{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T19:42:26Z","timestamp":1771875746615,"version":"3.50.1"},"reference-count":172,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T00:00:00Z","timestamp":1771804800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"DGAL","award":["EcoAntibio2, COLIPHAVI"],"award-info":[{"award-number":["EcoAntibio2, COLIPHAVI"]}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"crossref","award":["Projeto Universal 423.902\/2016\u20104"],"award-info":[{"award-number":["Projeto Universal 423.902\/2016\u20104"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004263","name":"FAPERGS","doi-asserted-by":"crossref","award":["PPSUS 21\/2551-0000079-1"],"award-info":[{"award-number":["PPSUS 21\/2551-0000079-1"]}],"id":[{"id":"10.13039\/501100004263","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002322","name":"CAPES","doi-asserted-by":"crossref","award":["DS 88887921543\/2023-00"],"award-info":[{"award-number":["DS 88887921543\/2023-00"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"crossref"}]},{"name":"F\u00e9d\u00e9ration de recherche en infectiologie","award":["training grant"],"award-info":[{"award-number":["training grant"]}]},{"DOI":"10.13039\/501100000038","name":"NSERC","doi-asserted-by":"crossref","award":["Discovery Grant 2019-06642"],"award-info":[{"award-number":["Discovery Grant 2019-06642"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    Extraintestinal pathogenic\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    (ExPEC) cause disease outside the gut and include avian pathogenic\n                    <jats:italic>E. coli<\/jats:italic>\n                    (APEC), a leading cause of bacterial infections in poultry. Among their highly diverse types, strain BEN2908 stands out for its significant invasive ability across various human and avian cell types. Aiming to investigate further aspects of this strain and its plasmid, we sequenced and assembled the complete genome of BEN2908 and compared it to 22\n                    <jats:italic>E. coli<\/jats:italic>\n                    strains, including other invasive strains such as adherent and invasive\n                    <jats:italic>E. coli<\/jats:italic>\n                    (AIEC) LF82 and NRG857c, by constructing a phylogenetic tree and using web-based characterization software. With these results, we selected eight strains closely related to BEN2908 to perform a ring comparison, including two APEC (APEC O1 and IMT5155), two neonatal meningitis\n                    <jats:italic>E. coli<\/jats:italic>\n                    (NMEC; RS218 and IHE3034), two uropathogenic\n                    <jats:italic>E. coli<\/jats:italic>\n                    (UPEC; 78-Pyelo and CFT073), one commensal\n                    <jats:italic>E. coli<\/jats:italic>\n                    (MG1655) and one adherent-invasive\n                    <jats:italic>E. coli<\/jats:italic>\n                    (AIEC; LF82). This revealed 20 genomic regions (GRs) of interest which were then analysed by CD-Search, BLASTp and KEGG Pathway databases. Many of the genes in these GRs had no previous description but showed similarity to known genes involved in sugar uptake, nitrogen metabolism, and dicarboxylate transport and processing, among other functions. These results were tabulated and used to infer possible pathways that could be involved in ExPEC pathogenesis, highlighting candidate genes that have been overlooked in ExPEC research.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0342894","type":"journal-article","created":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T18:27:29Z","timestamp":1771871249000},"page":"e0342894","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Sequencing of the invasive E. coli strain BEN2908 isolated from poultry: A comparative investigation of genomic regions shared with intestinal and extraintestinal model E. coli strains"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7487-1357","authenticated-orcid":true,"given":"Tobias Weber","family":"Martins","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ang\u00e9lina","family":"Trotereau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7064-3827","authenticated-orcid":true,"given":"Simone","family":"Lahnig-Jacques","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0982-5872","authenticated-orcid":true,"given":"Maxime","family":"Branger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S\u00e9bastien","family":"Houle","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles