosample_accession":"SAMN16520638","genbank_accessions":"CP064847,CP064848,CP064849,CP064850","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from the treated wastewater","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"Strain is confirmed ESBL producer resistant to CTX, CAZ, SXT, RL (EUCAST guidelines)","substrain":"","additional_metadata":"sample_type:cell culture","comments":"ESBL-E.coli isolated from the treated wastewater. Pathogenicity of the strain cannot be genotypically confirmed, due to the absence of distinctive virulence determinants. The strain carries large 130kb F-type conjugative plasmid, pHK01-1, that holds the key to the ESBL-phenotype (blaCTX-M-27) and resistance to sulfamethoxazole (sul1, sul2), alone and in the combination with trimethoprim.","n_reactions":2732,"n_metabolites":1944,"n_genes":1522,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"HKG","country":"Hong Kong"},{"gem_file":"562.16428.json.json","assembly_accession":"GCA_002120205.1","genome_id":"562.16428","genome_name":"Escherichia coli strain G199","strain":"strain G199","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"USA","geographic_location":"USA: Seattle","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5277911.0,"gc_content":50.62,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5488.0,"refseq_cds":5204.0,"sequencing_platform":"PacBio","sequencing_depth":"100.0x","assembly_method":"HGAP 3 (PacBio) v. 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This project involved sequencing a number of isolates with Inc L/M NDM plasmids using both minION and Illumina platforms to accurately determine the plasmid sequences and assess any potential transmission between organisms. The project included both epidemiologically related and unrelated isolates.;many frameshifted proteins","n_reactions":2734,"n_metabolites":1941,"n_genes":1530,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"83334.486.json.json","assembly_accession":"GCA_017165135.1","genome_id":"83334.486","genome_name":"Escherichia coli O157:H7 strain Z1766","strain":"O157:H7 strain Z1766","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5612573.0,"gc_content":50.48278,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5838.0,"refseq_cds":5433.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"227.2939398320672x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327598","genbank_accessions":"CP062736,CP062737,CP062738","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Roslin Institute","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.29088.json.json","assembly_accession":"GCA_003020885.1","genome_id":"562.29088","genome_name":"Escherichia coli strain MS7163","strain":"strain MS7163","serovar":"O45:K1:H7","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"urine","isolation_country":"Slovakia","geographic_location":"Slovakia","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5292507.0,"gc_content":50.67965,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5360.0,"refseq_cds":5031.0,"sequencing_platform":"PacBio","sequencing_depth":"100.0x","assembly_method":"HGAP v. 2.0","sequencing_centers":"University of Queensland","completion_date":"2018-03-27T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA427051","biosample_accession":"SAMN08469740","genbank_accessions":"CP026853,CP026854,CP026855","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Uropathogenic Escherichia coli (UPEC) are the most common cause of urinary tract infection. Curli are extracellular amyloid fibres that enhance UPEC virulence by their capacity to mediate adhesion and biofilm formation. In this study, we examined the function and regulation of curli in the UPEC pyelonephritis strain MS7163 that expressed these fibres at human physiological temperature. We also performed a large genetic screen and identified multiple genes involved in curli production, including several genes that were novel or poorly characterized with respect to curli synthesis.","n_reactions":2732,"n_metabolites":1944,"n_genes":1453,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"SVK","country":"Slovakia"},{"gem_file":"562.28201.json.json","assembly_accession":"GCA_002899535.1","genome_id":"562.28201","genome_name":"Escherichia coli strain CIT","strain":"strain CIT","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":21,"isolation_source":"Essential oils isolation","isolation_country":"Spain","geographic_location":"Spain","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4639673.0,"gc_content":50.7897,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4522.0,"refseq_cds":"","sequencing_platform":"Illumina HiSeq","sequencing_depth":"91.01x","assembly_method":"Burrows-Wheeler Alignment Tool v.","sequencing_centers":"Facultad de Veterinaria, Instituto Agroalimentario de Aragon (IA2)","completion_date":"2018-01-25T00:00:00Z","collection_date":"2014-08-05","bioproject_accession":"PRJNA430164","biosample_accession":"SAMN08367769","genbank_accessions":"CP026028","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:single cell","comments":"Eschericia coli str.K-12 substr. MG1655 mutant strain isolated after growth in presence of sub-inhibitory concentrations of citral","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"ESP","country":"Spain"},{"gem_file":"562.29118.json.json","assembly_accession":"GCA_003018535.1","genome_id":"562.29118","genome_name":"Escherichia coli strain 2013C-4081","strain":"strain 2013C-4081","serovar":"E. coli O111:H8","phylogroup":"B1","MLST":16,"mash_cluster":23,"isolation_source":"Stool","isolation_country":"United States","geographic_location":"United States","host_name":"","host_health":"","host_gender":"","host_age":"40-49","body_sample_site":"","disease":"","genome_length":5634505.0,"gc_content":50.46431,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5926.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"136.013x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Jun-2013","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN04558451","genbank_accessions":"CP027573,CP027574,CP027575,CP027576","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CDC","comments":"PulseNet STEC genome reference library","n_reactions":2731,"n_metabolites":1938,"n_genes":1513,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.67475.json.json","assembly_accession":"GCA_015508805.1","genome_id":"562.67475","genome_name":"Escherichia coli strain JE86-ST02","strain":"strain JE86-ST02","serovar":"O86","phylogroup":"B1","MLST":3570,"mash_cluster":26,"isolation_source":"","isolation_country":"Japan","geographic_location":"Japan","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5530044.0,"gc_content":50.668858,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5659.0,"refseq_cds":5294.0,"sequencing_platform":"Illumina MiSeq, PacBio RSII","sequencing_depth":"117.0X","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Department of Bacteriology, National Institute of Infectious Diseases","completion_date":"2020-11-06T00:00:00Z","collection_date":"1999","bioproject_accession":"PRJDB7390","biosample_accession":"SAMD00197816","genbank_accessions":"AP022811,AP022812,AP022813,AP022814","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"32678145","isolation_comments":"isolated in Japan","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Draft and compelete genome sequence analyses were performed in enterohemorrhagic Escherichia coli serogroup O86 isolated in Japan.","n_reactions":2732,"n_metabolites":1935,"n_genes":1511,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"JPN","country":"Japan"},{"gem_file":"991919.15.json.json","assembly_accession":"GCA_005037815.2","genome_id":"991919.15","genome_name":"Escherichia coli O145:NM strain FWSEC0002","strain":"O145:NM strain FWSEC0002","serovar":"O145:NM","phylogroup":"D","MLST":32,"mash_cluster":20,"isolation_source":"Clinical: Human (Homo sapiens)","isolation_country":"Canada","geographic_location":"Canada:Alberta","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5790057.0,"gc_content":50.641365,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":6315.0,"refseq_cds":6056.0,"sequencing_platform":"Illumina MiSeq;Oxford Nanopore MinION","sequencing_depth":"78.00x;124.40x","assembly_method":"Unicycler;Canu v. 0.4.4.0;1.7","sequencing_centers":"National Microbiology 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The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.","n_reactions":2732,"n_metabolites":1941,"n_genes":1487,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.60264.json.json","assembly_accession":"GCA_012934495.1","genome_id":"562.60264","genome_name":"Escherichia coli strain SCU-109","strain":"strain SCU-109","serovar":"","phylogroup":"D","MLST":963,"mash_cluster":15,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5144298.0,"gc_content":50.72255,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5050.0,"refseq_cds":4764.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"32x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-04-30T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609774","genbank_accessions":"CP051733,CP051734","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2732,"n_metabolites":1942,"n_genes":1521,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.63880.json.json","assembly_accession":"GCA_014216735.1","genome_id":"562.63880","genome_name":"Escherichia coli strain RH-045-WU","strain":"strain RH-045-WU","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"drinking water","isolation_country":"Bangladesh","geographic_location":"Bangladesh: 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This project involved sequencing a number of isolates with Inc L/M NDM plasmids using both minION and Illumina platforms to accurately determine the plasmid sequences and assess any potential transmission between organisms. The project included both epidemiologically related and unrelated isolates.","n_reactions":2732,"n_metabolites":1937,"n_genes":1526,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.50214.json.json","assembly_accession":"GCA_002951715.1","genome_id":"562.50214","genome_name":"Escherichia coli strain 13KWH46","strain":"strain 13KWH46","serovar":"","phylogroup":"B1","MLST":602,"mash_cluster":26,"isolation_source":"urine","isolation_country":"Hong Kong","geographic_location":"Hong Kong","host_name":"Human, Homo sapiens","host_health":"Urinary infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5386699.0,"gc_content":50.65124,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5782.0,"refseq_cds":5618.0,"sequencing_platform":"PacBio","sequencing_depth":"236.0x","assembly_method":"HGAP v. 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0.4.3","sequencing_centers":"","completion_date":"2020-06-29T00:00:00Z","collection_date":"2017","bioproject_accession":"PRJNA622869","biosample_accession":"SAMN14548319","genbank_accessions":"CP051158","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1940,"n_genes":1519,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.66609.json.json","assembly_accession":"GCA_014361285.1","genome_id":"562.66609","genome_name":"Escherichia coli strain EC96","strain":"strain EC96","serovar":"","phylogroup":"A","MLST":48,"mash_cluster":22,"isolation_source":"bile","isolation_country":"China","geographic_location":"China:Shanghai","host_name":"Human, Homo sapiens","host_health":"biliary tract infection","host_gender":"female","host_age":"69","body_sample_site":"","disease":"","genome_length":4939392.0,"gc_content":51.005245,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5078.0,"refseq_cds":4725.0,"sequencing_platform":"Illumina, PacBio","sequencing_depth":"200x","assembly_method":"SPAdes v. v3.11.1","sequencing_centers":"Huashan Hospital, Fudan University","completion_date":"2020-09-01T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA659360","biosample_accession":"SAMN15903653","genbank_accessions":"CP060748,CP060750,CP060749,CP060752,CP060751,CP060753","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Institute of Antibiotics Huashan Hospital, Fudan University","comments":"CTX-M-215-producing Escherichia coli strain EC96 and CTX-M-125-producing Klebsiella pneumoniae strain KP120","n_reactions":2730,"n_metabolites":1942,"n_genes":1488,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia 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Agency","completion_date":"2020-03-01T00:00:00Z","collection_date":"2015-12-31","bioproject_accession":"PRJNA606850","biosample_accession":"SAMN14115144","genbank_accessions":"CP049086,CP049087","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Cell culture;collected_by:Animal and Plant Quarantine Agency","comments":"Draft genome sequencing of Escherichia coli plasmid pK15EC053","n_reactions":2733,"n_metabolites":1940,"n_genes":1561,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"KOR","country":"South Korea"},{"gem_file":"562.28391.json.json","assembly_accession":"GCA_002951855.1","genome_id":"562.28391","genome_name":"Escherichia coli strain FHI_NMBU_03","strain":"strain FHI_NMBU_03","serovar":"O81:H6","phylogroup":"B2","MLST":28,"mash_cluster":6,"isolation_source":"Fecal sample","isolation_country":"Norway","geographic_location":"Norway: south east","host_name":"Human, Homo sapiens","host_health":"Diarrhea","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4844877.0,"gc_content":50.628242,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4957.0,"refseq_cds":4918.0,"sequencing_platform":"Oxford Nanopore MinION; Illumina MiSeq","sequencing_depth":"21.6x","assembly_method":"CANU v. 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university","completion_date":"2018-06-06T00:00:00Z","collection_date":"2012-10","bioproject_accession":"PRJNA384272","biosample_accession":"SAMN06833089","genbank_accessions":"CP021193,CP021194,CP021195,CP021196,CP021197,CP021198","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:SRRSH hospital","comments":"Antibiotic resistance of bacteria;many frameshifted proteins","n_reactions":2734,"n_metabolites":1949,"n_genes":1513,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia 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are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2750,"n_metabolites":2021,"n_genes":1672,"n_exchange":331,"n_with_gpr":2304,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.70766.json.json","assembly_accession":"GCA_016903935.1","genome_id":"562.70766","genome_name":"Escherichia coli strain FDAARGOS_1288 strain Not applicable","strain":"","serovar":"","phylogroup":"D","MLST":69,"mash_cluster":13,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5681879.0,"gc_content":50.653965,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":5853.0,"refseq_cds":5484.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"1384.73x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357430","genbank_accessions":"CP070007,CP070008,CP070009,CP070010,CP070011,CP070012,CP070013,CP070014","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1288","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.","n_reactions":2731,"n_metabolites":1938,"n_genes":1488,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.7247.json.json","assembly_accession":"GCA_000988425.1","genome_id":"562.7247","genome_name":"Escherichia coli strain SQ110","strain":"strain SQ110","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"United States","geographic_location":"United States","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4605135.0,"gc_content":50.78,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4584.0,"refseq_cds":4313.0,"sequencing_platform":"Illumina","sequencing_depth":"103x","assembly_method":"CLCBio Genomics Workbench v. 7.0.4","sequencing_centers":"AstraZeneca","completion_date":"2015-05-06T00:00:00Z","collection_date":"2008","bioproject_accession":"PRJNA241498","biosample_accession":"SAMN03276543","genbank_accessions":"CP011322","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:single cell","comments":"Genomic sequence of a ribosomal deletion construct of E. coli MG1655;missing tRNA genes","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.68766.json.json","assembly_accession":"GCA_016432805.1","genome_id":"562.68766","genome_name":"Escherichia coli strain 1EC187","strain":"strain 1EC187","serovar":"O8:H9","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"","isolation_country":"Ghana","geographic_location":"Ghana: Western region","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5054351.0,"gc_content":50.536774,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5065.0,"refseq_cds":4752.0,"sequencing_platform":"Illumina MiSeq; 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coli","country_iso":"BGD","country":"Bangladesh"},{"gem_file":"562.61707.json.json","assembly_accession":"GCA_013372365.1","genome_id":"562.61707","genome_name":"Escherichia coli strain EcPF15","strain":"strain EcPF15","serovar":"","phylogroup":"D","MLST":394,"mash_cluster":13,"isolation_source":"urine","isolation_country":"USA","geographic_location":"USA: Dallas, Texas","host_name":"Human, Homo sapiens","host_health":"Chronic Cystitis","host_gender":"female","host_age":"","body_sample_site":"","disease":"","genome_length":4938634.0,"gc_content":50.478897,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4770.0,"refseq_cds":4536.0,"sequencing_platform":"Illumina NextSeq, ONT MinION","sequencing_depth":"70x, 250x","assembly_method":"Unicycler v. v.0.4.11","sequencing_centers":"University of Texas at 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This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.","n_reactions":2731,"n_metabolites":1937,"n_genes":1495,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.410.json.json","assembly_accession":"GCA_016458905.1","genome_id":"83334.410","genome_name":"Escherichia coli O157:H7 strain ECP19-798","strain":"O157:H7 strain ECP19-798","serovar":"serovar O157","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5586183.0,"gc_content":50.443012,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5779.0,"refseq_cds":5378.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"100X","assembly_method":"Spades v. 3.12.1","sequencing_centers":"FDA Center for Food Safety and Applied Nutrition","completion_date":"2021-01-03T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA681235","biosample_accession":"SAMN16946947","genbank_accessions":"CP066756,CP066757,CP066758","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CDC","comments":"Whole genome sequencing of cultured foodborne bacterial pathogens collected from the 2019 GenomeTrakr/PulseNet proficiency testing exercise. Six isolates were distributed for sequencing: 4 Escherichia coli serovar O157:H7 and 2 Campylobacter jejuni isolates.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_016404325.2.json.json","assembly_accession":"GCF_016404325.2","genome_id":"GCF_016404325.2","genome_name":"Escherichia coli","strain":"S19-141","serovar":"","phylogroup":"B1","MLST":33,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN16993351","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1941,"n_genes":1520,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13552.json.json","assembly_accession":"GCF_001890225.1","genome_id":"562.13552","genome_name":"Escherichia coli strain 272","strain":"strain 272","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Human","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5568363.0,"gc_content":50.44,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":6024.0,"refseq_cds":5909.0,"sequencing_platform":"PacBio","sequencing_depth":"165X","assembly_method":"Celera 8.1 v. 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Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don\u2019t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.79123.json.json","assembly_accession":"GCA_019915525.1","genome_id":"562.79123","genome_name":"Escherichia coli strain SCAID WND1-2021 (1/128) strain SCAID WND1-2021 (1/128) strain SCAID WND1-2021 (1/128)","strain":"strain SCAID WND1-2021 (1/128) strain SCAID WND1-2021 (1/128) strain SCAID WND1-2021 (1/128)","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"Swab from Wound","isolation_country":"Kazakhstan","geographic_location":"Kazakhstan: Almaty","host_name":"Homo sapiens","host_health":"wound discharge","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5636010.0,"gc_content":50.61146,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5889.0,"refseq_cds":5465.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"334x","assembly_method":"Canu v. 2.0","sequencing_centers":"Scientific Center for Anti-infectious Drugs (SCAID)","completion_date":"2021-09-15T00:00:00Z","collection_date":"2021-02-16","bioproject_accession":"PRJNA754843","biosample_accession":"SAMN20982447","genbank_accessions":"CP082831,CP082832","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"Resistant;Susceptible;Intermediate","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2","comments":"Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon","n_reactions":2732,"n_metabolites":1945,"n_genes":1474,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"KAZ","country":"Kazakhstan"},{"gem_file":"562.68639.json.json","assembly_accession":"GCA_016026235.1","genome_id":"562.68639","genome_name":"Escherichia coli strain FDAARGOS_944 strain Not applicable","strain":"","serovar":"","phylogroup":"D","MLST":280,"mash_cluster":24,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5330898.0,"gc_content":50.54728,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5560.0,"refseq_cds":5118.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"891x","assembly_method":"SMRT v. 6.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2020-12-14T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN13450474","genbank_accessions":"CP065613,CP065614","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"DSM:9028","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:DSMZ","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2730,"n_metabolites":1940,"n_genes":1481,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13965.json.json","assembly_accession":"GCF_900096855.1","genome_id":"562.13965","genome_name":"Escherichia coli strain 108","strain":"strain 108","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4638126.0,"gc_content":50.83,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4522.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UNIVERSITY OF EXETER","completion_date":"2017-01-02T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB15352","biosample_accession":"SAMEA4444109","genbank_accessions":"LT615379","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli\u2019s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a \u2018trade-up\u2019 is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic\\; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.","n_reactions":2732,"n_metabolites":1935,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1385755.6.json.json","assembly_accession":"GCA_000826925.1","genome_id":"1385755.6","genome_name":"synthetic Escherichia coli C321.deltaA","strain":"coli C321.deltaA","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4650152.0,"gc_content":50.76,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4489.0,"refseq_cds":0.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Yale University","completion_date":"2015-01-21T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA272520","biosample_accession":"SAMN03283190","genbank_accessions":"CP010456.1","refseq_accessions":"-","genome_status":"Complete","taxon_id":1385755.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"25607356","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Construction of a series of genomically recoded organisms whose growth is restricted by the expression of essential genes dependent on exogenously supplied synthetic amino acids introduces novel ortho- gonal barriers between these engineered organisms and the environment, thereby creating safer gen- etically modified organisms.;partial","n_reactions":2732,"n_metabolites":1938,"n_genes":1560,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.11479.json.json","assembly_accession":"GCF_001693635.1","genome_id":"562.11479","genome_name":"Escherichia coli strain O177:H21","strain":"strain O177:H21","serovar":"O177:H21","phylogroup":"B1","MLST":359,"mash_cluster":26,"isolation_source":"faeces","isolation_country":"Netherlands","geographic_location":"Netherlands: Leiden","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5494878.0,"gc_content":50.41,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5852.0,"refseq_cds":5467.0,"sequencing_platform":"PacBio","sequencing_depth":"30.0x","assembly_method":"SMRT analysis v. 2.3.0","sequencing_centers":"Leiden University Medical Center","completion_date":"2016-07-26T00:00:00Z","collection_date":"13-Apr-2015","bioproject_accession":"PRJNA329265","biosample_accession":"SAMN05407982","genbank_accessions":"CP016546,CP016547,CP016548,CP016549,CP016550,CP016551","refseq_accessions":"NZ_CP016546.1,NZ_CP016547.1,NZ_CP016548.1,NZ_CP016549.1,NZ_CP016550.1,NZ_CP016551.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"ST 359","substrain":"","additional_metadata":"sample_type:whole organisme;biomaterial_provider:Leiden University Medical Center, department Medical microbiology, Albinusdreef 2, 2333ZA Leiden, the Netherlands;collected_by:Leiden University Medical Center, department Medical Microbiology, E.M. Terveer;identified_by:E.M. Terveer","comments":"The emergence of the newly discovered plasmid-mediated colistin resistance gene, mcr-1, poses a significant threat to hospitalized patients as well as to the community. The aim of this study was to determine the prevalence of mcr-1 mediated colistin resistance gene in fecal samples of patients attending a tertiary care hospital. From November 2014 until July 2015, fecal samples of patients attending the Leiden University Medical Center were collected and retrospectively screened for presence of mcr-1 using real-time PCR. Two of 576 patients were positive for mcr-1, resulting in a prevalence of 0.35%. One sample contained an ESBL negative, AmpC positive and mcr-1 (located on an IncX4 plasmid) containing E.coli. This strain belonged to Sequence Type 359 and serotype O177:H21. The mcr-1 containing E.coli was phenotypically susceptible to colistin with a MIC of \u2264 0.25mg/L, due to a 1329bp transposon IS10R inserted into the mcr-1 gene.","n_reactions":2731,"n_metabolites":1939,"n_genes":1511,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"562.33376.json.json","assembly_accession":"GCA_003336405.1","genome_id":"562.33376","genome_name":"Escherichia coli strain AMSCJX02","strain":"strain AMSCJX02","serovar":"","phylogroup":"B1","MLST":453,"mash_cluster":26,"isolation_source":"feces","isolation_country":"China","geographic_location":"China:Sichuan","host_name":"Giant panda","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5339431.0,"gc_content":50.70707,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5666.0,"refseq_cds":5532.0,"sequencing_platform":"PacBio","sequencing_depth":"120.0x","assembly_method":"HGAP v. 3","sequencing_centers":"Institute of Military Veterinary Medicine","completion_date":"2018-07-24T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA481171","biosample_accession":"SAMN09662618","genbank_accessions":"CP031105,CP031106,CP031107,CP031108,CP031109,CP031110,CP031111","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:fece sample","comments":"antimicrobial resistance of fecal isolate of E.coli from giant panda","n_reactions":2732,"n_metabolites":1938,"n_genes":1518,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.46749.json.json","assembly_accession":"GCA_005222425.1","genome_id":"562.46749","genome_name":"Escherichia coli strain 110","strain":"strain 110","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5542244.0,"gc_content":50.475132,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5945.0,"refseq_cds":5783.0,"sequencing_platform":"PacBio","sequencing_depth":"193x","assembly_method":"HGAP v. 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This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.72330.json.json","assembly_accession":"GCA_017355105.1","genome_id":"562.72330","genome_name":"Escherichia coli strain P8","strain":"strain P8","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"Cattle hide","isolation_country":"USA","geographic_location":"USA: South Central","host_name":"cattle","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4812117.0,"gc_content":50.685337,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4798.0,"refseq_cds":4526.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore","sequencing_depth":"186.0x","assembly_method":"Unicycler v. 