M.","family":"Dozois","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Brisotto Pavanelo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabiana","family":"Horn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3480-6278","authenticated-orcid":true,"given":"Catherine","family":"Schouler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,2,23]]},"reference":[{"issue":"15","key":"pone.0342894.ref001","doi-asserted-by":"crossref","DOI":"10.1093\/femsle\/fnv118","article-title":"Avian colibacillosis: still many black holes","volume":"362","author":"R Guabiraba","year":"2015","journal-title":"FEMS Microbiol Lett"},{"issue":"5","key":"pone.0342894.ref002","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1080\/03079457.2015.1060584","article-title":"The incidence and economic impact of the Escherichia coli peritonitis syndrome in Dutch poultry farming","volume":"44","author":"WJM Landman","year":"2015","journal-title":"Avian Pathol"},{"issue":"1","key":"pone.0342894.ref003","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1186\/s13567-021-00970-6","article-title":"DctR contributes to the virulence of avian pathogenic Escherichia coli through regulation of type III secretion system 2 expression","volume":"52","author":"Y Zhang","year":"2021","journal-title":"Vet Res"},{"issue":"1","key":"pone.0342894.ref004","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00333-18","article-title":"Diversity and population overlap between avian and human Escherichia coli belonging to Sequence Type 95","volume":"4","author":"SL Jorgensen","year":"2019","journal-title":"mSphere"},{"issue":"5","key":"pone.0342894.ref005","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1111\/j.1365-2958.2006.05172.x","article-title":"Sex and virulence in Escherichia coli: an evolutionary perspective","volume":"60","author":"T Wirth","year":"2006","journal-title":"Mol Microbiol"},{"issue":"7","key":"pone.0342894.ref006","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1016\/j.ijmm.2014.06.009","article-title":"Extraintestinal pathogenic Escherichia coli (ExPEC) of human and avian origin belonging to sequence type complex 95 (STC95) portray indistinguishable virulence features","volume":"304","author":"N Nandanwar","year":"2014","journal-title":"Int J Med Microbiol"},{"issue":"3","key":"pone.0342894.ref007","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00168-17","article-title":"Fine-scale structure analysis shows epidemic patterns of lonal Complex 95, a cosmopolitan Escherichia coli lineage responsible for extraintestinal infection","volume":"2","author":"DM Gordon","year":"2017","journal-title":"mSphere"},{"issue":"1","key":"pone.0342894.ref008","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/s13073-021-00892-0","article-title":"Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period","volume":"13","author":"G Royer","year":"2021","journal-title":"Genome Med"},{"issue":"4","key":"pone.0342894.ref009","doi-asserted-by":"crossref","first-page":"787","DOI":"10.2307\/1589865","article-title":"Escherichia coli colonization of the trachea in poultry: comparison of virulent and avirulent strains in gnotoxenic chickens","volume":"26","author":"M Dho","year":"1982","journal-title":"Avian Dis"},{"issue":"4","key":"pone.0342894.ref010","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0035475","article-title":"Effect of fructooligosaccharide metabolism on chicken colonization by an extra-intestinal pathogenic Escherichia coli strain","volume":"7","author":"G Porcheron","year":"2012","journal-title":"PLoS One"},{"issue":"1","key":"pone.0342894.ref011","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1128\/JB.01052-08","article-title":"A genomic island of an extraintestinal pathogenic Escherichia coli Strain enables the metabolism of fructooligosaccharides, which improves intestinal colonization","volume":"191","author":"C Schouler","year":"2009","journal-title":"J Bacteriol"},{"issue":"7","key":"pone.0342894.ref012","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0041031","article-title":"Infections with avian pathogenic and fecal Escherichia coli strains display similar lung histopathology and macrophage apoptosis","volume":"7","author":"F Horn","year":"2012","journal-title":"PLoS One"},{"issue":"1","key":"pone.0342894.ref013","doi-asserted-by":"crossref","first-page":"221","DOI":"10.2307\/1592463","article-title":"Dynamics of Escherichia coil infection in experimentally inoculated chickens","volume":"41","author":"SA Pourbakhsh","year":"1997","journal-title":"Avian