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This isolate was purchased from the American Type Culture Collection (ATCC), and the current sequence data was generated by both the Illumina MiSeq and Oxford Nanopore MinION platforms.For further information please see the following:https://www.atcc.org/products/all/BAA-1429.aspx#generalinformationhttps://doi.org/10.4315/0362-028x-68.12.2580","n_reactions":2733,"n_metabolites":1937,"n_genes":1530,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.60446.json.json","assembly_accession":"GCA_013122565.1","genome_id":"562.60446","genome_name":"Escherichia coli strain GF4-3","strain":"strain GF4-3","serovar":"","phylogroup":"B1","MLST":-1,"mash_cluster":20,"isolation_source":"Caecum","isolation_country":"Gambia","geographic_location":"Gambia","host_name":"Guinea fowl","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4821968.0,"gc_content":50.5129,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4593.0,"refseq_cds":4376.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"1.00x","assembly_method":"Hybrid v. 0.4.8.0","sequencing_centers":"Quadram Institute Biosciences","completion_date":"2020-05-17T00:00:00Z","collection_date":"2016","bioproject_accession":"PRJNA616250","biosample_accession":"SAMN14485325","genbank_accessions":"CP053258","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Whole organism","comments":"A study of the genomic diversity of E. coli and the burden of AMR in backyard poultry from rural Gambia.","n_reactions":2733,"n_metabolites":1936,"n_genes":1476,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GMB","country":"Gambia"},{"gem_file":"562.63092.json.json","assembly_accession":"GCA_902810385.1","genome_id":"562.63092","genome_name":"Escherichia coli strain SC475","strain":"strain SC475","serovar":"","phylogroup":"B1","MLST":297,"mash_cluster":26,"isolation_source":"Water","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4729401.0,"gc_content":50.76034,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4547.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"MASSEY UNIVERSITY","completion_date":"2020-06-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB36951","biosample_accession":"SAMEA6595241","genbank_accessions":"LR778148","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Mike Sadowsky","comments":"Here we report the complete genomes of 47 Escherichia coli natural isolates, sampled from watersheds located at (46\u00b042\u203204\"N, 92\u00b012\u203226\"W) in Duluth, Minnesota. 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The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.75941.json.json","assembly_accession":"GCA_900166955.1","genome_id":"562.75941","genome_name":"Escherichia coli strain KV7","strain":"strain KV7","serovar":"serovar O27","phylogroup":"E","MLST":57,"mash_cluster":20,"isolation_source":"pig feces","isolation_country":"Denmark","geographic_location":"Denmark","host_name":"Sus scrofa domestica","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5532158.0,"gc_content":50.45823,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5478.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UNIVERSITY OF CAMBRIDGE","completion_date":"2017-03-10T00:00:00Z","collection_date":"2006-08","bioproject_accession":"PRJEB19461","biosample_accession":"SAMEA95542918","genbank_accessions":"LT795502,LT795503,LT795504,LT795505,LT795506,LT795507,LT795508","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from a healthy pig that was treated prophylactically with ceftiofur","other_clinical":"host_health_state:not collected","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"We report the chromosome and plasmid sequences of a spontaneous nalidixic acid resistant derivative of the ESBL-producing E. coli strain KV7. 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Here we report the complete genome sequences of ten UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.","n_reactions":2731,"n_metabolites":1937,"n_genes":1510,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_900636305.1.json.json","assembly_accession":"GCF_900636305.1","genome_id":"GCF_900636305.1","genome_name":"Escherichia coli","strain":"NCTC10537","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMEA3492660","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2734,"n_metabolites":1939,"n_genes":1527,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.15206.json.json","assembly_accession":"GCF_002012205.1","genome_id":"562.15206","genome_name":"Escherichia coli strain Ecol_867","strain":"strain Ecol_867","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada: Toronto","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5065803.0,"gc_content":50.83,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5282.0,"refseq_cds":5263.0,"sequencing_platform":"PacBio","sequencing_depth":"XX","assembly_method":"HGAP v. unspecified","sequencing_centers":"University of Oxford","completion_date":"2017-03-03T00:00:00Z","collection_date":"2013","bioproject_accession":"PRJNA316786","biosample_accession":"SAMN05511148","genbank_accessions":"CP018983,CP018982,CP018980,CP018981","refseq_accessions":"NZ_CP018983.1,NZ_CP018982.1,NZ_CP018980.1,NZ_CP018981.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART)","comments":"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.","n_reactions":2711,"n_metabolites":1877,"n_genes":1402,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.63858.json.json","assembly_accession":"GCA_014170675.1","genome_id":"562.63858","genome_name":"Escherichia coli strain 64.1","strain":"strain 64.1","serovar":"","phylogroup":"G","MLST":3258,"mash_cluster":2,"isolation_source":"Turkey's","isolation_country":"Canada","geographic_location":"Canada","host_name":"Turkey","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5487002.0,"gc_content":50.752125,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5610.0,"refseq_cds":5219.0,"sequencing_platform":"Oxford Nanopore MinION","sequencing_depth":"80.9x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"University of Guelph","completion_date":"2020-08-12T00:00:00Z","collection_date":"2016/2017","bioproject_accession":"PRJNA596173","biosample_accession":"SAMN13613898","genbank_accessions":"CP059917,CP059918,CP059919,CP059920,CP059921","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from Turkey's in Canada","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:fecal","comments":"Chromosomes and plasmids were assembled from E. coli isolated from Turkey's in Canada. Both long reads (Oxford Nanopore) and short reads (Illumina) were used.","n_reactions":2733,"n_metabolites":1943,"n_genes":1485,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"83334.351.json.json","assembly_accession":"GCA_013167455.1","genome_id":"83334.351","genome_name":"Escherichia coli O157:H7 strain NE 1092-2","strain":"O157:H7 strain NE 1092-2","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle feces","isolation_country":"USA","geographic_location":"USA:Nebraska","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5802177.0,"gc_content":50.54527,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":6168.0,"refseq_cds":5868.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"219x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"2000","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN05360231","genbank_accessions":"CP038328,CP038332,CP038329,CP038330,CP038331","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. 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The fate and potential horizontal gene transfer of those genes into the host microbiome will have a crucial bearing on the eventual health risk of exposure to antibiotic resistance genes. In the present study, the effects of antibiotics on the in vivo transfer of \ud835\udefd-lactam resistance genes were evaluated in a mouse model by characterizing the microbiome in excreted feces. Mice were dosed with Escherichia coli, Salmonella enterica serovars Heidelberg or Bredeney referred to as donors. The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1936,"n_genes":1547,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.70738.json.json","assembly_accession":"GCA_016889505.1","genome_id":"562.70738","genome_name":"Escherichia coli strain ECY44","strain":"strain ECY44","serovar":"","phylogroup":"A","MLST":2973,"mash_cluster":26,"isolation_source":"","isolation_country":"China","geographic_location":"China:zhengzhou","host_name":"chicken","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5301216.0,"gc_content":50.282955,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5406.0,"refseq_cds":5055.0,"sequencing_platform":"Illumina HiSeq","sequencing_depth":"100.0x","assembly_method":"ABySS v. 2.0.2","sequencing_centers":"Henan Agricultural University","completion_date":"2021-02-15T00:00:00Z","collection_date":"2016-10-01","bioproject_accession":"PRJNA700460","biosample_accession":"SAMN17832021","genbank_accessions":"CP069706,CP069702,CP069703,CP069704,CP069705","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:pure culture","comments":"Escherichia coli strain ECY44, complete genome","n_reactions":2711,"n_metabolites":1877,"n_genes":1379,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.47720.json.json","assembly_accession":"GCA_005954625.1","genome_id":"562.47720","genome_name":"Escherichia coli strain EK2009","strain":"strain EK2009","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":21,"isolation_source":"chicken feces","isolation_country":"China","geographic_location":"China","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4605015.0,"gc_content":50.7713,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4597.0,"refseq_cds":4344.0,"sequencing_platform":"Illumina","sequencing_depth":"1.0x","assembly_method":"CLC NGS Cell v. 2.3","sequencing_centers":"Qingdao Agricultural University","completion_date":"2019-06-04T00:00:00Z","collection_date":"2009-05-01T17:50:02Z","bioproject_accession":"PRJNA543425","biosample_accession":"SAMN11774881","genbank_accessions":"CP040663","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from chicken feces in this laboratory is the host strain of bacteriophage Bp7, and the nucleic acid is extracted","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:single cell","comments":"The wild strain EK2009 isolated from chicken feces in this laboratory is the host strain of bacteriophage Bp7, and the nucleic acid is extracted. The genomic sequence is obtained by sequencing, and it is determined as E. coli K12 by comparison with NCBI database.","n_reactions":2732,"n_metabolites":1938,"n_genes":1550,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.55256.json.json","assembly_accession":"GCA_009909465.1","genome_id":"562.55256","genome_name":"Escherichia coli strain LD39-1","strain":"strain LD39-1","serovar":"","phylogroup":"A","MLST":2325,"mash_cluster":22,"isolation_source":"feces","isolation_country":"China","geographic_location":"China: Dafeng","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5077652.0,"gc_content":50.439926,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5166.0,"refseq_cds":4805.0,"sequencing_platform":"Illumina HiSeq; Oxford Nanopore MiniION","sequencing_depth":"100.0x","assembly_method":"Unicycler v. 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The fate and potential horizontal gene transfer of those genes into the host microbiome will have a crucial bearing on the eventual health risk of exposure to antibiotic resistance genes. In the present study, the effects of antibiotics on the in vivo transfer of \ud835\udefd-lactam resistance genes were evaluated in a mouse model by characterizing the microbiome in excreted feces. Mice were dosed with Escherichia coli, Salmonella enterica serovars Heidelberg or Bredeney referred to as donors. The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1936,"n_genes":1535,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.77494.json.json","assembly_accession":"GCA_019334645.1","genome_id":"562.77494","genome_name":"Escherichia coli strain GB2005","strain":"strain GB2005","serovar":"","phylogroup":"A","MLST":1060,"mash_cluster":21,"isolation_source":"","isolation_country":"China","geographic_location":"China","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4552324.0,"gc_content":50.77699,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4567.0,"refseq_cds":4309.0,"sequencing_platform":"PacBio","sequencing_depth":"100.0x","assembly_method":"Celera Assembler v. 07-2021","sequencing_centers":"shandongdaxue","completion_date":"2021-07-25T00:00:00Z","collection_date":"2021-06-15","bioproject_accession":"PRJNA747614","biosample_accession":"SAMN20286394","genbank_accessions":"CP079735","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Escherichia coli GB2005 wild type","n_reactions":2750,"n_metabolites":2025,"n_genes":1719,"n_exchange":331,"n_with_gpr":2304,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.63089.json.json","assembly_accession":"GCA_902810335.1","genome_id":"562.63089","genome_name":"Escherichia coli strain SC418","strain":"strain SC418","serovar":"","phylogroup":"G","MLST":2550,"mash_cluster":17,"isolation_source":"Sediment","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5222289.0,"gc_content":50.53513,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5045.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"MASSEY UNIVERSITY","completion_date":"2020-06-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB36951","biosample_accession":"SAMEA6595217","genbank_accessions":"LR778147","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Mike Sadowsky","comments":"Here we report the complete genomes of 47 Escherichia coli natural isolates, sampled from watersheds located at (46\u00b042\u203204\"N, 92\u00b012\u203226\"W) in Duluth, Minnesota. The genomes were assembled using a combination of Nanopore R9.4 and Illumina sequencing data.","n_reactions":2731,"n_metabolites":1942,"n_genes":1513,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_020883395.1.json.json","assembly_accession":"GCF_020883395.1","genome_id":"GCF_020883395.1","genome_name":"Escherichia 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This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of ten UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.","n_reactions":2752,"n_metabolites":2025,"n_genes":1733,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.61495.json.json","assembly_accession":"GCA_013315835.1","genome_id":"562.61495","genome_name":"Escherichia coli strain SCU-483","strain":"strain SCU-483","serovar":"","phylogroup":"B1","MLST":-1,"mash_cluster":26,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5084433.0,"gc_content":50.776184,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5879.0,"refseq_cds":4867.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore MinION","sequencing_depth":"43x","assembly_method":"Flye v. 2.6","sequencing_centers":"Santa Clara University","completion_date":"2020-06-10T00:00:00Z","collection_date":"2018","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609799","genbank_accessions":"CP054314,CP054316,CP054315","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2733,"n_metabolites":1953,"n_genes":1548,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.70524.json.json","assembly_accession":"GCA_016776285.1","genome_id":"562.70524","genome_name":"Escherichia coli strain RIVM_C028620","strain":"strain RIVM_C028620","serovar":"","phylogroup":"B2","MLST":127,"mash_cluster":6,"isolation_source":"","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5192168.0,"gc_content":50.432304,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5152.0,"refseq_cds":4833.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"National Institute for Public Health and the Environment","completion_date":"2021-02-01T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA691727","biosample_accession":"SAMN17373191","genbank_accessions":"CP068815","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:chromosome","comments":"OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2752,"n_metabolites":2023,"n_genes":1743,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"562.50974.json.json","assembly_accession":"GCA_901733115.1","genome_id":"562.50974","genome_name":"Escherichia coli strain EcMAD1","strain":"strain EcMAD1","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"","isolation_country":"France","geographic_location":"France","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4899891.0,"gc_content":50.598045,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":4805.0,"refseq_cds":4583.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"INSTITUT PASTEUR","completion_date":"2019-06-06T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB27293","biosample_accession":"SAMEA4732083","genbank_accessions":"LR595691,LR595692,LR595693,LR595694","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated in France","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology we have sequenced the genome of the Escherichia coli strain MAD. A carbapenemase producing isolate belonging to the ST410 isolated in France.;blaOXA-181 encoding Escherichia coli strain from the ST410 isolated in France (Bicetre Hospital-APHP) in 2013","n_reactions":2733,"n_metabolites":1939,"n_genes":1533,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"FRA","country":"France"},{"gem_file":"562.30991.json.json","assembly_accession":"GCA_003308955.1","genome_id":"562.30991","genome_name":"Escherichia coli strain 2017C-4109","strain":"strain 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septicemia","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Complete genome sequence of avian pathogenic Escherichia coli strain IMT5155 (O2:K1:H5) isolated from the internal organs of a laying hen with clinical symptoms of septicemia.","n_reactions":2733,"n_metabolites":1948,"n_genes":1463,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.76477.json.json","assembly_accession":"GCA_018972225.1","genome_id":"562.76477","genome_name":"Escherichia coli strain S21EC","strain":"strain S21EC","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"United Kingdom","geographic_location":"United Kingdom:Manchester","host_name":"Homo 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project, we described the diversity and prevalence of afa/dr fimbria genes in ST131, revealing the dominance of a new afaE-IX allelic variant. We additionally showed how different IS elements can alter the regulation of afa transcription and provide evidence for a more widespread impact of IS1 on ST131 genome evolution.The genomes in this BioProject are 4 ST131 representative strains with different IS elements located in the promoter region of afa operon. These genomes are assembled using Nanopore long reads and polished with Illumina short reads.","n_reactions":2732,"n_metabolites":1944,"n_genes":1466,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.50514.json.json","assembly_accession":"GCA_007108845.1","genome_id":"562.50514","genome_name":"Escherichia coli strain 131","strain":"strain 131","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"blood","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"Bloodstream infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5253264.0,"gc_content":50.70367,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5424.0,"refseq_cds":5179.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"162x","assembly_method":"HGAP v. 4","sequencing_centers":"Duke University","completion_date":"2019-07-18T00:00:00Z","collection_date":"2008","bioproject_accession":"PRJNA551684","biosample_accession":"SAMN12163096","genbank_accessions":"CP041541,CP041542,CP041543","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Vance G. Fowler Jr.","comments":"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2751,"n_metabolites":2021,"n_genes":1671,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.67476.json.json","assembly_accession":"GCA_015509005.1","genome_id":"562.67476","genome_name":"Escherichia coli strain JE86-ST05","strain":"strain JE86-ST05","serovar":"O86","phylogroup":"B1","MLST":3570,"mash_cluster":26,"isolation_source":"","isolation_country":"Japan","geographic_location":"Japan","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5590628.0,"gc_content":50.67862,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5791.0,"refseq_cds":5422.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MinION","sequencing_depth":"135.0X","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Department of Bacteriology, National Institute of Infectious Diseases","completion_date":"2020-11-06T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJDB7390","biosample_accession":"SAMD00197820","genbank_accessions":"AP022815,AP022816,AP022817,AP022818,AP022819,AP022820","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"32678145","isolation_comments":"isolated in Japan","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Draft and compelete genome sequence analyses were performed in enterohemorrhagic Escherichia coli serogroup O86 isolated in Japan.","n_reactions":2732,"n_metabolites":1936,"n_genes":1512,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"JPN","country":"Japan"},{"gem_file":"562.45404.json.json","assembly_accession":"GCA_004118895.1","genome_id":"562.45404","genome_name":"Escherichia coli strain BR43-DEC","strain":"strain BR43-DEC","serovar":"ST131","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"urine","isolation_country":"Brazil","geographic_location":"Brazil: Botucatu, Sao Paulo State","host_name":"Human, Homo sapiens","host_health":"Urinary tract infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5161342.0,"gc_content":50.58899,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5377.0,"refseq_cds":5155.0,"sequencing_platform":"Illumina NextSeq","sequencing_depth":"151.0x","assembly_method":"A5-miseq v. 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The plasmid-mediated qnrS1 gene is known to be situated on plasmids with different incompatibility (Inc) groups. In this study, the aim was to select QREC strains encoding qnrS1 situated on plasmids with different Inc-groups and to complete circular plasmid contigs. We created hybrid assemblies using data from Illumina and minION sequencing.","n_reactions":2733,"n_metabolites":1942,"n_genes":1507,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NOR","country":"Norway"},{"gem_file":"562.31030.json.json","assembly_accession":"GCA_900474495.1","genome_id":"562.31030","genome_name":"Escherichia coli strain NCTC11023","strain":"strain NCTC11023","serovar":"O160:K:H34","phylogroup":"A","MLST":218,"mash_cluster":22,"isolation_source":"Faeces","isolation_country":"Bahrain","geographic_location":"Bahrain: Arabian Gulf","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4705041.0,"gc_content":50.939003,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4620.0,"refseq_cds":4370.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"SC","completion_date":"2018-06-17T00:00:00Z","collection_date":"1967","bioproject_accession":"PRJEB6403","biosample_accession":"SAMEA3368272","genbank_accessions":"LS483297","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"NCTC:11023","publication":"","isolation_comments":"","other_clinical":"host_health_state:not available: to be reported later","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/","n_reactions":2731,"n_metabolites":1935,"n_genes":1511,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BHR","country":"Bahrain"},{"gem_file":"562.64246.json.json","assembly_accession":"GCA_014058445.1","genome_id":"562.64246","genome_name":"Escherichia coli strain MBT-5","strain":"strain MBT-5","serovar":"O26:H11","phylogroup":"B1","MLST":21,"mash_cluster":23,"isolation_source":"ready to eat mixed salad leaves (obtained from discount store)","isolation_country":"Germany","geographic_location":"Germany: Kiel","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5936184.0,"gc_content":50.5064,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":6452.0,"refseq_cds":5905.0,"sequencing_platform":"Illumina MiSeq; 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Both long reads (Oxford Nanopore) and short reads (Illumina) were used.","n_reactions":2731,"n_metabolites":1934,"n_genes":1533,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"1392854.3.json.json","assembly_accession":"GCA_003586045.1","genome_id":"1392854.3","genome_name":"Escherichia coli M8","strain":"M8","serovar":"","phylogroup":"B1","MLST":223,"mash_cluster":26,"isolation_source":"ob/ob mice","isolation_country":"Switzerland","geographic_location":"Switzerland","host_name":"Mus musculus C57Bl/6J","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5279597.0,"gc_content":50.597538,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5561.0,"refseq_cds":5475.0,"sequencing_platform":"Illumina; Sanger","sequencing_depth":"12.0x","assembly_method":"Newbler v. 2.9 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Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. 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Celera Assembler 8.1","sequencing_centers":"The Roslin Institute","completion_date":"2017-09-18T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA402083","biosample_accession":"SAMN07618120","genbank_accessions":"CP023388,CP023389","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from urinary tract infections in dogs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. 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University","completion_date":"2020-11-09T00:00:00Z","collection_date":"May-2017","bioproject_accession":"PRJNA673751","biosample_accession":"SAMN16622485","genbank_accessions":"CP063983,CP063984,CP063985","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Complete genome of Escherichia coli 25DN","n_reactions":2732,"n_metabolites":1947,"n_genes":1457,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia 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In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1939,"n_genes":1486,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"83334.194.json.json","assembly_accession":"GCF_001695515.1","genome_id":"83334.194","genome_name":"Escherichia coli O157:H7 strain FRIK944","strain":"O157:H7 strain FRIK944","serovar":"","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"calf feces","isolation_country":"USA","geographic_location":"USA: FL","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5866200.0,"gc_content":50.55,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":6321.0,"refseq_cds":5941.0,"sequencing_platform":"PacBio","sequencing_depth":"25x","assembly_method":"HGAP v. 3","sequencing_centers":"University of Florida","completion_date":"2016-07-27T00:00:00Z","collection_date":"16-Sep-2014","bioproject_accession":"PRJNA322195","biosample_accession":"SAMN04510563","genbank_accessions":"CP016625,CP016626","refseq_accessions":"NZ_CP016625.1,NZ_CP016626.1","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:FLUFL","comments":"Comparative genomics using PacBio sequencing","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_020827615.1.json.json","assembly_accession":"GCF_020827615.1","genome_id":"GCF_020827615.1","genome_name":"Escherichia coli","strain":"elppa6","serovar":"","phylogroup":"B1","MLST":58,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN21169129","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1941,"n_genes":1508,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.46722.json.json","assembly_accession":"GCA_005221705.1","genome_id":"562.46722","genome_name":"Escherichia coli strain 133","strain":"strain 133","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5553154.0,"gc_content":50.499626,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5967.0,"refseq_cds":5798.0,"sequencing_platform":"PacBio","sequencing_depth":"240x","assembly_method":"HGAP v. 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This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.60286.json.json","assembly_accession":"GCA_012955465.1","genome_id":"562.60286","genome_name":"Escherichia coli strain SCAID URN1-2019","strain":"strain SCAID URN1-2019","serovar":"","phylogroup":"B2","MLST":998,"mash_cluster":6,"isolation_source":"urine","isolation_country":"Kazakhstan","geographic_location":"Kazakhstan: Almaty","host_name":"Human, Homo sapiens","host_health":"Chronic cystitis","host_gender":"female","host_age":"71","body_sample_site":"","disease":"","genome_length":4937450.0,"gc_content":50.705578,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5028.0,"refseq_cds":4577.0,"sequencing_platform":"IonTorrent","sequencing_depth":"16x","assembly_method":"Bowtie v. 1.2.3","sequencing_centers":"Scientific Center for Anti-infectious Drugs (SCAID)","completion_date":"2020-05-03T00:00:00Z","collection_date":"08-March-2019","bioproject_accession":"PRJNA627194","biosample_accession":"SAMN14653305","genbank_accessions":"CP052057","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"Resistant;Susceptible","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"host_disease_outcome:Chronic disease;host_disease_stage:Chronic cystitis","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2","comments":"Creating experimental models on the basis of clinical isolates that are characterized by multiple drug resistance, in order to clarify the universality of the reversion phenomenon","n_reactions":2733,"n_metabolites":1956,"n_genes":1432,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"KAZ","country":"Kazakhstan"},{"gem_file":"930406.8.json.json","assembly_accession":"GCA_015571855.1","genome_id":"930406.8","genome_name":"Escherichia coli O157:H16 strain Res13-Lact-PEA12-26","strain":"O157:H16 strain Res13-Lact-PEA12-26","serovar":"O157:H16","phylogroup":"A","MLST":5502,"mash_cluster":22,"isolation_source":"feces","isolation_country":"Canada","geographic_location":"Canada: Quebec","host_name":"Pig, Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5213098.0,"gc_content":50.648598,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5417.0,"refseq_cds":5001.0,"sequencing_platform":"Oxford Nanopore MinION and Illumina MiSeq","sequencing_depth":"1.00x","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Government of Canada","completion_date":"2020-11-18T00:00:00Z","collection_date":"24-Apr-2017","bioproject_accession":"PRJNA662792","biosample_accession":"SAMN16304178","genbank_accessions":"CP062876,CP062877,CP062878,CP062879,CP062880,CP062881,CP062882","refseq_accessions":"","genome_status":"Complete","taxon_id":930406.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Agriculture and Agri-Food Canada","comments":"The majority of antibiotics sold are administered to livestock, presumably promoting the development and spread of antibiotic resistance genes in food-borne pathogens such as Enterobacteriaceae producing extended spectrum beta-lactamases (ESBL). Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. The major goal of the study was to characterize cefotaxime-resistant bacteria isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2733,"n_metabolites":1937,"n_genes":1491,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.60267.json.json","assembly_accession":"GCA_012934555.1","genome_id":"562.60267","genome_name":"Escherichia coli strain SCU-116","strain":"strain SCU-116","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5167467.0,"gc_content":50.760864,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5165.0,"refseq_cds":4877.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"21x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-04-30T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609778","genbank_accessions":"CP051719,CP051720,CP051721,CP051722,CP051723,CP051724","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2734,"n_metabolites":1948,"n_genes":1465,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.339.json.json","assembly_accession":"GCA_013167195.1","genome_id":"83334.339","genome_name":"Escherichia coli O157:H7 strain TX 265-1","strain":"O157:H7 strain TX 265-1","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle feces","isolation_country":"USA","geographic_location":"USA:Texas","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5688743.0,"gc_content":50.557495,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":6047.0,"refseq_cds":5738.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"236x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"2000","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN05360242","genbank_accessions":"CP038290,CP038291","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2732,"n_metabolites":1941,"n_genes":1487,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.70523.json.json","assembly_accession":"GCA_016776305.1","genome_id":"562.70523","genome_name":"Escherichia coli strain RIVM_C017887","strain":"strain RIVM_C017887","serovar":"","phylogroup":"B2","MLST":127,"mash_cluster":6,"isolation_source":"","isolation_country":"Netherlands","geographic_location":"Netherlands","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5227631.0,"gc_content":50.440823,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5203.0,"refseq_cds":4881.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"National Institute for Public Health and the Environment","completion_date":"2021-02-01T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA691727","biosample_accession":"SAMN17373172","genbank_accessions":"CP068799","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:chromosome","comments":"OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2752,"n_metabolites":2023,"n_genes":1743,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"562.77177.json.json","assembly_accession":"GCA_019091005.1","genome_id":"562.77177","genome_name":"Escherichia coli strain ST865","strain":"strain ST865","serovar":"","phylogroup":"B1","MLST":6198,"mash_cluster":26,"isolation_source":"diarrhea from outbreaks of food poisoning","isolation_country":"China","geographic_location":"China: Guangxi","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4944083.0,"gc_content":50.611084,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4933.0,"refseq_cds":4662.0,"sequencing_platform":"PacBio; 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The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1943,"n_genes":1443,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.30363.json.json","assembly_accession":"GCA_003204955.1","genome_id":"562.30363","genome_name":"Escherichia coli strain 2016C-3878","strain":"strain 2016C-3878","serovar":"","phylogroup":"F","MLST":457,"mash_cluster":11,"isolation_source":"Rectal swab","isolation_country":"United States","geographic_location":"United States","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5272336.0,"gc_content":50.392445,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5399.0,"refseq_cds":5296.0,"sequencing_platform":"PacBio","sequencing_depth":"45.0x","assembly_method":"HGAP v. 3","sequencing_centers":"Centers for Disease Control and Prevention","completion_date":"2018-06-10T00:00:00Z","collection_date":"31-May-2016","bioproject_accession":"PRJNA335991","biosample_accession":"SAMN05468123","genbank_accessions":"CP029747,CP029748","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Health Department","comments":"Raw sequence reads of Escherichia coli containing MCR-1 gene","n_reactions":2732,"n_metabolites":1943,"n_genes":1521,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.7244.json.json","assembly_accession":"GCF_000987875.1","genome_id":"562.7244","genome_name":"Escherichia coli strain SEC470","strain":"strain SEC470","serovar":"","phylogroup":"A","MLST":48,"mash_cluster":22,"isolation_source":"diarrhea piglet","isolation_country":"","geographic_location":"","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5153435.0,"gc_content":50.76,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5307.0,"refseq_cds":4941.0,"sequencing_platform":"Illumina","sequencing_depth":"50x","assembly_method":"de novo v. 4.11","sequencing_centers":"Institute of Subtropical Agriculture, Chinese Academy of Sciences","completion_date":"2015-05-04T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA244370","biosample_accession":"SAMN03576594","genbank_accessions":"CP007594","refseq_accessions":"NZ_CP007594.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from diarrhea piglet","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"This is a strain isolated from diarrhea piglet.","n_reactions":2734,"n_metabolites":1938,"n_genes":1530,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.178.json.json","assembly_accession":"GCA_001307215.1","genome_id":"83334.178","genome_name":"Escherichia coli O157:H7 strain WS4202","strain":"O157:H7 strain WS4202","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"derived from CIP 106327 (Collection de l'Institute Pasteur, Paris, France)","isolation_country":"France","geographic_location":"France: Paris","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5428108.0,"gc_content":50.48,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5676.0,"refseq_cds":5326.0,"sequencing_platform":"PacBio","sequencing_depth":"100.0x","assembly_method":"PacBio HGAP v. 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Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don\u2019t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.","n_reactions":2731,"n_metabolites":1938,"n_genes":1488,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"83333.1301.json.json","assembly_accession":"GCA_015534995.1","genome_id":"83333.1301","genome_name":"Escherichia coli K-12 strain BZKR3G40 strain not applicable","strain":"","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada: Manitoba","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4631476.0,"gc_content":50.778866,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4588.0,"refseq_cds":4340.0,"sequencing_platform":"Illumina","sequencing_depth":"30X","assembly_method":"Geneious v. 11.1.5","sequencing_centers":"University of Manitoba","completion_date":"2020-11-17T00:00:00Z","collection_date":"2018","bioproject_accession":"PRJNA646979","biosample_accession":"SAMN15572257","genbank_accessions":"CP064681","refseq_accessions":"","genome_status":"Complete","taxon_id":83333.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:pure culture","comments":"These isolates were created by gradually adapting an Escherichia coli K-12 BW25113 strain over 40 generations to one of two quaternary ammonium compounds, benzakonium (BZK) or cetrimide (CET). Three replicates were created for each compound, generating BZKR1, BZKR2, BZKR3, CETR1, CETR2, and CETR3, as well as an unadapted wild-type. At the end of the experiment, the BZK-adapted bacteria were tolerant to 72-144 ug/ml of BZK, and the CET-adapted bacteria were tolerant to 240 ug/ml of CET.;Benzalkonium adapted E.coli bioreplicate 3 derived from BW25113","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.60624.json.json","assembly_accession":"GCA_902825185.1","genome_id":"562.60624","genome_name":"Escherichia coli strain SC457","strain":"strain SC457","serovar":"","phylogroup":"B1","MLST":720,"mash_cluster":18,"isolation_source":"Soil","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4555909.0,"gc_content":50.92523,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4619.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"MASSEY UNIVERSITY","completion_date":"2020-03-11T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB36951","biosample_accession":"SAMEA6595235","genbank_accessions":"LR782231","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Mike Sadowsky","comments":"Here we report the complete genomes of 47 Escherichia coli natural isolates, sampled from watersheds located at (46\u00b042\u203204\"N, 92\u00b012\u203226\"W) in Duluth, Minnesota. 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Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.","n_reactions":2734,"n_metabolites":1939,"n_genes":1500,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"511145.186.json.json","assembly_accession":"GCF_001308065.1","genome_id":"511145.186","genome_name":"Escherichia coli str. K-12 substr. MG1655","strain":"str. K-12 substr. 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WGS was performed to determine genetic determinants in E.coli for different levels of heat resistance and determine the evolution regarding the emergence of heat resistant strains of E.coli in a meat plant setting.","n_reactions":2711,"n_metabolites":1877,"n_genes":1459,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.52635.json.json","assembly_accession":"GCA_009432415.1","genome_id":"562.52635","genome_name":"Escherichia coli strain 21B8 strain not applicable","strain":"","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"USA","geographic_location":"USA:Ohio","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5494884.0,"gc_content":50.498356,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5761.0,"refseq_cds":5444.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"171x","assembly_method":"HGAP v. v3.0","sequencing_centers":"University of Texas at San Antonio","completion_date":"2019-10-31T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA530317","biosample_accession":"SAMN11633025","genbank_accessions":"CP040309,CP040310","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:U.S. Meat Animal Research Center","comments":"The goal of this study is to comprehensively analyze the genomes and transcriptomes of Enterohemorrhagic Escherichia coli of the O157:H7 serotype and derived atypical non-shigatoxigenic strains","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.60268.json.json","assembly_accession":"GCA_012934575.1","genome_id":"562.60268","genome_name":"Escherichia coli strain SCU-118","strain":"strain SCU-118","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4702137.0,"gc_content":50.65988,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":4672.0,"refseq_cds":4397.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"30x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-04-30T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609779","genbank_accessions":"CP051716,CP051717,CP051718","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2733,"n_metabolites":1937,"n_genes":1535,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_004010675.1.json.json","assembly_accession":"GCF_004010675.1","genome_id":"GCF_004010675.1","genome_name":"Escherichia coli","strain":"2010C-3347","serovar":"","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN04549845","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.77344.json.json","assembly_accession":"GCA_019270115.1","genome_id":"562.77344","genome_name":"Escherichia coli strain Colony285","strain":"strain Colony285","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":22,"isolation_source":"Rectal Swab","isolation_country":"Thailand","geographic_location":"Thailand: Nakhon Ratchasima","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4733682.0,"gc_content":51.27647,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4319.0,"refseq_cds":"","sequencing_platform":"Illumina HiSeq","sequencing_depth":"88.522x","assembly_method":"idba_ud v. 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The genomes were assembled using a combination of Nanopore R9.4 and Illumina sequencing data.","n_reactions":2732,"n_metabolites":1940,"n_genes":1515,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.67265.json.json","assembly_accession":"GCA_015139155.1","genome_id":"562.67265","genome_name":"Escherichia coli strain THO-008","strain":"strain THO-008","serovar":"","phylogroup":"D","MLST":393,"mash_cluster":12,"isolation_source":"urine","isolation_country":"Japan","geographic_location":"Japan:Tokyo","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5231583.0,"gc_content":50.71501,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5078.0,"refseq_cds":4811.0,"sequencing_platform":"Sequel; NextSeq 500","sequencing_depth":"431x","assembly_method":"flye v. 2.5; 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Oxford Nanopore MinION","sequencing_depth":"100.0x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"Yangzhou University","completion_date":"2020-09-14T00:00:00Z","collection_date":"Aug-2018","bioproject_accession":"PRJNA661386","biosample_accession":"SAMN16056871","genbank_accessions":"CP061185,CP061187,CP061188,CP061186","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Xiaoyu Lu","comments":"Prevalence of plasmid Mediated Colistin Resistance Gene mcr-1 in E.coli from Deer in China","n_reactions":2733,"n_metabolites":1944,"n_genes":1519,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.13966.json.json","assembly_accession":"GCF_900096865.1","genome_id":"562.13966","genome_name":"Escherichia coli strain 101","strain":"strain 101","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4638126.0,"gc_content":50.82,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4511.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UNIVERSITY OF EXETER","completion_date":"2017-01-02T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB15352","biosample_accession":"SAMEA4444102","genbank_accessions":"LT615371","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli\u2019s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a \u2018trade-up\u2019 is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic\\; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.","n_reactions":2732,"n_metabolites":1935,"n_genes":1560,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"GCF_003031815.1.json.json","assembly_accession":"GCF_003031815.1","genome_id":"GCF_003031815.1","genome_name":"Escherichia coli","strain":"190","serovar":"","phylogroup":"C","MLST":90,"mash_cluster":25,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN04622917","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1936,"n_genes":1532,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.67700.json.json","assembly_accession":"GCA_904711295.1","genome_id":"562.67700","genome_name":"Escherichia coli strain 2015-01-466","strain":"strain 2015-01-466","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"pig","isolation_country":"Norway","geographic_location":"Norway","host_name":"Pig, Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4867812.0,"gc_content":50.599407,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":4806.0,"refseq_cds":4582.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"NORWEGIAN VETERINARY INSTITUTE","completion_date":"2020-09-28T00:00:00Z","collection_date":"2015-02-11","bioproject_accession":"PRJEB40078","biosample_accession":"SAMEA7287972","genbank_accessions":"LR882052,LR882053,LR882054,LR882055,LR882056","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"Norwegian Veterinary Institute","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The presence of quinolone resistant Escherichia coli (QREC) in the animal reservoir might be of public health concern especially related to acquired quinolone resistance genes encoded on plasmids as they might spread to more pathogenic and disease-causing bacteria. The plasmid-mediated qnrS1 gene is known to be situated on plasmids with different incompatibility (Inc) groups. In this study, the aim was to select QREC strains encoding qnrS1 situated on plasmids with different Inc-groups and to complete circular plasmid contigs. We created hybrid assemblies using data from Illumina and minION sequencing.","n_reactions":2734,"n_metabolites":1937,"n_genes":1528,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NOR","country":"Norway"},{"gem_file":"562.75744.json.json","assembly_accession":"GCA_018415975.1","genome_id":"562.75744","genome_name":"Escherichia coli strain TCM_B_2","strain":"strain TCM_B_2","serovar":"","phylogroup":"B1","MLST":448,"mash_cluster":26,"isolation_source":"intestinal and liver","isolation_country":"China","geographic_location":"China:Yangling","host_name":"swine","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5380316.0,"gc_content":50.446106,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5445.0,"refseq_cds":5121.0,"sequencing_platform":"Illumina Hiseq, oxford nanopore","sequencing_depth":"80.0x","assembly_method":"Unicycler v. v0.48","sequencing_centers":"Northwest A&F University","completion_date":"2021-05-20T00:00:00Z","collection_date":"2014-06-17","bioproject_accession":"PRJNA649866","biosample_accession":"SAMN15684126","genbank_accessions":"CP075061,CP075057,CP075060,CP075059,CP075056,CP075058","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:metagenomic assembly","comments":"Co-occurrence of mcr-1, blaCTX-M and blaCMY genes in multidrug-resistant ST448 Escherichia coli in China","n_reactions":2711,"n_metabolites":1877,"n_genes":1476,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.50569.json.json","assembly_accession":"GCA_007833875.1","genome_id":"562.50569","genome_name":"Escherichia coli strain UPEC132","strain":"strain UPEC132","serovar":"","phylogroup":"B2","MLST":-1,"mash_cluster":6,"isolation_source":"urinary","isolation_country":"China","geographic_location":"China: Tianjin","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5452963.0,"gc_content":50.514114,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5436.0,"refseq_cds":"","sequencing_platform":"PacBio Sequel","sequencing_depth":"50.0x","assembly_method":"FALCON v. 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RS_HGAP_Assembly.3","sequencing_centers":"United State Department of Agriculture","completion_date":"2019-05-07T00:00:00Z","collection_date":"2006","bioproject_accession":"PRJNA445267","biosample_accession":"SAMN08773033","genbank_accessions":"CP028656,CP028658,CP028657","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The aim of this project is to compare complete closed genomes with whole genome sequencing (WGS) using short reads. SNPs from WGS is used in many studies to determine relatedness of strains. These SNPs are in the core genome and don't reflect the diversity of the complete genome. This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.16427.json.json","assembly_accession":"GCA_002118095.1","genome_id":"562.16427","genome_name":"Escherichia coli strain HST04","strain":"strain HST04","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"TAKARA","isolation_country":"China","geographic_location":"China","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4567242.0,"gc_content":50.79,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4597.0,"refseq_cds":4405.0,"sequencing_platform":"SMRT PacBio","sequencing_depth":"180x","assembly_method":"HGAP v. 2.3.3","sequencing_centers":"Wuhan University","completion_date":"2017-04-28T00:00:00Z","collection_date":"27-Nov-2013","bioproject_accession":"PRJNA298687","biosample_accession":"SAMN04396805","genbank_accessions":"CP013952","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"28400512","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"C","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:single cell","comments":"SMRT sequencing of E. coli","n_reactions":2731,"n_metabolites":1933,"n_genes":1536,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.50508.json.json","assembly_accession":"GCA_007107705.1","genome_id":"562.50508","genome_name":"Escherichia coli strain 69","strain":"strain 69","serovar":"","phylogroup":"D","MLST":69,"mash_cluster":13,"isolation_source":"blood","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"Bloodstream infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5417941.0,"gc_content":50.725555,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5589.0,"refseq_cds":5311.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"74x","assembly_method":"HGAP v. 4","sequencing_centers":"Duke University","completion_date":"2019-07-18T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA551684","biosample_accession":"SAMN12163104","genbank_accessions":"CP041522,CP041523,CP041524,CP041525","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Vance G. Fowler Jr.","comments":"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2733,"n_metabolites":1942,"n_genes":1499,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.78003.json.json","assembly_accession":"GCA_019357435.1","genome_id":"562.78003","genome_name":"Escherichia coli strain ECJXMCRH7","strain":"strain ECJXMCRH7","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"food","isolation_country":"China","geographic_location":"China: Jiaxing, Zhejiang","host_name":"chicken","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5056324.0,"gc_content":50.548325,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5163.0,"refseq_cds":4838.0,"sequencing_platform":"PacBio Sequel; Illumina NovaSeq","sequencing_depth":"176.0x","assembly_method":"CANU v. v2.1","sequencing_centers":"Zhejiang Academy of Agricultural Sciences","completion_date":"2021-07-27T00:00:00Z","collection_date":"2020-07","bioproject_accession":"PRJNA689989","biosample_accession":"SAMN17224774","genbank_accessions":"CP067342,CP067343,CP067344","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from a chicken sample in a supermarket in Jiaxing, China","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:mixed culture","comments":"This strain was isolated from a chicken sample in a supermarket in Jiaxing, China. This strain showed a multidrug resistance phenotype and whole genome sequenceing was performed to investigate the characteristics of genome","n_reactions":2711,"n_metabolites":1877,"n_genes":1448,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.75681.json.json","assembly_accession":"GCA_018279125.1","genome_id":"562.75681","genome_name":"Escherichia coli strain 19-5","strain":"strain 19-5","serovar":"","phylogroup":"A","MLST":48,"mash_cluster":22,"isolation_source":"heart","isolation_country":"China","geographic_location":"China:Yangling","host_name":"swine","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5185965.0,"gc_content":50.63235,"contigs":9.0,"chromosomes":1.0,"plasmids":8.0,"patric_cds":5338.0,"refseq_cds":5005.0,"sequencing_platform":"Illumina HiSeq","sequencing_depth":"80.0x","assembly_method":"Unicycler Version v. v0.48","sequencing_centers":"Northwest A&F University","completion_date":"2021-05-05T00:00:00Z","collection_date":"2019-05-14","bioproject_accession":"PRJNA595647","biosample_accession":"SAMN13563036","genbank_accessions":"CP047010,CP047012,CP047017,CP047018,CP047016,CP047015,CP047011,CP047014,CP047013","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"comparative genomics","n_reactions":2752,"n_metabolites":2027,"n_genes":1757,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.66883.json.json","assembly_accession":"GCA_014854575.1","genome_id":"562.66883","genome_name":"Escherichia coli strain C311","strain":"strain C311","serovar":"","phylogroup":"B1","MLST":442,"mash_cluster":26,"isolation_source":"","isolation_country":"Hong Kong","geographic_location":"Hong Kong","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5358674.0,"gc_content":50.690113,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5481.0,"refseq_cds":5121.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore MinION","sequencing_depth":"25.0x","assembly_method":"Unicycler v. 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FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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region.","n_reactions":2732,"n_metabolites":1943,"n_genes":1473,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"JPN","country":"Japan"},{"gem_file":"562.51559.json.json","assembly_accession":"GCA_008761475.1","genome_id":"562.51559","genome_name":"Escherichia coli strain RM13745","strain":"strain RM13745","serovar":"","phylogroup":"B1","MLST":2217,"mash_cluster":25,"isolation_source":"","isolation_country":"USA","geographic_location":"USA: California","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5264698.0,"gc_content":50.964993,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5408.0,"refseq_cds":5132.0,"sequencing_platform":"PacBio","sequencing_depth":"86x","assembly_method":"Flye v. 2.4.1","sequencing_centers":"USDA-ARS, Western Regional Research 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The goal of this work was to identify which chloramphenicol concentrations promote the evolution of antibiotic resistance and how the presence of the AcrAB-TolC pump impacts this evolution.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_003956245.1.json.json","assembly_accession":"GCF_003956245.1","genome_id":"GCF_003956245.1","genome_name":"Escherichia coli","strain":"214-4","serovar":"","phylogroup":"A","MLST":398,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN08161344","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1945,"n_genes":1528,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.52636.json.json","assembly_accession":"GCA_009432635.1","genome_id":"562.52636","genome_name":"Escherichia coli strain F3398 strain not applicable","strain":"","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Ground beef","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5474637.0,"gc_content":50.467655,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5716.0,"refseq_cds":5385.