Dis"},{"issue":"8","key":"pone.0342894.ref014","doi-asserted-by":"crossref","DOI":"10.1128\/IAI.00241-18","article-title":"The periplasmic trehalase Affects Type 1 fimbria production and virulence of Extraintestinal Pathogenic Escherichia coli strain MT78","volume":"86","author":"DB Pavanelo","year":"2018","journal-title":"Infect Immun"},{"issue":"3","key":"pone.0342894.ref015","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1111\/j.1365-2958.2011.07725.x","article-title":"Regulation of fructooligosaccharide metabolism in an extra-intestinal pathogenic Escherichia coli strain","volume":"81","author":"G Porcheron","year":"2011","journal-title":"Mol Microbiol"},{"issue":"3","key":"pone.0342894.ref016","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1128\/JB.188.3.977-987.2006","article-title":"A selC-associated genomic island of the extraintestinal avian pathogenic Escherichia coli strain BEN2908 is involved in carbohydrate uptake and virulence","volume":"188","author":"I Chouikha","year":"2006","journal-title":"J Bacteriol"},{"issue":"2","key":"pone.0342894.ref017","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1111\/j.1574-6968.2011.02281.x","article-title":"The yicJI metabolic operon of Escherichia coli is involved in bacterial fitness","volume":"319","author":"M R\u00e9p\u00e9rant","year":"2011","journal-title":"FEMS Microbiol Lett"},{"issue":"13","key":"pone.0342894.ref018","doi-asserted-by":"crossref","first-page":"4427","DOI":"10.1128\/JB.00103-09","article-title":"A metabolic operon in extraintestinal pathogenic Escherichia coli promotes fitness under stressful conditions and invasion of eukaryotic cells","volume":"191","author":"G Rouquet","year":"2009","journal-title":"J Bacteriol"},{"key":"pone.0342894.ref019","doi-asserted-by":"crossref","first-page":"1414188","DOI":"10.3389\/fcimb.2024.1414188","article-title":"The osmoregulated metabolism of trehalose contributes to production of type 1 fimbriae and bladder colonization by extraintestinal Escherichia coli strain BEN2908","volume":"14","author":"VS Klemberg","year":"2024","journal-title":"Front Cell Infect Microbiol"},{"issue":"1","key":"pone.0342894.ref020","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.vetmic.2010.08.006","article-title":"Avian pathogenic Escherichia coli MT78 invades chicken fibroblasts","volume":"148","author":"LB Matter","year":"2011","journal-title":"Vet Microbiol"},{"key":"pone.0342894.ref021","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1016\/j.vetmic.2010.07.013","article-title":"The extra-intestinal avian pathogenic Escherichia coli strain BEN2908 invades avian and human epithelial cells and survives intracellularly","volume":"147","author":"NK Chanteloup","year":"2011","journal-title":"Vet Microbiol"},{"key":"pone.0342894.ref022","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1099\/mic.0.27809-0","article-title":"ibeA, a virulence factor of avian pathogenic Escherichia coli","volume":"151","author":"P Germon","year":"2005","journal-title":"Microbiology (Reading)"},{"issue":"16","key":"pone.0342894.ref023","doi-asserted-by":"crossref","first-page":"5813","DOI":"10.1128\/AEM.02614-10","article-title":"Adherent-invasive Escherichia coli phenotype displayed by intestinal pathogenic E. coli strains from cats, dogs, and swine","volume":"77","author":"M Martinez-Medina","year":"2011","journal-title":"Appl Environ Microbiol"},{"issue":"9","key":"pone.0342894.ref024","doi-asserted-by":"crossref","first-page":"4129","DOI":"10.1128\/IAI.00334-08","article-title":"Inactivation of ibeA and ibeT results in decreased expression of type 1 fimbriae in extraintestinal pathogenic Escherichia coli strain BEN2908","volume":"76","author":"MAM Cortes","year":"2008","journal-title":"Infect Immun"},{"issue":"17","key":"pone.0342894.ref025","doi-asserted-by":"crossref","first-page":"4550","DOI":"10.1128\/JB.00089-12","article-title":"New role for the ibeA gene in H2O2 stress resistance of Escherichia coli","volume":"194","author":"M Fl\u00e9chard","year":"2012","journal-title":"J Bacteriol"},{"issue":"6","key":"pone.0342894.ref026","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1016\/S0016-5085(98)70019-8","article-title":"Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn\u2019s disease","volume":"115","author":"A Darfeuille-Michaud","year":"1998","journal-title":"Gastroenterology"},{"key":"pone.0342894.ref027","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1186\/1471-2164-11-667","article-title":"Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes","volume":"11","author":"JH Nash","year":"2010","journal-title":"BMC