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"150x","assembly_method":"HGAP v. v3.0","sequencing_centers":"University of Texas at San Antonio","completion_date":"2019-10-31T00:00:00Z","collection_date":"2004","bioproject_accession":"PRJNA530317","biosample_accession":"SAMN11633024","genbank_accessions":"CP040311,CP040312","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Food Safety Inspection Service","comments":"The goal of this study is to comprehensively analyze the genomes and transcriptomes of Enterohemorrhagic Escherichia coli of the O157:H7 serotype and derived atypical non-shigatoxigenic strains","n_reactions":2752,"n_metabolites":2024,"n_genes":1681,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.51574.json.json","assembly_accession":"GCA_008807295.1","genome_id":"562.51574","genome_name":"Escherichia coli strain YPE3","strain":"strain YPE3","serovar":"","phylogroup":"A","MLST":761,"mash_cluster":22,"isolation_source":"Pork","isolation_country":"China","geographic_location":"China: Yangzhou","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4873760.0,"gc_content":50.664845,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":4880.0,"refseq_cds":4647.0,"sequencing_platform":"Oxford Nanopore MinION, Illumina","sequencing_depth":"80X","assembly_method":"Unicycler v. v0.4.4","sequencing_centers":"Yangzhou University","completion_date":"2019-10-03T00:00:00Z","collection_date":"Jun-2019","bioproject_accession":"PRJNA553293","biosample_accession":"SAMN12233487","genbank_accessions":"CP041452,CP041451,CP041453,CP041450","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Xiaoyu Lu","comments":"The emergence of plasmid-mediated tet(X) genes conferring resistance to tigecycline pose a public health concern. 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. 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In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2751,"n_metabolites":2021,"n_genes":1675,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.46743.json.json","assembly_accession":"GCA_005222305.1","genome_id":"562.46743","genome_name":"Escherichia coli strain 109","strain":"strain 109","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5542240.0,"gc_content":50.47517,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5943.0,"refseq_cds":5785.0,"sequencing_platform":"PacBio","sequencing_depth":"152x","assembly_method":"HGAP v. 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FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2732,"n_metabolites":1944,"n_genes":1454,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.45680.json.json","assembly_accession":"GCA_004301465.1","genome_id":"562.45680","genome_name":"Escherichia coli strain L725","strain":"strain L725","serovar":"","phylogroup":"B1","MLST":2161,"mash_cluster":26,"isolation_source":"feces","isolation_country":"China","geographic_location":"China: Hangzhou","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"32","body_sample_site":"","disease":"","genome_length":5069560.0,"gc_content":50.755962,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5130.0,"refseq_cds":4911.0,"sequencing_platform":"PacBio 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Three replicates were created for each compound, generating BZKR1G40, BZKR2G40, BZKR3G40, CETR1G40, CETR2G40, CETR3G40, CHXR1G20, CHXR2G20, CHXR3G20, COLR1G32, COLR2G32, COLR3G32 as well as an unadapted wild-type (WTG40). At the end of the experiment, the BZK-adapted bacteria were tolerant to 72-144 ug/ml of BZK, the CET-adapted bacteria were tolerant to 240 ug/ml of CET, the CHX-adapted bacteria were tolerant to 4.8-9.6 ug/ml of CHX, and the COL-adapted bacteria were tolerant to >300 ug/ml.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.46710.json.json","assembly_accession":"GCA_005153645.1","genome_id":"562.46710","genome_name":"Escherichia coli strain NRRL B-1109","strain":"strain NRRL B-1109","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4895196.0,"gc_content":50.471287,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5199.0,"refseq_cds":4711.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"412x","assembly_method":"HGAP v. 2","sequencing_centers":"Weill Cornell Medicine","completion_date":"2019-05-06T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA477598","biosample_accession":"SAMN09475312","genbank_accessions":"CP039753,CP039754","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"NRRL:B-1109","publication":"30718479","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism;biomaterial_provider:Zymo Research (https://www.zymoresearch.com/zymobiomics-community-standard);collected_by:Ehrlich, J. 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With m6A sites validated using PacBio, we train and test a new neural network-based method to detect m6A from nanopore data and show it can improve detection depending on sequence context.","n_reactions":2734,"n_metabolites":1947,"n_genes":1514,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.29131.json.json","assembly_accession":"GCA_003018215.1","genome_id":"562.29131","genome_name":"Escherichia coli strain 2015C-3905","strain":"strain 2015C-3905","serovar":"O181:H49","phylogroup":"B1","MLST":173,"mash_cluster":26,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5077047.0,"gc_content":50.861553,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4995.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"185.611x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Jun-2015","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08579573","genbank_accessions":"CP027371,CP027372","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2732,"n_metabolites":1939,"n_genes":1510,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.70601.json.json","assembly_accession":"GCA_016803855.1","genome_id":"562.70601","genome_name":"Escherichia coli strain RUT3575","strain":"strain RUT3575","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"Rectal swab of patient hospitalized for an unrelated disease","isolation_country":"Spain","geographic_location":"Spain: Barcelona","host_name":"Homo sapiens","host_health":"Human carrier","host_gender":"male","host_age":"63","body_sample_site":"","disease":"","genome_length":4986271.0,"gc_content":50.540073,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5000.0,"refseq_cds":4697.0,"sequencing_platform":"Illumina Miseq andOxford Nanopore MiniION","sequencing_depth":"64x","assembly_method":"Unicycler v. 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Escherichia coli IAI39 is a serotype O7:K1 strain from a urinary tract infection and will be used for comparative analysis.","n_reactions":2732,"n_metabolites":1948,"n_genes":1506,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.63857.json.json","assembly_accession":"GCA_014170695.1","genome_id":"562.63857","genome_name":"Escherichia coli strain 56.2","strain":"strain 56.2","serovar":"","phylogroup":"G","MLST":117,"mash_cluster":2,"isolation_source":"Turkey's","isolation_country":"Canada","geographic_location":"Canada","host_name":"Turkey","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5308724.0,"gc_content":50.721096,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5774.0,"refseq_cds":5092.0,"sequencing_platform":"Oxford Nanopore MinION","sequencing_depth":"277x","assembly_method":"Flye v. 2.6","sequencing_centers":"University of Guelph","completion_date":"2020-08-12T00:00:00Z","collection_date":"2016/2017","bioproject_accession":"PRJNA596173","biosample_accession":"SAMN13613897","genbank_accessions":"CP059922,CP059923,CP059924","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from Turkey's in Canada","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:fecal","comments":"Chromosomes and plasmids were assembled from E. coli isolated from Turkey's in Canada. 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Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. 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Sequencing of STECs from the agriculturally important region of the California central coast will address the diversity of genomic content and physiology of STECs compared to E. coli O157.","n_reactions":2731,"n_metabolites":1939,"n_genes":1520,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.29095.json.json","assembly_accession":"GCA_003019115.1","genome_id":"562.29095","genome_name":"Escherichia coli strain 07-4299","strain":"strain 07-4299","serovar":"O130:H11","phylogroup":"B1","MLST":297,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4972231.0,"gc_content":50.76367,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4884.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"120.31x","assembly_method":"FALCON v. v0.3.0","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08630964","genbank_accessions":"CP027462,CP027463","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2732,"n_metabolites":1940,"n_genes":1511,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.61514.json.json","assembly_accession":"GCA_013340825.1","genome_id":"562.61514","genome_name":"Escherichia coli strain TUM18781","strain":"strain TUM18781","serovar":"","phylogroup":"A","MLST":2040,"mash_cluster":26,"isolation_source":"Japanese patient with no history of travel abroad, we performed whole-genome sequencing using the illumina MiSeq and the Oxford Nanopore Technologies MinION","isolation_country":"Japan","geographic_location":"Japan:Tokyo, Meguro-ku","host_name":"Human, Homo sapiens","host_health":"no history of travel abroad, we performed whole-genome sequencing using the illumina MiSeq and the Oxford Nanopore Technologies MinION","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4803721.0,"gc_content":50.766792,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":4666.0,"refseq_cds":4419.0,"sequencing_platform":"MiSeq; 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This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.","n_reactions":2711,"n_metabolites":1877,"n_genes":1452,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"GCF_003956285.1.json.json","assembly_accession":"GCF_003956285.1","genome_id":"GCF_003956285.1","genome_name":"Escherichia 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In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.78282.json.json","assembly_accession":"GCA_019614135.1","genome_id":"562.78282","genome_name":"Escherichia coli strain 31HGR-CBG","strain":"strain 31HGR-CBG","serovar":"O101:H4","phylogroup":"A","MLST":44,"mash_cluster":22,"isolation_source":"urine","isolation_country":"Mexico","geographic_location":"Mexico","host_name":"Homo sapiens","host_health":"Urinary infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4820169.0,"gc_content":50.868523,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4963.0,"refseq_cds":4703.0,"sequencing_platform":"Illumina MiniSeq","sequencing_depth":"98x","assembly_method":"MEGAHIT v. 1.1.2","sequencing_centers":"INSTITUTO POLITECNICO NACIONAL","completion_date":"2021-08-16T00:00:00Z","collection_date":"2018","bioproject_accession":"PRJNA749581","biosample_accession":"SAMN20391559","genbank_accessions":"CP080645,CP080646","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"UPEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Laboratorio Interaccion Ambiente-Microorganismo","comments":"Antimicrobial resistance is a global concern around the world. Escherichia coli due to its genomic flexibility acquire antimicrobial resistance genes by horizontal gene transfer. 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Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2711,"n_metabolites":1877,"n_genes":1438,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"562.29113.json.json","assembly_accession":"GCA_003018675.1","genome_id":"562.29113","genome_name":"Escherichia coli strain 2014C-3550","strain":"strain 2014C-3550","serovar":"O118:H16","phylogroup":"B1","MLST":21,"mash_cluster":23,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5877677.0,"gc_content":50.672604,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":6183.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"104.403x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Apr-2014","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08579557","genbank_accessions":"CP027313,CP027314,CP027315,CP027316","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2731,"n_metabolites":1937,"n_genes":1514,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.361.json.json","assembly_accession":"GCA_013167715.1","genome_id":"83334.361","genome_name":"Escherichia coli O157:H7 strain F7349","strain":"O157:H7 strain F7349","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5615318.0,"gc_content":50.448578,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5900.0,"refseq_cds":5593.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"134x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN05360158","genbank_accessions":"CP038363,CP038364,CP038365","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CDC","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1938,"n_genes":1480,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.19208.json.json","assembly_accession":"GCA_002310675.1","genome_id":"562.19208","genome_name":"Escherichia coli strain 127","strain":"strain 127","serovar":"","phylogroup":"A","MLST":46,"mash_cluster":22,"isolation_source":"urinary tract infections","isolation_country":"United Kingdom","geographic_location":"United Kingdom: Scotland, Edinburgh","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":5091284.0,"gc_content":50.64,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5540.0,"refseq_cds":5402.0,"sequencing_platform":"PacBio","sequencing_depth":"20x","assembly_method":"De-novo v. Celera Assembler 8.4","sequencing_centers":"The Roslin Institute","completion_date":"2017-09-18T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA402083","biosample_accession":"SAMN07618123","genbank_accessions":"CP023377,CP023378,CP023379,CP023380,CP023381,CP023382","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from urinary tract infections in dogs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.","n_reactions":2731,"n_metabolites":1937,"n_genes":1477,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_020883355.1.json.json","assembly_accession":"GCF_020883355.1","genome_id":"GCF_020883355.1","genome_name":"Escherichia coli","strain":"RIVM_C037166","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN22569031","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1938,"n_genes":1521,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"83334.493.json.json","assembly_accession":"GCA_017165295.1","genome_id":"83334.493","genome_name":"Escherichia coli O157:H7 strain Z903","strain":"O157:H7 strain Z903","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"Bovine Faeces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5613910.0,"gc_content":50.480522,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5828.0,"refseq_cds":5427.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"108.36536654520619x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327591","genbank_accessions":"CP062755,CP062756,CP062757","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:IPRAVE Consortium","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.68638.json.json","assembly_accession":"GCA_016026195.1","genome_id":"562.68638","genome_name":"Escherichia coli strain FDAARGOS_946 strain Not applicable","strain":"","serovar":"","phylogroup":"E","MLST":7444,"mash_cluster":19,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5389640.0,"gc_content":50.408524,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5436.0,"refseq_cds":5107.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"644x","assembly_method":"SMRT v. 6.0.0, HGAP v. 4, SPAdes v. 3.11.1","sequencing_centers":"US Food and Drug Administration","completion_date":"2020-12-14T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN13450476","genbank_accessions":"CP065607,CP065606,CP065608,CP065609","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"DSM:4779","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:DSMZ","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2711,"n_metabolites":1877,"n_genes":1435,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"2697517.3.json.json","assembly_accession":"GCA_016803935.1","genome_id":"2697517.3","genome_name":"Escherichia coli O84:H7 strain Trh52","strain":"O84:H7 strain Trh52","serovar":"O84:H7","phylogroup":"B2","MLST":28,"mash_cluster":6,"isolation_source":"feces","isolation_country":"Norway","geographic_location":"Norway: Trondelag","host_name":"Homo sapiens","host_health":"Diarrhea","host_gender":"","host_age":"<5","body_sample_site":"","disease":"","genome_length":4926859.0,"gc_content":50.58391,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4863.0,"refseq_cds":4617.0,"sequencing_platform":"Oxford Nanopore MiniION; Illumina 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This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2731,"n_metabolites":1938,"n_genes":1484,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.74553.json.json","assembly_accession":"GCA_017639145.1","genome_id":"562.74553","genome_name":"Escherichia coli strain ABW_A32","strain":"strain ABW_A32","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"waste water","isolation_country":"Switzerland","geographic_location":"Switzerland: Basel","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4805372.0,"gc_content":50.69283,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":4840.0,"refseq_cds":4526.0,"sequencing_platform":"Illumina MiniSeq, Oxford Nanopore MinIon","sequencing_depth":"100x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"University of Zurich","completion_date":"2021-03-30T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA689691","biosample_accession":"SAMN17214838","genbank_accessions":"CP067303,CP067304,CP067305,CP067306","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture;collected_by:ILS, University of Zurich","comments":"Long- and short-read sequencing of fosfomycin-resistant and ESBL-producing Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae, Klebsiella variicola) to determine the genetic environment of resistance genes","n_reactions":2733,"n_metabolites":1939,"n_genes":1513,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHE","country":"Switzerland"},{"gem_file":"GCF_000464955.2.json.json","assembly_accession":"GCF_000464955.2","genome_id":"GCF_000464955.2","genome_name":"Escherichia coli O104:H21 str. 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In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_900636245.1.json.json","assembly_accession":"GCF_900636245.1","genome_id":"GCF_900636245.1","genome_name":"Escherichia coli","strain":"NCTC9107","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMEA3451127","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1935,"n_genes":1525,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1033813.3.json.json","assembly_accession":"GCA_000214765.2","genome_id":"1033813.3","genome_name":"Escherichia coli NA114","strain":"NA114","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4935241.0,"gc_content":51.16,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4889.0,"refseq_cds":4873.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Pathogen Biology Laboratory, Department of Biotechnology, University of Hyderabad","completion_date":"2011-05-25T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA66975","biosample_accession":"SAMN02603711","genbank_accessions":"CP002797","refseq_accessions":"-","genome_status":"Complete","taxon_id":1033813.0,"organism_name":"Escherichia coli NA114","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"-","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Bacterial culture archived with Pathogen Biology Laboratory, Department of Biotechnology, University of Hyderabad, India","n_reactions":2732,"n_metabolites":1943,"n_genes":1455,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"544404.4.json.json","assembly_accession":"GCA_000022225.1","genome_id":"544404.4","genome_name":"Escherichia coli O157:H7 str. 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EHEC attaches and effaces to cells in the large intestine.There are numerous differences that distinguish O157:H7 from K-12, hundreds of them associated with genomic islands in either strain, including at least 9 large PAIs in O157:H7 that encode virulence factors. A type III secretion system, the locus of enterocyte effacement, numerous toxins and adhesins, as well as fimbrial gene clusters and iron uptake systems are found in these PAIs. Pathogenicity genes are also found on the plasmid pO157.i&gt\\;Escherichia coli O157:H7 str. TW14359. This strain was isolated from spinach during the E. coli outbreak in 2006 and will be used for comparative analysis.","n_reactions":2731,"n_metabolites":1938,"n_genes":1484,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13960.json.json","assembly_accession":"GCF_900096805.1","genome_id":"562.13960","genome_name":"Escherichia coli strain 107","strain":"strain 107","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4638126.0,"gc_content":50.83,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4520.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UNIVERSITY OF EXETER","completion_date":"2017-01-02T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB15352","biosample_accession":"SAMEA4444108","genbank_accessions":"LT615375","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli\u2019s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a \u2018trade-up\u2019 is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic\\; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.","n_reactions":2732,"n_metabolites":1935,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.46718.json.json","assembly_accession":"GCA_005221625.1","genome_id":"562.46718","genome_name":"Escherichia coli strain 137","strain":"strain 137","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5555913.0,"gc_content":50.501026,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5969.0,"refseq_cds":5802.0,"sequencing_platform":"PacBio","sequencing_depth":"190x","assembly_method":"HGAP v. 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This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.46069.json.json","assembly_accession":"GCA_004771235.1","genome_id":"562.46069","genome_name":"Escherichia coli strain PF9285","strain":"strain PF9285","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":22,"isolation_source":"Rectal swab from healthy swiss fattening veal calves","isolation_country":"Switzerland","geographic_location":"Switzerland","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5441892.0,"gc_content":50.670025,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5696.0,"refseq_cds":5363.0,"sequencing_platform":"Illumina MiSeq; MinION Oxford Nanopore","sequencing_depth":"100.0x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"University of Bern","completion_date":"2019-04-11T00:00:00Z","collection_date":"2017","bioproject_accession":"PRJNA530748","biosample_accession":"SAMN11333172","genbank_accessions":"CP038791,CP038792,CP038793,CP038794,CP038795","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"ST10","substrain":"","additional_metadata":"sample_type:Pure culture","comments":"Investigation of the unknown mechanism of trimethoprim resistance in the Escherichia coli strain PF9285. The dissemination of the gene dfrA35 and other resistance genes may further jeopardize the efficacy of antibiotics.","n_reactions":2734,"n_metabolites":1939,"n_genes":1554,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHE","country":"Switzerland"},{"gem_file":"562.46735.json.json","assembly_accession":"GCA_005221965.1","genome_id":"562.46735","genome_name":"Escherichia coli strain 138","strain":"strain 138","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5555919.0,"gc_content":50.50106,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5969.0,"refseq_cds":5802.0,"sequencing_platform":"PacBio","sequencing_depth":"192x","assembly_method":"HGAP v. 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This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.78023.json.json","assembly_accession":"GCA_019428525.1","genome_id":"562.78023","genome_name":"Escherichia coli strain Dog168","strain":"strain Dog168","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"dog, faeces","isolation_country":"Kenya","geographic_location":"Kenya","host_name":"dog","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5112272.0,"gc_content":50.77099,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5132.0,"refseq_cds":4861.0,"sequencing_platform":"Illumina MiSeq; PacBio Sequel","sequencing_depth":"300x","assembly_method":"SMRT Link v. 6.0","sequencing_centers":"University of Veterinary Sciences Brno","completion_date":"2021-07-31T00:00:00Z","collection_date":"2009","bioproject_accession":"PRJNA748602","biosample_accession":"SAMN20339880","genbank_accessions":"CP080116","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The whole-genome sequences of Escherichia coli ST131 H30Rx subclone of human, animal and environmental origin","n_reactions":2732,"n_metabolites":1943,"n_genes":1469,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"KEN","country":"Kenya"},{"gem_file":"562.70756.json.json","assembly_accession":"GCA_016903375.1","genome_id":"562.70756","genome_name":"Escherichia coli strain FDAARGOS_1286 strain Not applicable","strain":"","serovar":"","phylogroup":"G","MLST":117,"mash_cluster":2,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:WA","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5168953.0,"gc_content":50.77771,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":5187.0,"refseq_cds":4881.0,"sequencing_platform":"Pacbio; Illumina","sequencing_depth":"1520.67x","assembly_method":"SMRT v. 8.0.0, HGAP v. 4","sequencing_centers":"US Food and Drug Administration","completion_date":"2021-02-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN16357428","genbank_accessions":"CP069893,CP069894,CP069895,CP069896,CP069897,CP069898,CP069899,CP069900","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_1286","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:ARMADA","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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Carbapenems are considered a last-resort antibiotic, however the spread of plasmid-encoded carbapenemases such as the New-Delhi Metallo-beta-Lactamase (blaNDM-1) challenges their effectiveness. E. coli ST101 is an emerging, atypical multidrug resistant ExPEC lineage, highly associated with the carriage of blaNDM-1. In this study we analysed the phylogeny and antimicrobial resistance of ST101 isolates from the UK and India.","n_reactions":2733,"n_metabolites":1941,"n_genes":1499,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"IND","country":"India"},{"gem_file":"562.58460.json.json","assembly_accession":"GCA_011492985.1","genome_id":"562.58460","genome_name":"Escherichia coli strain T16R","strain":"strain T16R","serovar":"","phylogroup":"A","MLST":48,"mash_cluster":22,"isolation_source":"","isolation_country":"China","geographic_location":"China: Henan","host_name":"pet dog","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5035953.0,"gc_content":50.632504,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5099.0,"refseq_cds":4776.0,"sequencing_platform":"Illumina; Oxford Nanopore MinilON","sequencing_depth":"80.0x","assembly_method":"unicycler v. v. 0.4.4","sequencing_centers":"Henan Agricultural University","completion_date":"2020-03-19T00:00:00Z","collection_date":"2019-08","bioproject_accession":"PRJNA594788","biosample_accession":"SAMN13530296","genbank_accessions":"CP046716,CP046717,CP046718,CP046719","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:faecal sample","comments":"whole genome sequences of an E. coli strain harboring tet(X4) and mcr-1","n_reactions":2732,"n_metabolites":1939,"n_genes":1508,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"GCF_003999795.1.json.json","assembly_accession":"GCF_003999795.1","genome_id":"GCF_003999795.1","genome_name":"Escherichia coli","strain":"L65","serovar":"","phylogroup":"B1","MLST":3076,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN10623993","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2732,"n_metabolites":1937,"n_genes":1515,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.33455.json.json","assembly_accession":"GCA_003346835.1","genome_id":"562.33455","genome_name":"Escherichia coli strain Es_ST80_L1_NDM_10_2017","strain":"strain Es_ST80_L1_NDM_10_2017","serovar":"O2:H7","phylogroup":"B2","MLST":80,"mash_cluster":6,"isolation_source":"rectal swab","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"Human, Homo sapiens","host_health":"screen","host_gender":"male","host_age":"64","body_sample_site":"","disease":"","genome_length":5313245.0,"gc_content":50.328903,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5634.0,"refseq_cds":5386.0,"sequencing_platform":"Oxford Nanopore MiniION; Illumina HiSeq","sequencing_depth":"500.0x","assembly_method":"miniasm v. 0.2-r168-dirty; racon","sequencing_centers":"Public Health England","completion_date":"2018-07-31T00:00:00Z","collection_date":"26-Oct-2017","bioproject_accession":"PRJNA482002","biosample_accession":"SAMN09710898","genbank_accessions":"CP031215,CP031216","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"ST80","substrain":"","additional_metadata":"collected_by:Hospital in London","comments":"Inc L/M NDM plasmids are currently relatively rare, yet we have observed a number (in multiple bacterial genera) of late. This project involved sequencing a number of isolates with Inc L/M NDM plasmids using both minION and Illumina platforms to accurately determine the plasmid sequences and assess any potential transmission between organisms. The project included both epidemiologically related and unrelated isolates.","n_reactions":2733,"n_metabolites":1946,"n_genes":1463,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.50512.json.json","assembly_accession":"GCA_007108505.1","genome_id":"562.50512","genome_name":"Escherichia coli strain 95","strain":"strain 95","serovar":"","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"blood","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"Bloodstream infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5279974.0,"gc_content":50.63761,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5478.0,"refseq_cds":5213.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"151x","assembly_method":"HGAP v. 4","sequencing_centers":"Duke University","completion_date":"2019-07-18T00:00:00Z","collection_date":"2010","bioproject_accession":"PRJNA551684","biosample_accession":"SAMN12163098","genbank_accessions":"CP041535,CP041536,CP041537","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Vance G. Fowler Jr.","comments":"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2752,"n_metabolites":2019,"n_genes":1676,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.61487.json.json","assembly_accession":"GCA_013315715.1","genome_id":"562.61487","genome_name":"Escherichia coli strain SCU-171","strain":"strain SCU-171","serovar":"","phylogroup":"G","MLST":657,"mash_cluster":2,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5370190.0,"gc_content":50.76628,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5522.0,"refseq_cds":5168.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"74x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-06-10T00:00:00Z","collection_date":"2017","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14943544","genbank_accessions":"CP054363,CP054364,CP054365,CP054366,CP054367","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2733,"n_metabolites":1942,"n_genes":1471,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"469008.117.json.json","assembly_accession":"GCA_019754155.1","genome_id":"469008.117","genome_name":"Escherichia coli BL21(DE3) strain BL21(DE3) strain BL21(DE3) strain BL21(DE3)","strain":"BL21(DE3) strain BL21(DE3) strain BL21(DE3) strain BL21(DE3)","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"Not Applicable","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4498411.0,"gc_content":50.797337,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4480.0,"refseq_cds":4274.0,"sequencing_platform":"Illumina MiniSeq","sequencing_depth":"60X","assembly_method":"SPAdes v. 3.9.0","sequencing_centers":"Gennova Biopharmaceuticals Ltd","completion_date":"2021-08-25T00:00:00Z","collection_date":"2021","bioproject_accession":"PRJNA749934","biosample_accession":"SAMN20703503","genbank_accessions":"CP081489","refseq_accessions":"","genome_status":"Complete","taxon_id":469008.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Whole Genome Sequencing of Competent cells","n_reactions":2733,"n_metabolites":1935,"n_genes":1511,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.11293.json.json","assembly_accession":"GCF_001677495.1","genome_id":"562.11293","genome_name":"Escherichia coli strain 09-00049","strain":"strain 09-00049","serovar":"O168","phylogroup":"B1","MLST":718,"mash_cluster":26,"isolation_source":"lettuce","isolation_country":"USA","geographic_location":"USA:MI","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5511850.0,"gc_content":50.5,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5784.0,"refseq_cds":5393.0,"sequencing_platform":"PacBio RS","sequencing_depth":"169X","assembly_method":"SMRT Portal HGAP v. 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Six isolates were distributed for sequencing: 4 Salmonella enterica subsp. enterica serovar Typhimurium and 2 E.coli O157:H7 isolates.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.59215.json.json","assembly_accession":"GCA_012221365.1","genome_id":"562.59215","genome_name":"Escherichia coli strain 8-3-DC15","strain":"strain 8-3-DC15","serovar":"","phylogroup":"B1","MLST":270,"mash_cluster":24,"isolation_source":"colonoscopy","isolation_country":"Australia","geographic_location":"Australia: Canberra","host_name":"Human, Homo sapiens","host_health":"Crohn's disease","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5142316.0,"gc_content":50.824005,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5456.0,"refseq_cds":5140.0,"sequencing_platform":"Illumina NextSeq; Oxford Nanopore MiniION","sequencing_depth":"34x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Monash University","completion_date":"2020-04-09T00:00:00Z","collection_date":"2010","bioproject_accession":"PRJNA616136","biosample_accession":"SAMN14482837","genbank_accessions":"CP050862,CP050863,CP050864","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"29266651","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:David Gordon","comments":"Completion of two ST270 EIEC genomes for use as references","n_reactions":2732,"n_metabolites":1940,"n_genes":1460,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"2067421.3.json.json","assembly_accession":"GCA_016756455.1","genome_id":"2067421.3","genome_name":"Escherichia coli O25:H4 strain 18044","strain":"O25:H4 strain 18044","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"persons infected with HNoV","isolation_country":"Japan","geographic_location":"Japan","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5256311.0,"gc_content":50.861755,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5285.0,"refseq_cds":4988.0,"sequencing_platform":"Sequel; GridION X5; MiSeq","sequencing_depth":"56x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"Fukuoka Institute of Health and Environmental Sciences","completion_date":"2020-12-22T00:00:00Z","collection_date":"2018","bioproject_accession":"PRJDB9114","biosample_accession":"SAMD00199041","genbank_accessions":"AP022326,AP022327,AP022328,AP022329,AP022330,AP022331","refseq_accessions":"","genome_status":"Complete","taxon_id":2067421.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"32866241","isolation_comments":"derived from persons infected with HNoV","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The proportion of Enterobacteriaceae such as Escherichia coli increases in human gut microbiota after infection with norovirus (HNoV). This shows that HNoV-infected persons are susceptible to Enterobacteriaceae. When a HNoV-infected person is further infected with Enterobacteriaceae possessing strong pathogenicity and/or showing multiple antimicrobial-resistances, health condition of the person may be worse. Aims of this project are to evaluate pathogenicity and antimicrobial resistance of Enterobacteriaceae which derived from persons infected with HNoV.","n_reactions":2732,"n_metabolites":1943,"n_genes":1470,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"JPN","country":"Japan"},{"gem_file":"562.13962.json.json","assembly_accession":"GCF_900096825.1","genome_id":"562.13962","genome_name":"Escherichia coli strain 104","strain":"strain 104","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4638126.0,"gc_content":50.39,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4481.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UNIVERSITY OF EXETER","completion_date":"2017-01-02T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB15352","biosample_accession":"SAMEA4444105","genbank_accessions":"LT615374","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. 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The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic\\; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.","n_reactions":2732,"n_metabolites":1935,"n_genes":1560,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.58143.json.json","assembly_accession":"GCA_010365485.1","genome_id":"562.58143","genome_name":"Escherichia coli strain 53","strain":"strain 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Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1940,"n_genes":1489,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.61725.json.json","assembly_accession":"GCA_013376575.1","genome_id":"562.61725","genome_name":"Escherichia coli strain ARL09/232","strain":"strain ARL09/232","serovar":"","phylogroup":"B1","MLST":7505,"mash_cluster":26,"isolation_source":"urine","isolation_country":"New Zealand","geographic_location":"New Zealand","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5322305.0,"gc_content":50.690235,"contigs":9.0,"chromosomes":1.0,"plasmids":8.0,"patric_cds":5439.0,"refseq_cds":5125.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore MiniION","sequencing_depth":"100.0x","assembly_method":"Unicycler v. 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Previously published short-read DNA sequence of pMG101 showed that it was a 183.5 Kb IncHI plasmid, where a Tn7-mediated transposition of pco/sil resistance genes into the chromosome of the E. coli K-12 J53 host strain had occurred. We noticed differences in streptomycin resistance and plasmid size between two stocks of E. coli K-12 J53 pMG101 we possessed, which we had obtained from two different laboratories. We sequenced the strains to identify whether they were in fact identical. Long-read sequencing (PacBio) of the two strains shows significant differences between them. pMG101-A is a non-transmissible 383 Kb closed-circular plasmid consisting of an IncHI2 plasmid sequence fused to an IncFI/FIIA plasmid. pMG101-B is a mobile closed-circular 168 Kb IncFI/FIIA plasmid. Sequence identity of pMG101-B with the fused IncFI/IncFIIA region of pMG101-A was >99%. Assembled host sequence reads of pMG101-B showed Tn7-mediated transposition of pco/sil into the E. coli J53 chromosome between yhiM and yhiN. Long read sequence data in combination with laboratory experiments has demonstrated large scale changes in pMG101, loss of resistance and conjugation function, and movement of resistance genes into the chromosome- similar to plasmid variations seen in recently isolated plasmids- suggesting that changes in the plasmids in the laboratory strains are similar to those that occur naturally. This study emphasises the importance of utilising long read sequencing technologies of plasmids and host strains at the earliest opportunity.","n_reactions":2752,"n_metabolites":2027,"n_genes":1744,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.9022.json.json","assembly_accession":"GCF_001542675.2","genome_id":"562.9022","genome_name":"Escherichia coli strain MRE600","strain":"strain MRE600","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":24,"isolation_source":"environmental","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4980796.0,"gc_content":50.78,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5428.0,"refseq_cds":5026.0,"sequencing_platform":"Pacific 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Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.50217.json.json","assembly_accession":"GCA_002951755.1","genome_id":"562.50217","genome_name":"Escherichia coli strain 13TMH22","strain":"strain 13TMH22","serovar":"","phylogroup":"B1","MLST":453,"mash_cluster":26,"isolation_source":"urine","isolation_country":"Hong Kong","geographic_location":"Hong Kong","host_name":"Human, Homo sapiens","host_health":"Urinary infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4901615.0,"gc_content":50.783016,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5150.0,"refseq_cds":5100.0,"sequencing_platform":"PacBio","sequencing_depth":"175.0x","assembly_method":"HGAP v. 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Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.","n_reactions":2731,"n_metabolites":1939,"n_genes":1490,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"511145.185.json.json","assembly_accession":"GCF_000801205.1","genome_id":"511145.185","genome_name":"Escherichia coli str. K-12 substr. MG1655","strain":"str. K-12 substr. 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With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2751,"n_metabolites":2021,"n_genes":1710,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.13752.json.json","assembly_accession":"GCF_001900615.1","genome_id":"562.13752","genome_name":"Escherichia coli strain D2","strain":"strain D2","serovar":"","phylogroup":"A","MLST":373,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4876911.0,"gc_content":50.66,"contigs":3.0,"chromosomes":3.0,"plasmids":"","patric_cds":4874.0,"refseq_cds":4599.0,"sequencing_platform":"Illumina Miseq; Roche 454 GS Junior","sequencing_depth":"30-80x","assembly_method":"Newbler v. 2.7","sequencing_centers":"Nanjing Agricultural University","completion_date":"2016-12-12T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA269191","biosample_accession":"SAMN03252420","genbank_accessions":"CP010137,CP010138,CP010139","refseq_accessions":"NZ_CP010137.1,NZ_CP010138.1,NZ_CP010139.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"env_biome:faeces","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments","n_reactions":2734,"n_metabolites":1939,"n_genes":1522,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13958.json.json","assembly_accession":"GCF_900096785.1","genome_id":"562.13958","genome_name":"Escherichia coli strain 102","strain":"strain 102","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4638126.0,"gc_content":50.82,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4512.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"UNIVERSITY OF EXETER","completion_date":"2017-01-02T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB15352","biosample_accession":"SAMEA4444103","genbank_accessions":"LT615372","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli\u2019s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a \u2018trade-up\u2019 is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic\\; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.","n_reactions":2732,"n_metabolites":1935,"n_genes":1560,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.13740.json.json","assembly_accession":"GCF_001900375.1","genome_id":"562.13740","genome_name":"Escherichia coli strain D7","strain":"strain D7","serovar":"","phylogroup":"B1","MLST":224,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4827779.0,"gc_content":50.93,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4767.0,"refseq_cds":4557.0,"sequencing_platform":"Illumina Miseq; Roche 454 GS Junior","sequencing_depth":"30-80x","assembly_method":"Newbler v. 2.7","sequencing_centers":"Nanjing Agricultural University","completion_date":"2016-12-12T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA269191","biosample_accession":"SAMN03252425","genbank_accessions":"CP010150","refseq_accessions":"NZ_CP010150.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"env_biome:faeces","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments","n_reactions":2731,"n_metabolites":1935,"n_genes":1507,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.50218.json.json","assembly_accession":"GCA_002951795.1","genome_id":"562.50218","genome_name":"Escherichia coli strain 13C1079T","strain":"strain 13C1079T","serovar":"","phylogroup":"B1","MLST":155,"mash_cluster":26,"isolation_source":"feces","isolation_country":"Hong Kong","geographic_location":"Hong Kong","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4938616.0,"gc_content":50.603024,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5113.0,"refseq_cds":5031.0,"sequencing_platform":"PacBio","sequencing_depth":"179.0x","assembly_method":"HGAP v. 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We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced these samples with shotgun metagenomics at high depth (~200 million reads per sample). Alongside this, we cultured multiple single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data.","n_reactions":2734,"n_metabolites":1937,"n_genes":1538,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"83334.349.json.json","assembly_accession":"GCA_013167395.1","genome_id":"83334.349","genome_name":"Escherichia coli O157:H7 strain NE122","strain":"O157:H7 strain NE122","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA:Nebraska","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5547743.0,"gc_content":50.54468,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5803.0,"refseq_cds":5504.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"243x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11229495","genbank_accessions":"CP038319,CP038320","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1940,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"1954351.6.json.json","assembly_accession":"GCA_001021635.2","genome_id":"1954351.6","genome_name":"Escherichia coli APEC O2-211 strain APEC O2-211","strain":"APEC O2-211 strain APEC O2-211","serovar":"serovar fully","phylogroup":"G","MLST":117,"mash_cluster":2,"isolation_source":"air sac","isolation_country":"United States","geographic_location":"United States","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5112508.0,"gc_content":50.63,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5139.0,"refseq_cds":4661.0,"sequencing_platform":"454; Illumina","sequencing_depth":"","assembly_method":"Newbler v. 2.7; Velvet v. 1.1; ELANDv2e v.","sequencing_centers":"Iowa State University","completion_date":"2017-02-08T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA219410","biosample_accession":"SAMN03761814","genbank_accessions":"CP006834","refseq_accessions":"","genome_status":"Complete","taxon_id":1954351.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from the air sac of a chicken","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting turkeys, layers, and broilers. Here we describe the sequence of first APEC O2 serotype fully complete and closed. This O2 strain was isolated from the air sac of a chicken. Functional analysis of the genome will enhance the community\u2019s knowledge of the pathogenesis of avian pathogenic E. coli.","n_reactions":2732,"n_metabolites":1941,"n_genes":1485,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.61491.json.json","assembly_accession":"GCA_013315995.1","genome_id":"562.61491","genome_name":"Escherichia coli strain SCU-104","strain":"strain SCU-104","serovar":"","phylogroup":"A","MLST":8125,"mash_cluster":21,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5245988.0,"gc_content":50.71895,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5308.0,"refseq_cds":4960.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"47x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"Santa Clara University","completion_date":"2020-06-10T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609769","genbank_accessions":"CP053284,CP053285","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. 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MG1655 mutant strain isolated after growth in presence of sub-inhibitory concentrations of citral","n_reactions":2732,"n_metabolites":1936,"n_genes":1555,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"ESP","country":"Spain"},{"gem_file":"562.79202.json.json","assembly_accession":"GCA_019970955.1","genome_id":"562.79202","genome_name":"Escherichia coli strain CX12","strain":"strain CX12","serovar":"","phylogroup":"A","MLST":3202,"mash_cluster":22,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada: Alberta","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4868473.0,"gc_content":51.07511,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4973.0,"refseq_cds":4681.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"84x","assembly_method":"flye v. 2.8.2","sequencing_centers":"Agriculture & Agri-Food Canada","completion_date":"2021-09-14T00:00:00Z","collection_date":"2014/2015","bioproject_accession":"PRJNA716667","biosample_accession":"SAMN18446044","genbank_accessions":"CP073719","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The presence of locus of heat resistance is a common way of screening heat resistance in E.coli, however harboring LHR does not always confer extreme heat resistance suggesting other genetic components may play a role in heat resistance. WGS was performed to determine genetic determinants in E.coli for different levels of heat resistance and determine the evolution regarding the emergence of heat resistant strains of E.coli in a meat plant setting.","n_reactions":2733,"n_metabolites":1941,"n_genes":1505,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.7249.json.json","assembly_accession":"GCF_000988465.1","genome_id":"562.7249","genome_name":"Escherichia coli strain SQ2203","strain":"strain SQ2203","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"United States","geographic_location":"United States","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4605301.0,"gc_content":50.78,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4587.0,"refseq_cds":4313.0,"sequencing_platform":"Illumina","sequencing_depth":"50x","assembly_method":"CLCBio Genomics Workbench v. 7.0.4","sequencing_centers":"AstraZeneca","completion_date":"2015-05-06T00:00:00Z","collection_date":"2008","bioproject_accession":"PRJNA241498","biosample_accession":"SAMN03276542","genbank_accessions":"CP011324","refseq_accessions":"NZ_CP011324.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:single cell","comments":"Genomic sequence of a ribosomal deletion construct of E. coli MG1655","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.13745.json.json","assembly_accession":"GCF_001900475.1","genome_id":"562.13745","genome_name":"Escherichia coli strain H10","strain":"strain H10","serovar":"","phylogroup":"B1","MLST":297,"mash_cluster":26,"isolation_source":"river water","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4805164.0,"gc_content":50.76,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4758.0,"refseq_cds":4558.0,"sequencing_platform":"Illumina Miseq; 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The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2733,"n_metabolites":1944,"n_genes":1513,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"481805.51.json.json","assembly_accession":"GCA_016864475.1","genome_id":"481805.51","genome_name":"Escherichia coli ATCC 8739","strain":"ATCC 8739","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4920540.0,"gc_content":50.700024,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4919.0,"refseq_cds":4673.0,"sequencing_platform":"PacBio; 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rate.","n_reactions":2752,"n_metabolites":2024,"n_genes":1729,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.58148.json.json","assembly_accession":"GCA_010365425.1","genome_id":"562.58148","genome_name":"Escherichia coli strain 10","strain":"strain 10","serovar":"","phylogroup":"A","MLST":656,"mash_cluster":21,"isolation_source":"environment","isolation_country":"Switzerland","geographic_location":"Switzerland","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5126529.0,"gc_content":50.77207,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5274.0,"refseq_cds":4913.0,"sequencing_platform":"Oxford Nanopore/illumina minniseq","sequencing_depth":"80x","assembly_method":"unicycler v. 0.4.8","sequencing_centers":"University of 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coli","country_iso":"","country":""},{"gem_file":"562.76466.json.json","assembly_accession":"GCA_018884545.1","genome_id":"562.76466","genome_name":"Escherichia coli strain DS26-1","strain":"strain DS26-1","serovar":"","phylogroup":"C","MLST":423,"mash_cluster":25,"isolation_source":"feces","isolation_country":"Saudi Arabia","geographic_location":"Saudi Arabia","host_name":"Homo sapiens","host_health":"diarrhea","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5294813.0,"gc_content":50.785458,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5342.0,"refseq_cds":"","sequencing_platform":"PacBio RSII","sequencing_depth":"29.67x","assembly_method":"Canu v. v.1.2","sequencing_centers":"University of Maryland, School of 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3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"Jul-2005","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08579574","genbank_accessions":"CP027373,CP027374,CP027375","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2732,"n_metabolites":1938,"n_genes":1521,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia 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producing extended spectrum beta-lactamases (ESBL). Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. The major goal of the study was to characterize cefotaxime-resistant bacteria isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2732,"n_metabolites":1943,"n_genes":1506,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.33453.json.json","assembly_accession":"GCA_003344465.1","genome_id":"562.33453","genome_name":"Escherichia coli strain MCJCHV-1","strain":"strain MCJCHV-1","serovar":"O75:H5:K1","phylogroup":"B2","MLST":1193,"mash_cluster":6,"isolation_source":"CSF","isolation_country":"USA","geographic_location":"USA: Nashville, TN","host_name":"Human, Homo sapiens","host_health":"Neonatal bacterial meningitis","host_gender":"female","host_age":"30 days","body_sample_site":"","disease":"","genome_length":5042521.0,"gc_content":50.59128,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5213.0,"refseq_cds":5113.0,"sequencing_platform":"PacBio","sequencing_depth":"320.0x","assembly_method":"Canu v. 1.5","sequencing_centers":"University of Georgia","completion_date":"2018-07-27T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA476955","biosample_accession":"SAMN09462202","genbank_accessions":"CP030111,CP030112,CP030113,CP030114,CP030115,CP030116","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"NMEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"host_disease_outcome:death","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Monroe Carell Jr. Children's Hospital at Vanderbilt University","comments":"Neonatal meningitis Escherichia coli (NMEC) is the second-leading cause of neonatal bacterial meningitis (NBM) worldwide. We report the genome sequence of a multi-drug resistant, NMEC serotype O75:H5:K1 strain mcjchv-1 (NMEC-O75), which resulted in the death of an infant. The O75 serogroup is rare among NMEC isolates.","n_reactions":2733,"n_metabolites":1947,"n_genes":1468,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.19203.json.json","assembly_accession":"GCA_002310575.1","genome_id":"562.19203","genome_name":"Escherichia coli strain 317","strain":"strain 317","serovar":"","phylogroup":"B2","MLST":127,"mash_cluster":6,"isolation_source":"urinary tract infections","isolation_country":"United Kingdom","geographic_location":"United Kingdom: Scotland, Edinburgh","host_name":"Dog, Canis lupus familiaris","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Urinary tract infection","genome_length":5135913.0,"gc_content":50.54,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5255.0,"refseq_cds":5129.0,"sequencing_platform":"PacBio","sequencing_depth":"20x","assembly_method":"De-novo v. Celera Assembler 8.9","sequencing_centers":"The Roslin Institute","completion_date":"2017-09-18T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA402083","biosample_accession":"SAMN07618128","genbank_accessions":"CP023357,CP023358","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from urinary tract infections in dogs","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.","n_reactions":2733,"n_metabolites":1946,"n_genes":1450,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_905332365.1.json.json","assembly_accession":"GCF_905332365.1","genome_id":"GCF_905332365.1","genome_name":"Escherichia coli","strain":"","serovar":"","phylogroup":"B2","MLST":127,"mash_cluster":6,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMEA8065773","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2733,"n_metabolites":1946,"n_genes":1451,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.22323.json.json","assembly_accession":"GCA_002634895.1","genome_id":"562.22323","genome_name":"Escherichia coli strain FDAARGOS_434","strain":"FDAARGOS_434","serovar":"","phylogroup":"A","MLST":167,"mash_cluster":21,"isolation_source":"Rectal","isolation_country":"Canada","geographic_location":"Canada:BC","host_name":"Human, Homo sapiens","host_health":"Screening","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5059202.0,"gc_content":50.88,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5219.0,"refseq_cds":5095.0,"sequencing_platform":"PacBio; Illumina","sequencing_depth":"24.87x","assembly_method":"Celera v. 8.2, SPAdes v. 3.6.0","sequencing_centers":"US Food and Drug Administration","completion_date":"2017-10-18T00:00:00Z","collection_date":"2014-08","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN07312478","genbank_accessions":"CP023870,CP023868,CP023869,CP023872,CP023871","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_434","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:BC Centre for Disease Control","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: \u2022Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. \u2022Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). \u2022Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2711,"n_metabolites":1877,"n_genes":1480,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.22307.json.json","assembly_accession":"GCA_002591135.1","genome_id":"562.22307","genome_name":"Escherichia coli strain FDAARGOS_448","strain":"FDAARGOS_448","serovar":"","phylogroup":"D","MLST":405,"mash_cluster":16,"isolation_source":"urine","isolation_country":"Canada","geographic_location":"Canada:BC","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5446833.0,"gc_content":50.55,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5653.0,"refseq_cds":5561.0,"sequencing_platform":"PacBio; Illumina","sequencing_depth":"20.01x","assembly_method":"Celera v. 8.2, SPAdes v. 3.6.0","sequencing_centers":"US Food and Drug Administration","completion_date":"2017-10-18T00:00:00Z","collection_date":"2014-08","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN07312492","genbank_accessions":"CP023960,CP023959,CP023961,CP023957,CP023958","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_448","publication":"","isolation_comments":"","other_clinical":"host_description:Not applicable","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:BC Centre for Disease Control","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: \u2022Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. \u2022Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). \u2022Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2711,"n_metabolites":1877,"n_genes":1454,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.7388.json.json","assembly_accession":"GCF_001183685.1","genome_id":"562.7388","genome_name":"Escherichia coli strain DH1Ec169","strain":"strain DH1Ec169","serovar":"","phylogroup":"A","MLST":1060,"mash_cluster":21,"isolation_source":"","isolation_country":"USA","geographic_location":"USA: Walnut Creek","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4609522.0,"gc_content":50.82,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4602.0,"refseq_cds":4348.0,"sequencing_platform":"Illumina","sequencing_depth":">200x","assembly_method":"Geneious v. 8.1.2","sequencing_centers":"Joint Genome Institute","completion_date":"2015-07-21T00:00:00Z","collection_date":"01-Jul-2014","bioproject_accession":"PRJNA290012","biosample_accession":"SAMN03863378","genbank_accessions":"CP012127","refseq_accessions":"NZ_CP012127.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"C","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Whole genome sequencing to detect off-target changes (if any) after CRISPR-Cas9 editings","n_reactions":2732,"n_metabolites":1940,"n_genes":1558,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.28209.json.json","assembly_accession":"GCA_002903105.1","genome_id":"562.28209","genome_name":"Escherichia coli strain ECONIH5","strain":"strain ECONIH5","serovar":"","phylogroup":"A","MLST":399,"mash_cluster":22,"isolation_source":"patients and hospital environment","isolation_country":"United States","geographic_location":"United States","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":6028201.0,"gc_content":50.755207,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":6590.0,"refseq_cds":6406.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"234x","assembly_method":"canu v. 1.4","sequencing_centers":"NIH","completion_date":"2018-01-29T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA430813","biosample_accession":"SAMN06040386","genbank_accessions":"CP026202,CP026208,CP026203,CP026206,CP026207,CP026204,CP026205,CP026209","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from patients and hospital environment","other_clinical":"","other_environmental":"env_biome:wastewater/sludge","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.","n_reactions":2732,"n_metabolites":1944,"n_genes":1514,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.60464.json.json","assembly_accession":"GCA_013166935.1","genome_id":"562.60464","genome_name":"Escherichia coli strain NEBExpress","strain":"strain NEBExpress","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4476291.0,"gc_content":50.80791,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4440.0,"refseq_cds":4200.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"219x","assembly_method":"HGAP v. 3","sequencing_centers":"New England Biolabs","completion_date":"2020-05-26T00:00:00Z","collection_date":"2010-01-01","bioproject_accession":"PRJNA341475","biosample_accession":"SAMN14933842","genbank_accessions":"CP053599","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"28654677","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Closed and finished genome of NEB 5-alpha, an immediate fhuA derivative of (E. coli K-12) DH5alpha.","n_reactions":2731,"n_metabolites":1931,"n_genes":1506,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.55131.json.json","assembly_accession":"GCA_009873355.1","genome_id":"562.55131","genome_name":"Escherichia coli strain NCCP 15739","strain":"strain NCCP 15739","serovar":"","phylogroup":"E","MLST":-1,"mash_cluster":19,"isolation_source":"feces","isolation_country":"South Korea","geographic_location":"South Korea: Busan","host_name":"Human, Homo sapiens","host_health":"diarrhea","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5567406.0,"gc_content":50.486385,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":6125.0,"refseq_cds":5562.0,"sequencing_platform":"PacBio; IonTorrent","sequencing_depth":"181.0x","assembly_method":"SPAdes v. 3.1","sequencing_centers":"Korea Centers for Disease Control and Prevention","completion_date":"2020-01-14T00:00:00Z","collection_date":"19-jul-2010","bioproject_accession":"PRJNA555173","biosample_accession":"SAMN12302771","genbank_accessions":"CP041747,CP041748","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Korea National Institute of Health","comments":"A clinical isolate of the genus Escherichia","n_reactions":2731,"n_metabolites":1948,"n_genes":1496,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"KOR","country":"South Korea"},{"gem_file":"1355100.3.json.json","assembly_accession":"GCA_000493755.1","genome_id":"1355100.3","genome_name":"Escherichia coli JJ1886","strain":"JJ1886","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"Patient","isolation_country":"United States","geographic_location":"United States","host_name":"Human, Homo sapiens","host_health":"fatal urosepsis","host_gender":"","host_age":"","body_sample_site":"","disease":"Urosepsis","genome_length":5308284.0,"gc_content":50.7667,"contigs":6.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5323.0,"refseq_cds":5049.0,"sequencing_platform":"454; Illumina; PacBio","sequencing_depth":"50x","assembly_method":"MIRA v. 3.9.9; ABySS v. 1.3.4; PBJelly v.","sequencing_centers":"Statens Serum Institut","completion_date":"2013-10-29T00:00:00Z","collection_date":"2007","bioproject_accession":"PRJNA218163","biosample_accession":"SAMN02603887","genbank_accessions":"CP006784.1,CP006789.1,CP006785.1,CP006788.1,CP006786.1,CP006787.1","refseq_accessions":"NC_022648.1,NC_022651.1,NC_022661.1,NC_022650.1,NC_022649.1,NC_022662.1","genome_status":"Complete","taxon_id":1355100.0,"organism_name":"Escherichia coli JJ1886","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"24309736","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"Bacilli","motility":"Motile","temperature_range":"Mesophilic","optimal_temperature":"37C","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"Complete Genome of the Epidemic and Highly Virulent CTX-M-15-Producing H30-Rx Subclone of Escherichia coli ST131.","n_reactions":2732,"n_metabolites":1943,"n_genes":1472,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.50216.json.json","assembly_accession":"GCA_002951775.1","genome_id":"562.50216","genome_name":"Escherichia coli strain 13C1065T","strain":"strain 13C1065T","serovar":"","phylogroup":"A","MLST":4542,"mash_cluster":22,"isolation_source":"feces","isolation_country":"Hong Kong","geographic_location":"Hong Kong","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5378331.0,"gc_content":50.501205,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":5840.0,"refseq_cds":5600.0,"sequencing_platform":"PacBio","sequencing_depth":"161.0x","assembly_method":"HGAP v. NOV-2016","sequencing_centers":"The University of Hong Kong","completion_date":"2018-02-05T00:00:00Z","collection_date":"Aug-2013","bioproject_accession":"PRJNA361032","biosample_accession":"SAMN06219550","genbank_accessions":"CP019259,CP019260,CP019261,CP019262,CP019263,CP019264,CP019265,CP019266","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism;biomaterial_provider:Ho Pak-Leung","comments":"oqxAB positive Escherichia coli Genome sequencing and assembly","n_reactions":2733,"n_metabolites":1942,"n_genes":1517,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"HKG","country":"Hong Kong"},{"gem_file":"591946.4.json.json","assembly_accession":"GCA_000284495.1","genome_id":"591946.4","genome_name":"Escherichia coli LF82","strain":"LF82","serovar":"","phylogroup":"B2","MLST":135,"mash_cluster":6,"isolation_source":"patient with Crohn's disease","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"Crohn's disease","host_gender":"","host_age":"","body_sample_site":"","disease":"Enterocolitis","genome_length":4773108.0,"gc_content":50.7,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4555.0,"refseq_cds":4376.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Genoscope","completion_date":"2009-01-27T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA33825","biosample_accession":"SAMEA3138414","genbank_accessions":"CU651637","refseq_accessions":"NC_011993.1","genome_status":"Complete","taxon_id":591946.0,"organism_name":"Escherichia coli LF82","pathovar":"AIEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from a patient with Crohn's disease","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"Yes","temperature_range":"Mesophilic","optimal_temperature":"-","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"Escherichia coli LF82. Escherichia coli LF82 is an adherent-invasive E. coli (AIEC) strain isolated from a patient with Crohn's disease. AIEC strains adhere and colonize the intestinal mucosa and are able to invade and replicate in intestinal epithelial cells. This strain will be used for comparative analysis with other E. coli strains.","n_reactions":2733,"n_metabolites":1946,"n_genes":1449,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"930406.3.json.json","assembly_accession":"GCA_000827105.1","genome_id":"930406.3","genome_name":"Escherichia coli O157:H16 Santai","strain":"O157:H16 Santai","serovar":"","phylogroup":"D","MLST":1011,"mash_cluster":20,"isolation_source":"rectum of clinical healthy adult layingduck","isolation_country":"China","geographic_location":"China: Santai, mianyang city, sichuan province","host_name":"Duck, Anas platyrhynchos","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5104557.0,"gc_content":50.6,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4843.0,"refseq_cds":0.0,"sequencing_platform":"Illumina HiSeq","sequencing_depth":"275.0x","assembly_method":"SOAPdenovo v. 2.4","sequencing_centers":"BGI","completion_date":"2015-01-21T00:00:00Z","collection_date":"2011-08-03","bioproject_accession":"PRJNA240262","biosample_accession":"SAMN02673556","genbank_accessions":"CP007592.1","refseq_accessions":"NZ_CP007592.1","genome_status":"Complete","taxon_id":930406.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Presence and isolation of a special pathogenic EHEC O157 in clinical healthy adult laying duck","n_reactions":2732,"n_metabolites":1942,"n_genes":1497,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.66554.json.json","assembly_accession":"GCA_014295295.1","genome_id":"562.66554","genome_name":"Escherichia coli strain G5","strain":"strain G5","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":22,"isolation_source":"feces from healthy individual","isolation_country":"Germany","geographic_location":"Germany","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5052732.0,"gc_content":50.94036,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":5153.0,"refseq_cds":4786.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"696x","assembly_method":"Unicycler v. 0.4.8","sequencing_centers":"University of Arkansas for Medical Sciences","completion_date":"2020-08-25T00:00:00Z","collection_date":"1954","bioproject_accession":"PRJNA650131","biosample_accession":"SAMN15693148","genbank_accessions":"CP060065,CP060070,CP060072,CP060069,CP060071,CP060068,CP060066,CP060067","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:isolate;passage_history:multiple passages","comments":"Some Escherichia coli strains have been shown to provide beneficial effects on human and animal health. Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.","n_reactions":2734,"n_metabolites":1940,"n_genes":1529,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"331111.12.json.json","assembly_accession":"GCA_000017745.1","genome_id":"331111.12","genome_name":"Escherichia coli E24377A","strain":"E24377A","serovar":"serovar O139","phylogroup":"B1","MLST":1132,"mash_cluster":26,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Diarrhea","genome_length":5249288.0,"gc_content":50.6,"contigs":7.0,"chromosomes":1.0,"plasmids":6.0,"patric_cds":5196.0,"refseq_cds":4991.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"TIGR","completion_date":"2007-09-11T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA13960","biosample_accession":"","genbank_accessions":"CP000800,CP000796,CP000797,CP000798,CP000799,CP000801,CP000795","refseq_accessions":"NC_009801,NC_009787,NC_009788,NC_009789,NC_009790,NC_009791,NC_009786","genome_status":"Complete","taxon_id":331111.0,"organism_name":"Escherichia coli E24377A","pathovar":"ETEC","antimicrobial_resistance":"","culture_collection":"","publication":"18676672","isolation_comments":"obtained from Maj. Carl Brinkley at Walter Reed Army Institute of Research","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"Yes","temperature_range":"Mesophilic","optimal_temperature":"37","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"Escherichia coli strain E24377A. This is an enterotoxigenic E. coli (ETEC) strain (E24377A\\; serotype O139:H28) and was obtained from Maj. Carl Brinkley at Walter Reed Army Institute of Research. ETEC is the leading cause of traveler's diarrhea, characterized by a large volume of watery diarrhea.  ETEC primarily colonizes  the small intestine by way of the pili. Colonization factor antigens (CFA) in this strain include two pili types (coli surface antigen one and three\\; CS1 and CS3). Additionally two toxins are thought to be responsible for the virulence, heat stable and heat labile enterotoxins. Other virulence factors include the O139:H28 serotype as well as genes carried on a number of uncharacterized plasmids. The stocks used for genomic DNA preparation were obtained from a master- and  production cGMP cell bank available at WRAIR/NMRC. Pathogenicity has been confirmed in human challenge experiments.","n_reactions":2711,"n_metabolites":1877,"n_genes":1470,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.55128.json.json","assembly_accession":"GCA_009866945.1","genome_id":"562.55128","genome_name":"Escherichia coli strain 29957","strain":"strain 29957","serovar":"","phylogroup":"A","MLST":167,"mash_cluster":21,"isolation_source":"Bovine adult","isolation_country":"France","geographic_location":"France","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5536879.0,"gc_content":50.54396,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5848.0,"refseq_cds":5659.0,"sequencing_platform":"PacBio","sequencing_depth":"30.0x","assembly_method":"CANU v. 1.6","sequencing_centers":"University College Dublin","completion_date":"2020-01-14T00:00:00Z","collection_date":"03-May-2007","bioproject_accession":"PRJNA433820","biosample_accession":"SAMN08522730","genbank_accessions":"CP026932,CP026933,CP026934","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Cell Culture","comments":"Genetic diversity of E. coli isolated from diseased animals","n_reactions":2731,"n_metabolites":1942,"n_genes":1542,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"FRA","country":"France"},{"gem_file":"562.79629.json.json","assembly_accession":"GCA_020149465.1","genome_id":"562.79629","genome_name":"Escherichia coli strain SUISSEKPC3NDM5","strain":"strain SUISSEKPC3NDM5","serovar":"","phylogroup":"A","MLST":361,"mash_cluster":22,"isolation_source":"urine","isolation_country":"Switzerland","geographic_location":"Switzerland: Basel","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5614810.0,"gc_content":50.82749,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":5936.0,"refseq_cds":5498.0,"sequencing_platform":"Oxford Nanopore MinION; 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Therefore, this study screened for (LHR) among meat borne E. coli isolated from different stages of meat processing. 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The fate and potential horizontal gene transfer of those genes into the host microbiome will have a crucial bearing on the eventual health risk of exposure to antibiotic resistance genes. In the present study, the effects of antibiotics on the in vivo transfer of \ud835\udefd-lactam resistance genes were evaluated in a mouse model by characterizing the microbiome in excreted feces. Mice were dosed with Escherichia coli, Salmonella enterica serovars Heidelberg or Bredeney referred to as donors. The in vivo transfer of the antibiotic resistance genes (blaTEM-1B, blaCMY-2, blaCTX-M1, etc.) from these donor bacteria to an exogenously introduced or endogenously present Escherichia coli strains (i.e. recipients) in the mouse gut was evaluated with or without a clinical dosage of ampicillin.","n_reactions":2732,"n_metabolites":1936,"n_genes":1547,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.59071.json.json","assembly_accession":"GCA_009950475.1","genome_id":"562.59071","genome_name":"Escherichia coli strain STEC367 strain not applicable","strain":"","serovar":"","phylogroup":"B1","MLST":1611,"mash_cluster":26,"isolation_source":"Raw mutton","isolation_country":"China","geographic_location":"China: 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AUGUST-2016; MeDuSa v. 1.6;","sequencing_centers":"Sao Paulo State University","completion_date":"2019-01-29T00:00:00Z","collection_date":"2015","bioproject_accession":"PRJNA511007","biosample_accession":"SAMN10748603","genbank_accessions":"CP035339,CP035335,CP035345,CP035346,CP035347,CP035348,CP035336,CP035337,CP035338,CP035340,CP035341,CP035342","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"Susceptible;Resistant;Intermediate","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Hospital das Clinincas Botucatu","comments":"11 uropathogenic Escherichia coli genomes isolated in \"Hospital da Clinicas de Botucatu\", Sao Paulo - Brazil","n_reactions":2711,"n_metabolites":1877,"n_genes":1459,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BRA","country":"Brazil"},{"gem_file":"562.58441.json.json","assembly_accession":"GCA_011306375.1","genome_id":"562.58441","genome_name":"Escherichia coli strain 15RDA-Livestock feces-ECO087","strain":"strain 15RDA-Livestock feces-ECO087","serovar":"","phylogroup":"B1","MLST":224,"mash_cluster":26,"isolation_source":"feces","isolation_country":"South Korea","geographic_location":"South Korea: Goyang-si, Gyeonggi-do","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5572079.0,"gc_content":50.817997,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5847.0,"refseq_cds":5605.0,"sequencing_platform":"Illumina MiSeq","sequencing_depth":"8.0x","assembly_method":"RAST v. 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V1.1.3","sequencing_centers":"Ministry of Public Health-Thailand","completion_date":"2021-07-19T00:00:00Z","collection_date":"Not collected","bioproject_accession":"PRJNA668870","biosample_accession":"SAMN17771329","genbank_accessions":"CP078587","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Department of Disease Control, Ministry of Public Health","comments":"Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand","n_reactions":2730,"n_metabolites":1935,"n_genes":1451,"n_exchange":331,"n_with_gpr":2284,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"THA","country":"Thailand"},{"gem_file":"562.45389.json.json","assembly_accession":"GCA_004114395.1","genome_id":"562.45389","genome_name":"Escherichia coli strain RS571","strain":"strain RS571","serovar":"","phylogroup":"F","MLST":648,"mash_cluster":9,"isolation_source":"rectal swab","isolation_country":"Bangladesh","geographic_location":"Bangladesh: Dhaka","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5348132.0,"gc_content":50.346157,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5468.0,"refseq_cds":5164.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"627.0x","assembly_method":"Unicycler v. 0.4.6","sequencing_centers":"Cardiff University","completion_date":"2019-01-25T00:00:00Z","collection_date":"16-May-2018","bioproject_accession":"PRJNA509034","biosample_accession":"SAMN10535911","genbank_accessions":"CP034389,CP034390,CP034391,CP034392","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:Pure culture one microbial species","comments":"First report of mcr-1 carried by IncH12 plasmid in Escherichia coli from human normal flora in Bangladesh","n_reactions":2732,"n_metabolites":1941,"n_genes":1511,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BGD","country":"Bangladesh"},{"gem_file":"83334.350.json.json","assembly_accession":"GCA_013167435.1","genome_id":"83334.350","genome_name":"Escherichia coli O157:H7 strain NE 1169-1","strain":"O157:H7 strain NE 1169-1","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle feces","isolation_country":"USA","geographic_location":"USA:Nebraska","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5757794.0,"gc_content":50.49698,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":6073.0,"refseq_cds":5771.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"236x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"2000","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN05360232","genbank_accessions":"CP038324,CP038327,CP038325,CP038326","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1940,"n_genes":1481,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"1403831.3.json.json","assembly_accession":"GCA_000499485.1","genome_id":"1403831.3","genome_name":"Escherichia coli str. K-12 substr. MC4100","strain":"str. K-12 substr. 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This was done by variant calling, variant incorporation and manual curation of changes to the reference annotation.","n_reactions":2732,"n_metabolites":1935,"n_genes":1529,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"741093.3.json.json","assembly_accession":"GCA_000262125.1","genome_id":"741093.3","genome_name":"Escherichia coli Xuzhou21","strain":"Xuzhou21","serovar":"","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"China","geographic_location":"China","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Hemolytic uremic syndrome (HUS)","genome_length":5516736.0,"gc_content":50.3828,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5540.0,"refseq_cds":5183.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention","completion_date":"2011-04-08T00:00:00Z","collection_date":"1999","bioproject_accession":"PRJNA45823","biosample_accession":"SAMN02603645","genbank_accessions":"CP001925.1,CP001927.1,CP001926.1","refseq_accessions":"NC_017906.1,NC_017903.1,NC_017907.1","genome_status":"Complete","taxon_id":741093.0,"organism_name":"Escherichia coli Xuzhou21","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"22558360","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"Bacilli","motility":"No","temperature_range":"Mesophilic","optimal_temperature":"","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"-","n_reactions":2731,"n_metabolites":1938,"n_genes":1486,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.33990.json.json","assembly_accession":"GCA_003443815.1","genome_id":"562.33990","genome_name":"Escherichia coli strain E308","strain":"strain E308","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":22,"isolation_source":"Broiler chicken farm","isolation_country":"China","geographic_location":"China","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5166180.0,"gc_content":50.639004,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5588.0,"refseq_cds":5402.0,"sequencing_platform":"PacBio","sequencing_depth":"50.0x","assembly_method":"SOAPdenovo v. 2.03","sequencing_centers":"Sichuan Agricultural University","completion_date":"2018-09-04T00:00:00Z","collection_date":"2014","bioproject_accession":"PRJNA478107","biosample_accession":"SAMN09499316","genbank_accessions":"CP030281,CP030282,CP030283,CP030284,CP030285","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Sichuan Agricultural University","comments":"Complete Sequence of Four Plasmids from Escherichia coli Carrying Multidrug Resistance Genes from Broiler Chickens Farm in China","n_reactions":2732,"n_metabolites":1940,"n_genes":1509,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"2810404.4.json.json","assembly_accession":"GCA_017570585.1","genome_id":"2810404.4","genome_name":"Escherichia coli O7:H4 strain MIN14","strain":"O7:H4 strain MIN14","serovar":"O7:H4","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"upper respiratory tract","isolation_country":"Poland","geographic_location":"Poland: Bialystok","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5032262.0,"gc_content":50.624413,"contigs":11.0,"chromosomes":1.0,"plasmids":10.0,"patric_cds":5124.0,"refseq_cds":4783.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore MinION","sequencing_depth":"100x","assembly_method":"Unicycler hybrid assembly v. v0.4.8-beta","sequencing_centers":"Medical University of Bialystok","completion_date":"2021-03-23T00:00:00Z","collection_date":"2016-07-21","bioproject_accession":"PRJNA700422","biosample_accession":"SAMN17831486","genbank_accessions":"CP069646,CP069647,CP069648,CP069649,CP069651,CP069652,CP069653,CP069654,CP069655,CP069656,CP069650","refseq_accessions":"","genome_status":"Complete","taxon_id":2810404.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"ST-93","substrain":"","additional_metadata":"","comments":"Genome and mobilome structures of extraintestinal E. coli strains isolated in Poland","n_reactions":2733,"n_metabolites":1933,"n_genes":1523,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"POL","country":"Poland"},{"gem_file":"562.51577.json.json","assembly_accession":"GCA_008823185.1","genome_id":"562.51577","genome_name":"Escherichia coli strain PK6","strain":"strain PK6","serovar":"O162:O89:H10","phylogroup":"A","MLST":1695,"mash_cluster":21,"isolation_source":"Healthy pig from farm","isolation_country":"Cuba","geographic_location":"Cuba: Matanzas","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4789129.0,"gc_content":50.79721,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":4848.0,"refseq_cds":4582.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore MiniION","sequencing_depth":"100.0x","assembly_method":"Unicycler v. 0.4.4","sequencing_centers":"University of Bern","completion_date":"2019-10-04T00:00:00Z","collection_date":"Jul-2016","bioproject_accession":"PRJNA559061","biosample_accession":"SAMN12512712","genbank_accessions":"CP042588,CP042589,CP042590,CP042591,CP042592","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from pig in Cuba harboring blaCTX-M-32/IncX1 plasmid","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"ST1695","substrain":"","additional_metadata":"sample_type:whole organism;biomaterial_provider:National Centre for Animal and Plant Health (CENSA). Autopista Nacional y Carretera de Jamaica, San Jose de las Lajas Mayabeque, Cuba.;collected_by:Carelia Martha Marrero Moreno;identified_by:Rosa Elena Hernandez Fillor","comments":"First complete genome of a multidrug-resistant E. coli isolated from pig in Cuba harboring blaCTX-M-32/IncX1 plasmid.","n_reactions":2752,"n_metabolites":2026,"n_genes":1662,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CUB","country":"Cuba"},{"gem_file":"562.50522.json.json","assembly_accession":"GCA_007109425.1","genome_id":"562.50522","genome_name":"Escherichia coli strain 131","strain":"strain 131","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5398583.0,"gc_content":50.763596,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5667.0,"refseq_cds":5380.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"50x","assembly_method":"HGAP v. 4","sequencing_centers":"Duke University","completion_date":"2019-07-18T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA551684","biosample_accession":"SAMN12163088","genbank_accessions":"CP041578,CP041579,CP041580","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Deverick Anderson","comments":"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (\u226525%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.","n_reactions":2732,"n_metabolites":1943,"n_genes":1471,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.68602.json.json","assembly_accession":"GCA_015843075.1","genome_id":"562.68602","genome_name":"Escherichia coli strain W60","strain":"strain W60","serovar":"","phylogroup":"A","MLST":167,"mash_cluster":21,"isolation_source":"Urine sample","isolation_country":"China","geographic_location":"China: Jinan, The Second Hospital of Shandong University","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5043978.0,"gc_content":50.835354,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5050.0,"refseq_cds":4698.0,"sequencing_platform":"PacBio","sequencing_depth":"120X","assembly_method":"HGAP v. 3","sequencing_centers":"ShanDong University","completion_date":"2020-12-08T00:00:00Z","collection_date":"2018-07-02","bioproject_accession":"PRJNA642190","biosample_accession":"SAMN15391109","genbank_accessions":"CP058342,CP058343,CP058344","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:genomic assembly","comments":"E. coli W60 sequencing assembly results, including chromosome and two plasmids","n_reactions":2732,"n_metabolites":1942,"n_genes":1538,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"83334.411.json.json","assembly_accession":"GCA_016458925.1","genome_id":"83334.411","genome_name":"Escherichia coli O157:H7 strain ECP19-598","strain":"O157:H7 strain ECP19-598","serovar":"serovar O157","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5772391.0,"gc_content":50.450012,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":6037.0,"refseq_cds":5595.0,"sequencing_platform":"PacBio Sequel","sequencing_depth":"100X","assembly_method":"Spades v. 3.12.1","sequencing_centers":"FDA Center for Food Safety and Applied Nutrition","completion_date":"2021-01-03T00:00:00Z","collection_date":"2019","bioproject_accession":"PRJNA681235","biosample_accession":"SAMN16946946","genbank_accessions":"CP066753,CP066754,CP066755","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CDC","comments":"Whole genome sequencing of cultured foodborne bacterial pathogens collected from the 2019 GenomeTrakr/PulseNet proficiency testing exercise. 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We believe this is occurring through a mobile genetic element amplification mechanism with concomitant outer membrane porin disruption.","n_reactions":2732,"n_metabolites":1943,"n_genes":1471,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.78279.json.json","assembly_accession":"GCA_019599065.1","genome_id":"562.78279","genome_name":"Escherichia coli strain TOP10","strain":"strain TOP10","serovar":"","phylogroup":"A","MLST":1060,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"Not Applicable","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4513232.0,"gc_content":50.739094,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4551.0,"refseq_cds":4311.0,"sequencing_platform":"Illumina MiniSeq","sequencing_depth":"60X","assembly_method":"SPAdes v. 3.9.0","sequencing_centers":"Gennova Biopharmaceuticals Ltd","completion_date":"2021-08-15T00:00:00Z","collection_date":"2021","bioproject_accession":"PRJNA749934","biosample_accession":"SAMN20587896","genbank_accessions":"CP080620","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Whole Genome Sequencing of Competent cells","n_reactions":2732,"n_metabolites":1940,"n_genes":1542,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"2810408.4.json.json","assembly_accession":"GCA_017570665.1","genome_id":"2810408.4","genome_name":"Escherichia coli O176:H45 strain MIN9","strain":"O176:H45 strain MIN9","serovar":"O176:H45","phylogroup":"A","MLST":6856,"mash_cluster":22,"isolation_source":"wound","isolation_country":"Poland","geographic_location":"Poland: Bialystok","host_name":"Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5032799.0,"gc_content":50.551075,"contigs":10.0,"chromosomes":1.0,"plasmids":9.0,"patric_cds":5126.0,"refseq_cds":4789.0,"sequencing_platform":"Illumina MiSeq; Oxford Nanopore MinION","sequencing_depth":"100x","assembly_method":"Unicycler hybrid assembly v. v0.4.8-beta","sequencing_centers":"Medical University of Bialystok","completion_date":"2021-03-23T00:00:00Z","collection_date":"2018-03-05","bioproject_accession":"PRJNA700422","biosample_accession":"SAMN17831482","genbank_accessions":"CP069682,CP069683,CP069684,CP069686,CP069687,CP069688,CP069689,CP069690,CP069691,CP069685","refseq_accessions":"","genome_status":"Complete","taxon_id":2810408.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"ST-6856","substrain":"","additional_metadata":"","comments":"Genome and mobilome structures of extraintestinal E. coli strains isolated in Poland","n_reactions":2734,"n_metabolites":1941,"n_genes":1511,"n_exchange":331,"n_with_gpr":2288,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"POL","country":"Poland"},{"gem_file":"562.46745.json.json","assembly_accession":"GCA_005222345.1","genome_id":"562.46745","genome_name":"Escherichia coli strain 106","strain":"strain 106","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5531321.0,"gc_content":50.469788,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5918.0,"refseq_cds":5760.0,"sequencing_platform":"PacBio","sequencing_depth":"197x","assembly_method":"HGAP v. 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RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1939,"n_genes":1485,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"562.61497.json.json","assembly_accession":"GCA_013315935.1","genome_id":"562.61497","genome_name":"Escherichia coli strain SCU-120","strain":"strain SCU-120","serovar":"","phylogroup":"F","MLST":648,"mash_cluster":9,"isolation_source":"rectal swab from healthy college student","isolation_country":"USA","geographic_location":"USA: California","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5457435.0,"gc_content":50.55694,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":6180.0,"refseq_cds":5202.0,"sequencing_platform":"Illumina MiSeq, Oxford Nanopore MiniION","sequencing_depth":"35x","assembly_method":"Flye v. 2.6","sequencing_centers":"Santa Clara University","completion_date":"2020-06-10T00:00:00Z","collection_date":"2016","bioproject_accession":"PRJNA624897","biosample_accession":"SAMN14609780","genbank_accessions":"CP054335,CP054336,CP054337,CP054338,CP054339,CP054340,CP054341,CP054342","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:whole organism","comments":"This study explores genomic diversity in commensal E. coli isolates from healthy college students. 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FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.","n_reactions":2731,"n_metabolites":1936,"n_genes":1515,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NLD","country":"Netherlands"},{"gem_file":"562.33465.json.json","assembly_accession":"GCA_003352425.1","genome_id":"562.33465","genome_name":"Escherichia coli strain FORC 064","strain":"strain FORC 064","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"cucumber","isolation_country":"South Korea","geographic_location":"South Korea: Chungcheongbuk-do","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5093756.0,"gc_content":50.368942,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5270.0,"refseq_cds":5259.0,"sequencing_platform":"PacBio","sequencing_depth":"274x","assembly_method":"SMRT Analysis v. 2.3.0","sequencing_centers":"Seoul National University","completion_date":"2018-08-01T00:00:00Z","collection_date":"01-Jan-2014","bioproject_accession":"PRJNA395606","biosample_accession":"SAMN07411561","genbank_accessions":"CP022664,CP023732,CP023733,CP023734","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Chungcheongbuk-do Institute of Health Environment","comments":"As a food-borne pathogen, Escherichia coli exhibits profound food-poisoning activities with high prevalence, every year. 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In so doing, many off-target mutations leftover from the original recoding efforts were corrected as either direct reversions, or more often compensatory adaptive mutations. Additionally, mutations known to be endemic to all MG1655-derived strains, including the mutation to rph which causes pyrimidine starvation in minimal media, were corrected or compensated for. We present here the genome of a recoded C321 strain with no TAG codons adapted for fast growth in M9 and other defined media.","n_reactions":2732,"n_metabolites":1938,"n_genes":1559,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.33716.json.json","assembly_accession":"GCA_003367575.1","genome_id":"562.33716","genome_name":"Escherichia coli strain ST410","strain":"strain ST410","serovar":"","phylogroup":"C","MLST":410,"mash_cluster":25,"isolation_source":"urine","isolation_country":"Ghana","geographic_location":"Ghana: Tamale","host_name":"Human, Homo sapiens","host_health":"Urinary tract infection","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4938383.0,"gc_content":50.539185,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5173.0,"refseq_cds":5020.0,"sequencing_platform":"PacBio","sequencing_depth":"142.7x","assembly_method":"HGAP v. 3","sequencing_centers":"Tokyo Medical and Dental University","completion_date":"2018-08-08T00:00:00Z","collection_date":"Jun-2015","bioproject_accession":"PRJNA473419","biosample_accession":"SAMN09273490","genbank_accessions":"CP029630,CP029631","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Tamale Teaching Hospital","comments":"AMR-GhanaOur aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana\uff0c and further to explore major resistance mechanisms involved.","n_reactions":2736,"n_metabolites":1950,"n_genes":1540,"n_exchange":331,"n_with_gpr":2290,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GHA","country":"Ghana"},{"gem_file":"562.76469.json.json","assembly_accession":"GCA_018966785.1","genome_id":"562.76469","genome_name":"Escherichia coli strain MSI001","strain":"strain MSI001","serovar":"","phylogroup":"A","MLST":2854,"mash_cluster":22,"isolation_source":"","isolation_country":"China","geographic_location":"China:Guangzhou","host_name":"Mus musculus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5013406.0,"gc_content":50.80598,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5060.0,"refseq_cds":4755.0,"sequencing_platform":"PacBio; Illumina HiSeq","sequencing_depth":"120.0x","assembly_method":"HGAP v. 2.3","sequencing_centers":"Southern Medical University","completion_date":"2021-06-20T00:00:00Z","collection_date":"2016-10-12","bioproject_accession":"PRJNA736706","biosample_accession":"SAMN19656307","genbank_accessions":"CP076645","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"We have identified a novel strain of E. coli that can induce severe sepsis.","n_reactions":2752,"n_metabolites":2026,"n_genes":1750,"n_exchange":331,"n_with_gpr":2306,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"83334.515.json.json","assembly_accession":"GCA_017357545.1","genome_id":"83334.515","genome_name":"Escherichia coli O157:H7 strain TT12A strain not applicable","strain":"","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"feces","isolation_country":"Japan","geographic_location":"Japan: Yokosuka","host_name":"Homo sapiens","host_health":"Hemorrhagic colitis","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5593719.0,"gc_content":50.44313,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5893.0,"refseq_cds":5586.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"154x","assembly_method":"HGAP v. v2.3","sequencing_centers":"University of Texas at San Antonio","completion_date":"2021-03-16T00:00:00Z","collection_date":"1994-10-25","bioproject_accession":"PRJNA530317","biosample_accession":"SAMN11310480","genbank_accessions":"CP038496,CP038497","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:National Children's Medical Research Center","comments":"The goal of this study is to comprehensively analyze the genomes and transcriptomes of Enterohemorrhagic Escherichia coli of the O157:H7 serotype and derived atypical non-shigatoxigenic strains","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"JPN","country":"Japan"},{"gem_file":"1401688.5.json.json","assembly_accession":"GCA_001021615.1","genome_id":"1401688.5","genome_name":"Escherichia coli APEC O18 strain APEC O18","strain":"APEC O18 strain APEC O18","serovar":"serovar fully","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"pericardium/lung","isolation_country":"United States","geographic_location":"United States","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5006568.0,"gc_content":50.7,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4961.0,"refseq_cds":4581.0,"sequencing_platform":"454; 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The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.28199.json.json","assembly_accession":"GCA_002899495.1","genome_id":"562.28199","genome_name":"Escherichia coli strain CAR","strain":"strain CAR","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"Essential oils isolation","isolation_country":"Spain","geographic_location":"Spain","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4544646.0,"gc_content":50.80211,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4443.0,"refseq_cds":"","sequencing_platform":"Illumina HiSeq","sequencing_depth":"95.48x","assembly_method":"Burrows-Wheeler Alignment Tool v.","sequencing_centers":"Facultad de Veterinaria, Instituto Agroalimentario de Aragon (IA2)","completion_date":"2018-01-25T00:00:00Z","collection_date":"2014-08-05","bioproject_accession":"PRJNA430164","biosample_accession":"SAMN08367764","genbank_accessions":"CP026026","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:single cell","comments":"Eschericia coli str.K-12 substr. 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Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.","n_reactions":2731,"n_metabolites":1939,"n_genes":1485,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"83334.345.json.json","assembly_accession":"GCA_013167315.1","genome_id":"83334.345","genome_name":"Escherichia coli O157:H7 strain SS NE 1040-1","strain":"O157:H7 strain SS NE 1040-1","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle feces","isolation_country":"USA","geographic_location":"USA:Nebraska","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5630167.0,"gc_content":50.453396,"contigs":4.0,"chromosomes":1.0,"plasmids":3.0,"patric_cds":5944.0,"refseq_cds":5663.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"228x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"2000","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN05360230","genbank_accessions":"CP038305,CP038308,CP038306,CP038307","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2732,"n_metabolites":1941,"n_genes":1486,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.50634.json.json","assembly_accession":"GCA_007998005.1","genome_id":"562.50634","genome_name":"Escherichia coli strain NCYU-29-19 strain not collected","strain":"","serovar":"","phylogroup":"A","MLST":-1,"mash_cluster":22,"isolation_source":"","isolation_country":"Taiwan","geographic_location":"Taiwan","host_name":"Pig, Sus scrofa","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4793217.0,"gc_content":50.878983,"contigs":9.0,"chromosomes":1.0,"plasmids":8.0,"patric_cds":6438.0,"refseq_cds":4678.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"80x","assembly_method":"CCBGpipe v. 1","sequencing_centers":"national health research institutes","completion_date":"2019-08-15T00:00:00Z","collection_date":"2017","bioproject_accession":"PRJNA558860","biosample_accession":"SAMN12500849","genbank_accessions":"CP042606,CP042607,CP042608,CP042609,CP042610,CP042611,CP042612,CP042613,CP042614","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:National Chiayi University","comments":"To survey the prevalence of mcr-like genes in diseased animals and patients in Taiwan","n_reactions":2738,"n_metabolites":1980,"n_genes":1585,"n_exchange":331,"n_with_gpr":2292,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"TWN","country":"Taiwan"},{"gem_file":"562.63086.json.json","assembly_accession":"GCA_902810305.1","genome_id":"562.63086","genome_name":"Escherichia coli strain SC368","strain":"strain SC368","serovar":"","phylogroup":"B1","MLST":58,"mash_cluster":26,"isolation_source":"Water","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5101998.0,"gc_content":50.65266,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5259.0,"refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"MASSEY UNIVERSITY","completion_date":"2020-06-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJEB36951","biosample_accession":"SAMEA6595206","genbank_accessions":"LR778144","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Mike Sadowsky","comments":"Here we report the complete genomes of 47 Escherichia coli natural isolates, sampled from watersheds located at (46\u00b042\u203204\"N, 92\u00b012\u203226\"W) in Duluth, Minnesota. 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The IHE3034 strain sequenced in this work has lost its plasmids during laboratory passages and is more virulent than the ancestor strain in the sepsis mouse model.","n_reactions":2733,"n_metabolites":1946,"n_genes":1457,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"FIN","country":"Finland"},{"gem_file":"562.75680.json.json","assembly_accession":"GCA_018279085.1","genome_id":"562.75680","genome_name":"Escherichia coli strain J-8","strain":"strain J-8","serovar":"","phylogroup":"B1","MLST":156,"mash_cluster":26,"isolation_source":"intestinal and liver","isolation_country":"China","geographic_location":"China:Yangling","host_name":"chicken","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5210909.0,"gc_content":50.587433,"contigs":8.0,"chromosomes":1.0,"plasmids":7.0,"patric_cds":5214.0,"refseq_cds":4906.0,"sequencing_platform":"Illumina HiSeq","sequencing_depth":"80.0x","assembly_method":"Unicycler Version v. v0.48","sequencing_centers":"Northwest A&F University","completion_date":"2021-05-05T00:00:00Z","collection_date":"2017-04-14","bioproject_accession":"PRJNA595645","biosample_accession":"SAMN13563033","genbank_accessions":"CP047002,CP047007,CP047008,CP047009,CP047004,CP047006,CP047003,CP047005","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"ST156","substrain":"","additional_metadata":"sample_type:whole organism","comments":"NDM-5-harbouring plasmid and mcr-1-harboring chromosome","n_reactions":2753,"n_metabolites":2027,"n_genes":1758,"n_exchange":331,"n_with_gpr":2307,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"562.79203.json.json","assembly_accession":"GCA_019970975.1","genome_id":"562.79203","genome_name":"Escherichia coli strain AH04","strain":"strain AH04","serovar":"","phylogroup":"A","MLST":3202,"mash_cluster":22,"isolation_source":"","isolation_country":"Canada","geographic_location":"Canada: Alberta","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5049771.0,"gc_content":50.940132,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5208.0,"refseq_cds":4891.0,"sequencing_platform":"Oxford Nanopore MiniION","sequencing_depth":"65x","assembly_method":"flye v. 2.8.2","sequencing_centers":"Agriculture & Agri-Food Canada","completion_date":"2021-09-14T00:00:00Z","collection_date":"2013","bioproject_accession":"PRJNA716667","biosample_accession":"SAMN18446036","genbank_accessions":"CP081706,CP081707,CP081708,CP081709,CP081710","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The presence of locus of heat resistance is a common way of screening heat resistance in E.coli, however harboring LHR does not always confer extreme heat resistance suggesting other genetic components may play a role in heat resistance. WGS was performed to determine genetic determinants in E.coli for different levels of heat resistance and determine the evolution regarding the emergence of heat resistant strains of E.coli in a meat plant setting.","n_reactions":2733,"n_metabolites":1942,"n_genes":1500,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"83334.384.json.json","assembly_accession":"GCA_013168235.1","genome_id":"83334.384","genome_name":"Escherichia coli O157:H7 strain 2571","strain":"O157:H7 strain 2571","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"Cow, Bos taurus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5668040.0,"gc_content":50.508255,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":6007.0,"refseq_cds":5696.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"85x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN11229478","genbank_accessions":"CP038425,CP038426,CP038427","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.","n_reactions":2731,"n_metabolites":1938,"n_genes":1488,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.15198.json.json","assembly_accession":"GCF_002012045.1","genome_id":"562.15198","genome_name":"Escherichia coli strain Ecol_545","strain":"strain Ecol_545","serovar":"","phylogroup":"D","MLST":38,"mash_cluster":15,"isolation_source":"","isolation_country":"Viet Nam","geographic_location":"Viet Nam: Ho Chi Minh City","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5276034.0,"gc_content":50.63,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5495.0,"refseq_cds":5440.0,"sequencing_platform":"PacBio","sequencing_depth":"XX","assembly_method":"HGAP v. unspecified","sequencing_centers":"University of Oxford","completion_date":"2017-03-03T00:00:00Z","collection_date":"2011","bioproject_accession":"PRJNA316786","biosample_accession":"SAMN05511169","genbank_accessions":"CP018976,CP018975,CP018973,CP018972,CP018971,CP018974","refseq_accessions":"NZ_CP018976.1,NZ_CP018975.1,NZ_CP018973.1,NZ_CP018972.1,NZ_CP018971.1,NZ_CP018974.1","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART)","comments":"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.","n_reactions":2711,"n_metabolites":1877,"n_genes":1465,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"VNM","country":"Vietnam"},{"gem_file":"83334.477.json.json","assembly_accession":"GCA_017164995.1","genome_id":"83334.477","genome_name":"Escherichia coli O157:H7 strain Z1813","strain":"O157:H7 strain Z1813","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"feces","isolation_country":"United Kingdom","geographic_location":"United Kingdom","host_name":"Homo sapiens","host_health":"Gastroenteritis Escherichia coli","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5684358.0,"gc_content":50.52548,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5932.0,"refseq_cds":5531.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"205.9768441748391x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2021-03-04T00:00:00Z","collection_date":"2002","bioproject_accession":"PRJNA666790","biosample_accession":"SAMN16327604","genbank_accessions":"CP062725,CP062726","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Socttish E. coli Reference Laboratory (SERL)","comments":"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.","n_reactions":2731,"n_metabolites":1938,"n_genes":1487,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"GCF_020149685.1.json.json","assembly_accession":"GCF_020149685.1","genome_id":"GCF_020149685.1","genome_name":"Escherichia coli","strain":"NDM3","serovar":"","phylogroup":"A","MLST":167,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":"","gc_content":"","contigs":"","chromosomes":"","plasmids":"","patric_cds":"","refseq_cds":"","sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"","completion_date":"","collection_date":"","bioproject_accession":"PRJNA224116","biosample_accession":"SAMN21398204","genbank_accessions":"","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"Escherichia coli","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"","n_reactions":2731,"n_metabolites":1938,"n_genes":1528,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"405955.13.json.json","assembly_accession":"GCA_000014845.1","genome_id":"405955.13","genome_name":"Escherichia coli APEC O1","strain":"APEC O1","serovar":"serovar O1","phylogroup":"B2","MLST":95,"mash_cluster":4,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"Chicken, Gallus gallus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Colibacillosis","genome_length":5497653.0,"gc_content":50.3,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5417.0,"refseq_cds":4851.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Iowa State University","completion_date":"2006-10-04T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA16718","biosample_accession":"SAMN02603424","genbank_accessions":"CP000468,DQ517526,DQ381420","refseq_accessions":"NC_008563,NC_009838,NC_009837","genome_status":"Complete","taxon_id":405955.0,"organism_name":"Escherichia coli APEC O1","pathovar":"APEC","antimicrobial_resistance":"","culture_collection":"","publication":"16940062,17293413,16885466","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"Yes","temperature_range":"Mesophilic","optimal_temperature":"-","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"Escherichia coli APEC O1. This strain (serovar O1) is an avian pathogenic strain and causes respiratory, blood, and enteric infections primarily in poultry. 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Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.","n_reactions":2732,"n_metabolites":1940,"n_genes":1526,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.34089.json.json","assembly_accession":"GCA_003571825.1","genome_id":"562.34089","genome_name":"Escherichia coli strain AR_0089","strain":"strain AR_0089","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5245490.0,"gc_content":50.679153,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5457.0,"refseq_cds":5352.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"185x","assembly_method":"canu v. 1.6","sequencing_centers":"Centers for Disease Control and Prevention","completion_date":"2018-09-17T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA292904","biosample_accession":"SAMN04014930","genbank_accessions":"CP032265,CP032263,CP032264","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"Susceptible;Resistant;Not defined","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria","n_reactions":2711,"n_metabolites":1877,"n_genes":1403,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.62729.json.json","assembly_accession":"GCA_013390265.1","genome_id":"562.62729","genome_name":"Escherichia coli strain M1/5","strain":"strain M1/5","serovar":"","phylogroup":"B2","MLST":550,"mash_cluster":6,"isolation_source":"feces","isolation_country":"Germany","geographic_location":"Germany","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5288136.0,"gc_content":50.627876,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5354.0,"refseq_cds":5023.0,"sequencing_platform":"PacBio RS; Illumina MiSeq","sequencing_depth":"230.0x","assembly_method":"HGAP v. 3","sequencing_centers":"University of Muenster","completion_date":"2020-07-06T00:00:00Z","collection_date":"1994","bioproject_accession":"PRJNA630566","biosample_accession":"SAMN14840032","genbank_accessions":"CP053296,CP053298,CP053297","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolate from a healthy human donor","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:pure culture","comments":"Comparative genome sequence analysis should help to better understand genomic differences between extraintestinal pathogenic and commensal Escherichia coli strains. For this purpose, we sequenced the complete genome of a fecal E. coli isolate from a healthy human donor.","n_reactions":2732,"n_metabolites":1945,"n_genes":1465,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"DEU","country":"Germany"},{"gem_file":"562.29096.json.json","assembly_accession":"GCA_003019095.1","genome_id":"562.29096","genome_name":"Escherichia coli strain 95-3322","strain":"strain 95-3322","serovar":"O22:H5","phylogroup":"B2","MLST":646,"mash_cluster":6,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5095223.0,"gc_content":50.631443,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5016.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"149.21x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08579587","genbank_accessions":"CP027461","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2732,"n_metabolites":1941,"n_genes":1459,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.28697.json.json","assembly_accession":"GCA_003017765.1","genome_id":"562.28697","genome_name":"Escherichia coli strain 2013C-3033","strain":"strain 2013C-3033","serovar":"O146:H21","phylogroup":"B1","MLST":442,"mash_cluster":26,"isolation_source":"feces","isolation_country":"","geographic_location":"","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5553868.0,"gc_content":50.78079,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5650.0,"refseq_cds":"","sequencing_platform":"PacBio","sequencing_depth":"230.753x","assembly_method":"HGAP v. 3","sequencing_centers":"CDC","completion_date":"2018-03-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA218110","biosample_accession":"SAMN08579559","genbank_accessions":"CP027323,CP027324","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"PulseNet STEC genome reference library","n_reactions":2732,"n_metabolites":1941,"n_genes":1512,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1038927.31.json.json","assembly_accession":"GCA_002209105.2","genome_id":"1038927.31","genome_name":"Escherichia coli O104:H4 strain FDAARGOS_348","strain":"FDAARGOS_348","serovar":"O104:H4","phylogroup":"B1","MLST":678,"mash_cluster":26,"isolation_source":"Stool","isolation_country":"USA","geographic_location":"USA: Georgia","host_name":"Human, Homo sapiens","host_health":"Bloody diarrhea complicated hemolytic uremic syndrome (HUS)","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5442181.0,"gc_content":50.58,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5899.0,"refseq_cds":5662.0,"sequencing_platform":"PacBio","sequencing_depth":"18.1565653439553x","assembly_method":"SMRT v. 2.3.0, HGAP v. 3.0","sequencing_centers":"US Food and Drug Administration","completion_date":"2017-06-27T00:00:00Z","collection_date":"2009","bioproject_accession":"PRJNA231221","biosample_accession":"SAMN06173361","genbank_accessions":"CP022086,CP022085,CP022087","refseq_accessions":"","genome_status":"Complete","taxon_id":1038927.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"FDA:FDAARGOS_348","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USAMRIID < CDC-Atlanta","comments":"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: \u2022Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. \u2022Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). \u2022Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2711,"n_metabolites":1877,"n_genes":1467,"n_exchange":331,"n_with_gpr":2265,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.61706.json.json","assembly_accession":"GCA_013372325.1","genome_id":"562.61706","genome_name":"Escherichia coli strain EcPF18","strain":"strain EcPF18","serovar":"","phylogroup":"B2","MLST":131,"mash_cluster":3,"isolation_source":"urine","isolation_country":"USA","geographic_location":"USA: Dallas, Texas","host_name":"Human, Homo sapiens","host_health":"Chronic Cystitis","host_gender":"female","host_age":"","body_sample_site":"","disease":"","genome_length":5232916.0,"gc_content":50.70009,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5287.0,"refseq_cds":4987.0,"sequencing_platform":"Illumina NextSeq, ONT MinION","sequencing_depth":"310x, 161x","assembly_method":"Unicycler v. v.0.4.13","sequencing_centers":"University of Texas at Dallas","completion_date":"2020-06-24T00:00:00Z","collection_date":"July-2018","bioproject_accession":"PRJNA636382","biosample_accession":"SAMN15075997","genbank_accessions":"CP054219,CP054220,CP054221,CP054222,CP054223","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"UPEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"host_description:Postmenopausal","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:UT Southwestern Medical Center/ UT Dallas","comments":"Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.","n_reactions":2732,"n_metabolites":1943,"n_genes":1472,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.28403.json.json","assembly_accession":"GCA_002953075.1","genome_id":"562.28403","genome_name":"Escherichia coli strain 2FA","strain":"2FA","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4651848.0,"gc_content":50.80501,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4540.0,"refseq_cds":"","sequencing_platform":"illumina","sequencing_depth":"100x","assembly_method":"unknown v. not applicable","sequencing_centers":"University of Texas at Austin","completion_date":"2018-02-01T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA430697","biosample_accession":"SAMN08380006","genbank_accessions":"CP026356","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:not applicable","comments":"We have carried out directed evolution experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine across from amber codons, creating a 21 amino acid genetic code in which the amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. The 21 amino acid code is enforced throughthe inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical.","n_reactions":2732,"n_metabolites":1936,"n_genes":1561,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1330457.6.json.json","assembly_accession":"GCA_000803705.1","genome_id":"1330457.6","genome_name":"Escherichia coli O157:H7 str. SS52","strain":"O157:H7 str. SS52","serovar":"","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5583430.0,"gc_content":50.47,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5675.0,"refseq_cds":5745.0,"sequencing_platform":"Ion Torrent PGM sequencer","sequencing_depth":"168.4x","assembly_method":"DNASTAR SeqMan NGen v. 11.0.0;","sequencing_centers":"Penn State","completion_date":"2014-12-18T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA201344","biosample_accession":"SAMN03265100","genbank_accessions":"CP010304.1,CP010305.1","refseq_accessions":"NZ_CP010304.1,NZ_CP010305.1","genome_status":"Complete","taxon_id":1330457.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"Bacilli","motility":"Yes","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"This Escherichia coli O157:H7 isolate was obtained from the recto-anal junction of a cow which produced the isolate at &gt\\; 6.8X10^5 CFU/g of feces classifying both the cow and the isolate as a super-shedder.","n_reactions":2731,"n_metabolites":1938,"n_genes":1483,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.67026.json.json","assembly_accession":"GCA_014863785.1","genome_id":"562.67026","genome_name":"Escherichia coli strain AML003_par","strain":"strain AML003_par","serovar":"","phylogroup":"A","MLST":10,"mash_cluster":21,"isolation_source":"not applicable","isolation_country":"USA","geographic_location":"USA: Boston","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4631469.0,"gc_content":50.778683,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":4506.0,"refseq_cds":"","sequencing_platform":"Illumina NextSeq","sequencing_depth":"50x","assembly_method":"breseq v. 0.35.1","sequencing_centers":"Boston University","completion_date":"2020-10-08T00:00:00Z","collection_date":"28-Aug-2019","bioproject_accession":"PRJNA666010","biosample_accession":"SAMN16090667","genbank_accessions":"CP062246","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolate from each separate evolution experiment and the parent strains are provided here","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture;biomaterial_provider:M.J. Dunlop, Boston University, 44 Cummington Mall, Boston, MA 02219;collected_by:A.M. Langevin","comments":"In this work, we evolved strains of Escherichia coli with different genotypes related to the AcrAB-TolC efflux pump. Parent strains were either wild type, had the pump overexpressed, or had the pump knocked out. We evolved these three strains under different levels of chloramphenicol. Each parent strain was evolved in an evolution experiment using three biological replicates. The most resistant isolate from each separate evolution experiment and the parent strains are provided here. The goal of this work was to identify which chloramphenicol concentrations promote the evolution of antibiotic resistance and how the presence of the AcrAB-TolC pump impacts this evolution.","n_reactions":2732,"n_metabolites":1936,"n_genes":1557,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"562.67510.json.json","assembly_accession":"GCA_015571615.1","genome_id":"562.67510","genome_name":"Escherichia coli strain Res13-Lact-PER12-33-A","strain":"strain Res13-Lact-PER12-33-A","serovar":"O-untypeable:H4","phylogroup":"A","MLST":761,"mash_cluster":22,"isolation_source":"feces","isolation_country":"Canada","geographic_location":"Canada: Quebec","host_name":"Pig, Sus scrofa domesticus","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5113968.0,"gc_content":50.625072,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5198.0,"refseq_cds":4850.0,"sequencing_platform":"Oxford Nanopore MinION and Illumina MiSeq","sequencing_depth":"1.00x","assembly_method":"Unicycler v. 0.4.7","sequencing_centers":"Government of Canada","completion_date":"2020-11-18T00:00:00Z","collection_date":"27-Mar-2017","bioproject_accession":"PRJNA662792","biosample_accession":"SAMN16304239","genbank_accessions":"CP062826,CP062827,CP062828,CP062829,CP062830,CP062831","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Agriculture and Agri-Food Canada","comments":"The majority of antibiotics sold are administered to livestock, presumably promoting the development and spread of antibiotic resistance genes in food-borne pathogens such as Enterobacteriaceae producing extended spectrum beta-lactamases (ESBL). Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. The major goal of the study was to characterize cefotaxime-resistant bacteria isolated from feed, faeces, manures and carcasses of quebecker pigs reared with penicillin-using or antibiotic-free husbandries. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays.","n_reactions":2732,"n_metabolites":1940,"n_genes":1526,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CAN","country":"Canada"},{"gem_file":"562.46731.json.json","assembly_accession":"GCA_005221885.1","genome_id":"562.46731","genome_name":"Escherichia coli strain 143","strain":"strain 143","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5697472.0,"gc_content":50.503628,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":6185.0,"refseq_cds":5985.0,"sequencing_platform":"PacBio","sequencing_depth":"193x","assembly_method":"Celera Assembler v. Canu version 1.2","sequencing_centers":"United State Department of Agriculture","completion_date":"2019-05-07T00:00:00Z","collection_date":"2009","bioproject_accession":"PRJNA445267","biosample_accession":"SAMN08773050","genbank_accessions":"CP028607,CP028608","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"STEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:USMARC","comments":"The aim of this project is to compare complete closed genomes with whole genome sequencing (WGS) using short reads. SNPs from WGS is used in many studies to determine relatedness of strains. These SNPs are in the core genome and don't reflect the diversity of the complete genome. This study provides insight into how core SNPs relates to the structure and sequence of the complete genome.","n_reactions":2731,"n_metabolites":1938,"n_genes":1488,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.60460.json.json","assembly_accession":"GCA_013166895.1","genome_id":"562.60460","genome_name":"Escherichia coli strain T7Express_LysY","strain":"strain T7Express_LysY","serovar":"","phylogroup":"A","MLST":93,"mash_cluster":22,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4486677.0,"gc_content":50.802856,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":4449.0,"refseq_cds":4211.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"163x","assembly_method":"HGAP v. 3","sequencing_centers":"New England Biolabs","completion_date":"2020-05-26T00:00:00Z","collection_date":"2010-01-01","bioproject_accession":"PRJNA341475","biosample_accession":"SAMN14933843","genbank_accessions":"CP053597,CP053598","refseq_accessions":"","genome_status":"Complete","taxon_id":562.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"sample_type:cell culture","comments":"Closed and finished genome of NEB 5-alpha, an immediate fhuA derivative of (E. coli K-12) DH5alpha.","n_reactions":2731,"n_metabolites":1931,"n_genes":1506,"n_exchange":331,"n_with_gpr":2285,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"USA","country":"United States of America"},{"gem_file":"83334.359.json.json","assembly_accession":"GCA_013167615.1","genome_id":"83334.359","genome_name":"Escherichia coli O157:H7 strain F8798","strain":"O157:H7 strain F8798","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"","isolation_country":"USA","geographic_location":"USA","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5662137.0,"gc_content":50.481293,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":6010.0,"refseq_cds":5704.0,"sequencing_platform":"PacBio RSII","sequencing_depth":"121x","assembly_method":"HGAP v. 3","sequencing_centers":"United State Department of Agriculture","completion_date":"2020-05-26T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA528413","biosample_accession":"SAMN05360171","genbank_accessions":"CP038351,CP038352","refseq_accessions":"","genome_status":"Complete","taxon_id":83334.0,"organism_name":"","pathovar":"EHEC","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:CDC","comments":"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. 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The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic\\; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.","n_reactions":2732,"n_metabolites":1935,"n_genes":1560,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"562.46727.json.json","assembly_accession":"GCA_005221805.1","genome_id":"562.46727","genome_name":"Escherichia coli strain 120","strain":"strain 120","serovar":"O157:H7","phylogroup":"E","MLST":11,"mash_cluster":19,"isolation_source":"cattle","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5555919.0,"gc_content":50.50106,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5966.0,"refseq_cds":5803.0,"sequencing_platform":"PacBio","sequencing_depth":"129x","assembly_method":"HGAP v. 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University","completion_date":"2017-10-04T00:00:00Z","collection_date":"1988","bioproject_accession":"PRJNA382451","biosample_accession":"SAMN06706581","genbank_accessions":"CP020753","refseq_accessions":"","genome_status":"Complete","taxon_id":1935181.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"28899344","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Nils I. A. Carlin","comments":"Shigella species cause bacillary dysentery \u2013 a severe form of diarrhoea, characterized by acute colonic and rectal mucosal inflammation leading to fever, abdominal cramps and bloody mucoid stools. Out of four species of Shigella, S. flexneri is the most prevalent enteric pathogen in developing countries. Shigella is transmitted through faecal-oral route and can cause gastrointestinal infection via an exceptionally low infectious dose (as many as 10 bacteria). S. flexneri is classified into different serotypes based on the O-antigen structure of its lipopolysaccharide. The serotype conversion is mediated by bacteriophages and plasmids carrying genes that modify the O-antigen. The S. flexneri serotype 1c is a novel serotype, which has now been found to be prevalent in many developing countries. However, little is known about its virulence signatures and evolution. Here, we provide the unique features of this serotype through the whole genome sequencing and bioinformatics tools. We also identified it as a highly adaptive pathogen with unique O-antigen modification possibly mediated by three different bacteriophages during its evolution. Furthermore, this serotype possesses several hypothetical genes and putative bacteriophage regions that will guide future investigation to identify novel genes involved in pathogen\u2019s virulence and its survival in the host environment.;many frameshifted proteins","n_reactions":2732,"n_metabolites":1942,"n_genes":1430,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BGD","country":"Bangladesh"},{"gem_file":"591020.3.json.json","assembly_accession":"GCA_000022245.1","genome_id":"591020.3","genome_name":"Shigella flexneri 2002017","strain":"2002017","serovar":"","phylogroup":"A","MLST":245,"mash_cluster":24,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Dysentery","genome_length":4894492.0,"gc_content":50.6,"contigs":6.0,"chromosomes":1.0,"plasmids":5.0,"patric_cds":5524.0,"refseq_cds":4706.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Chinese Center for Disease Control and Prevention|TEDA School of Biological Sciences and Biotechnology, Nankai University","completion_date":"2009-12-24T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA33639","biosample_accession":"SAMN02603122","genbank_accessions":"CP001383,CP001385,CP001386,CP001387,CP001388,CP001384","refseq_accessions":"NC_017328.1,NC_017319.1,NC_017320.1,NC_017329.1,NC_017321.1,NC_017330.1","genome_status":"Complete","taxon_id":591020.0,"organism_name":"Shigella flexneri 2002017","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"19955273","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"Yes","temperature_range":"Mesophilic","optimal_temperature":"-","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"Shigella flexneri 200217. This strain will be used for comparative analysis with other Shigella species.","n_reactions":2733,"n_metabolites":1942,"n_genes":1426,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"1282357.3.json.json","assembly_accession":"GCA_000743955.1","genome_id":"1282357.3","genome_name":"Shigella flexneri 2003036","strain":"2003036","serovar":"","phylogroup":"A","MLST":245,"mash_cluster":24,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4595814.0,"gc_content":50.9,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":4885.0,"refseq_cds":4891.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Institute for Communicable Disease Control and Prevention","completion_date":"2014-08-27T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA186498","biosample_accession":"SAMN02999960","genbank_accessions":"CP004056.1","refseq_accessions":"NZ_CP004056.1","genome_status":"Complete","taxon_id":1282357.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"","comments":"Genome announcement;many frameshifted proteins","n_reactions":2733,"n_metabolites":1941,"n_genes":1429,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"198215.6.json.json","assembly_accession":"GCA_000007405.1","genome_id":"198215.6","genome_name":"Shigella flexneri 2a str. 2457T","strain":"2a str. 2457T","serovar":"","phylogroup":"A","MLST":245,"mash_cluster":24,"isolation_source":"","isolation_country":"","geographic_location":"","host_name":"","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Dysentery","genome_length":4599354.0,"gc_content":50.9,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5131.0,"refseq_cds":4061.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"University of Wisconsin-Madison, USA","completion_date":"2003-04-22T00:00:00Z","collection_date":"","bioproject_accession":"PRJNA408","biosample_accession":"","genbank_accessions":"AE014073","refseq_accessions":"NC_004741","genome_status":"Complete","taxon_id":198215.0,"organism_name":"Shigella flexneri 2a str. 2457T","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"","temperature_range":"Mesophilic","optimal_temperature":"37","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":" Shigella flexneri 2a str. 2457T. This is a highly virulent strain that has been widely used for genetic and clinical research. It is similar to pathogenic Escherichia coli except for the more numerous insertion sequences and contains 4 plasmids pINV-2457T, pSf2, and pSf4, and pSf-R27. Plasmid pINV-2457T is similar to plasmids pWR100, pWR501, and pCP301 whereas plasmid pSf-R27 is similar to R27. Plasmids pSf2 and pSf4 are small ColE1-like plasmids. pSf2 is similar to plasmid p2457TS2 found in RefSeq Accession Number NC_002773.;many frameshifted proteins","n_reactions":2733,"n_metabolites":1942,"n_genes":1434,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"198214.7.json.json","assembly_accession":"GCA_000006925.2","genome_id":"198214.7","genome_name":"Shigella flexneri 2a str. 301","strain":"2a str. 301","serovar":"","phylogroup":"A","MLST":245,"mash_cluster":24,"isolation_source":"patient","isolation_country":"China","geographic_location":"China: Beijing","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"Dysentery","genome_length":4828821.0,"gc_content":50.7,"contigs":2.0,"chromosomes":1.0,"plasmids":1.0,"patric_cds":5527.0,"refseq_cds":4440.0,"sequencing_platform":"","sequencing_depth":"","assembly_method":"","sequencing_centers":"Microbial Genome Center of ChMPH","completion_date":"2002-10-18T00:00:00Z","collection_date":"1984","bioproject_accession":"PRJNA310","biosample_accession":"SAMN02603599","genbank_accessions":"AE005674,AF386526","refseq_accessions":"NC_004337,NC_004851","genome_status":"Complete","taxon_id":198214.0,"organism_name":"Shigella flexneri 2a str. 301","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"12384590","isolation_comments":"isolated in 1984 from a patient in Beijing, China","other_clinical":"","other_environmental":"","cell_shape":"Rod","motility":"","temperature_range":"Mesophilic","optimal_temperature":"37","oxygen_requirement":"Facultative","genotype":"","substrain":"","additional_metadata":"","comments":"  Shigella flexneri 2a str. 301. This strain was isolated in 1984 from a patient in Beijing, China. It is similar to pathogenic Escherichia coli except for the more numerous insertion sequences and contains a virulence plasmid (pCP301).","n_reactions":2733,"n_metabolites":1941,"n_genes":1435,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"CHN","country":"China"},{"gem_file":"42897.88.json.json","assembly_accession":"GCA_003324695.1","genome_id":"42897.88","genome_name":"Shigella flexneri 2a strain 1508","strain":"2a strain 1508","serovar":"2a","phylogroup":"A","MLST":245,"mash_cluster":24,"isolation_source":"hospitalized patients","isolation_country":"China","geographic_location":"China: Hangzhou","host_name":"Human, Homo sapiens","host_health":"","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":5028868.0,"gc_content":50.67749,"contigs":3.0,"chromosomes":1.0,"plasmids":2.0,"patric_cds":5858.0,"refseq_cds":5383.0,"sequencing_platform":"PacBio; Illumina HiSeq; 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Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.","n_reactions":2733,"n_metabolites":1941,"n_genes":1436,"n_exchange":331,"n_with_gpr":2287,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"AUS","country":"Australia"},{"gem_file":"424717.5.json.json","assembly_accession":"GCA_016598675.1","genome_id":"424717.5","genome_name":"Shigella flexneri 3a strain 888048","strain":"3a strain 888048","serovar":"","phylogroup":"A","MLST":245,"mash_cluster":24,"isolation_source":"stool","isolation_country":"United Kingdom","geographic_location":"United Kingdom: London","host_name":"Human, Homo sapiens","host_health":"shigellosis","host_gender":"male","host_age":"","body_sample_site":"","disease":"","genome_length":4519004.0,"gc_content":50.90664,"contigs":1.0,"chromosomes":1.0,"plasmids":0.0,"patric_cds":5146.0,"refseq_cds":4401.0,"sequencing_platform":"Oxford Nanopore MinION; Illumina HiSeq","sequencing_depth":"28.0x","assembly_method":"Flye v. 2.7.1","sequencing_centers":"University of Bath","completion_date":"2021-01-10T00:00:00Z","collection_date":"Jan-2020","bioproject_accession":"PRJNA687663","biosample_accession":"SAMN17152196","genbank_accessions":"CP066809","refseq_accessions":"","genome_status":"Complete","taxon_id":424717.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"","publication":"","isolation_comments":"","other_clinical":"","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:Public Health England","comments":"Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK. This study aimed to look at the location of AMR determinants in CTX-M-27-positive Shigella isolates spread through MSM in England and their relation to known plasmids in Shigella","n_reactions":2732,"n_metabolites":1944,"n_genes":1411,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"GBR","country":"United Kingdom"},{"gem_file":"1617964.8.json.json","assembly_accession":"GCA_002240095.1","genome_id":"1617964.8","genome_name":"Shigella flexneri 4c","strain":"4c","serovar":"","phylogroup":"A","MLST":245,"mash_cluster":24,"isolation_source":"hospitalized patients","isolation_country":"China","geographic_location":"China: 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With funding support from FDA\u2019s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","n_reactions":2732,"n_metabolites":1937,"n_genes":1384,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"NGA","country":"Nigeria"},{"gem_file":"623.1270.json.json","assembly_accession":"GCA_013402835.1","genome_id":"623.1270","genome_name":"Shigella flexneri strain M2901","strain":"strain M2901","serovar":"2b","phylogroup":"A","MLST":245,"mash_cluster":24,"isolation_source":"feces","isolation_country":"Australia","geographic_location":"Australia: Queensland","host_name":"Human, Homo sapiens","host_health":"shigellosis","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4995595.0,"gc_content":50.628082,"contigs":5.0,"chromosomes":1.0,"plasmids":4.0,"patric_cds":5756.0,"refseq_cds":4956.0,"sequencing_platform":"Illumina NextSeq; Oxford Nanopore","sequencing_depth":"50.0x","assembly_method":"Flye v. 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It is a Shigella flexneri serotype 2a that was isolated in 1915 from the reputed first case of dysentery on the Western Front in WWI.;many frameshifted proteins","n_reactions":2751,"n_metabolites":2014,"n_genes":1742,"n_exchange":331,"n_with_gpr":2305,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"","country":""},{"gem_file":"623.1082.json.json","assembly_accession":"GCA_004171185.1","genome_id":"623.1082","genome_name":"Shigella flexneri strain SFL1520","strain":"strain SFL1520","serovar":"3b","phylogroup":"A","MLST":1025,"mash_cluster":24,"isolation_source":"Stool","isolation_country":"Bangladesh","geographic_location":"Bangladesh: Dhaka","host_name":"Human, Homo sapiens","host_health":"Shigellosis","host_gender":"","host_age":"","body_sample_site":"","disease":"","genome_length":4575536.0,"gc_content":50.892944,"contigs":1.0,"chromosomes":1.0,"plasmids":"","patric_cds":5183.0,"refseq_cds":4725.0,"sequencing_platform":"Oxford Nanopore MiniION; Illumina MiSeq","sequencing_depth":"410.0x","assembly_method":"SPAdes v. 3.12.0","sequencing_centers":"Australian National University","completion_date":"2019-02-12T00:00:00Z","collection_date":"1984","bioproject_accession":"PRJNA492813","biosample_accession":"SAMN10106138","genbank_accessions":"CP032513","refseq_accessions":"","genome_status":"Complete","taxon_id":623.0,"organism_name":"","pathovar":"","antimicrobial_resistance":"","culture_collection":"not applicable","publication":"","isolation_comments":"","other_clinical":"host_description:not collected;host_disease_outcome:not collected;host_disease_stage:not collected;host_health_state:not collected;host_subject_id:not collected","other_environmental":"","cell_shape":"","motility":"","temperature_range":"","optimal_temperature":"","oxygen_requirement":"","genotype":"","substrain":"","additional_metadata":"collected_by:International Centre for Diarrhoeal Disease Research, Bangladesh;passage_history:not collected;specimen_voucher:not applicable","comments":"We report the first complete genome analysis of S. flexneri serotype 3b strain SFL1520 using both long read MinION Flow (Oxford Nanopore Technologies) and short read MiSeq v3 300 bp (Illumina) sequencing platforms. The subsequent genome analysis aimed to provide a broader understanding of the genomic signatures of S. flexneri serotype 3b- an important serotype of developing countries.","n_reactions":2732,"n_metabolites":1945,"n_genes":1403,"n_exchange":331,"n_with_gpr":2286,"dataset":"EcopanGEM","organism":"Escherichia coli","gtdb_species":"Escherichia coli","country_iso":"BGD","country":"Bangladesh"},{"gem_file":"623.1589.json.json","assembly_accession":"GCA_019793575.1","genome_id":"623.1589","genome_name":"Shigella flexneri strain WW1","strain":"strain WW1","serovar":"","phylogroup":"B1","MLST":942,"mash_cluster":26,"isolation_source":"sludge from the aeration tanks of urban wastewater treatment 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FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. 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