Genomics"},{"issue":"9","key":"pone.0342894.ref028","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0012714","article-title":"Complete genome sequence of Crohn\u2019s disease-associated adherent-invasive E. coli strain LF82","volume":"5","author":"S Miquel","year":"2010","journal-title":"PLoS One"},{"issue":"5","key":"pone.0342894.ref029","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1111\/cmi.12539","article-title":"The Vat-AIEC protease promotes crossing of the intestinal mucus layer by Crohn\u2019s disease-associated Escherichia coli","volume":"18","author":"L Gibold","year":"2016","journal-title":"Cell Microbiol"},{"issue":"9","key":"pone.0342894.ref030","doi-asserted-by":"crossref","first-page":"5087","DOI":"10.1128\/IAI.71.9.5087-5096.2003","article-title":"A novel pathogenicity island integrated adjacent to the thrW tRNA gene of avian pathogenic Escherichia coli encodes a vacuolating autotransporter toxin","volume":"71","author":"VR Parreira","year":"2003","journal-title":"Infect Immun"},{"issue":"1","key":"pone.0342894.ref031","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/s42003-021-02161-7","article-title":"The Crohn\u2019s disease-related bacterial strain LF82 assembles biofilm-like communities to protect itself from phagolysosomal attack","volume":"4","author":"V Prudent","year":"2021","journal-title":"Commun Biol"},{"issue":"6","key":"pone.0342894.ref032","doi-asserted-by":"crossref","first-page":"3183","DOI":"10.1128\/IAI.00656-06","article-title":"The salmochelin siderophore receptor IroN contributes to invasion of urothelial cells by extraintestinal pathogenic Escherichia coli in vitro","volume":"75","author":"F Feldmann","year":"2007","journal-title":"Infect Immun"},{"issue":"5","key":"pone.0342894.ref033","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1007\/s101420100039","article-title":"A novel genetic island of meningitic Escherichia coli K1 containing the ibeA invasion gene (GimA): functional annotation and carbon-source-regulated invasion of human brain microvascular endothelial cells","volume":"1","author":"SH Huang","year":"2001","journal-title":"Funct Integr Genomics"},{"issue":"8","key":"pone.0342894.ref034","doi-asserted-by":"crossref","first-page":"2655","DOI":"10.1128\/IAI.00457-12","article-title":"Role of the vpe carbohydrate permease in Escherichia coli urovirulence and fitness in vivo","volume":"80","author":"V Martinez-J\u00e9hanne","year":"2012","journal-title":"Infect Immun"},{"issue":"9","key":"pone.0342894.ref035","doi-asserted-by":"crossref","first-page":"5335","DOI":"10.1128\/IAI.70.9.5335-5337.2002","article-title":"Yersinia high-pathogenicity island contributes to virulence in Escherichia coli causing extraintestinal infections","volume":"70","author":"S Schubert","year":"2002","journal-title":"Infect Immun"},{"issue":"1","key":"pone.0342894.ref036","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1080\/21505594.2019.1573491","article-title":"Characterization of multiple type-VI secretion system (T6SS) VgrG proteins in the pathogenicity and antibacterial activity of porcine extra-intestinal pathogenic Escherichia coli","volume":"10","author":"B Zong","year":"2019","journal-title":"Virulence"},{"issue":"15","key":"pone.0342894.ref037","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: visualizing and processing long-read sequencing data","volume":"34","author":"W De Coster","year":"2018","journal-title":"Bioinformatics"},{"issue":"15","key":"pone.0342894.ref038","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"pone.0342894.ref039","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae410","article-title":"The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update","volume":"52","author":"Galaxy Community","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"14","key":"pone.0342894.ref040","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"5","key":"pone.0342894.ref041","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"S Koren","year":"2017","journal-title":"Genome Res"},{"issue":"11","key":"pone.0342894.ref042","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"BJ Walker","year":"2014","journal-title":"PLoS One"},{"key":"pone.0342894.ref043","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology","volume":"9","author":"RK Aziz","year":"2008","journal-title":"BMC Genomics"},{"issue":"8","key":"pone.0342894.ref044","doi-asserted-by":"crossref","first-page":"3228","DOI":"10.1128\/JB.01726-06","article-title":"The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes","volume":"189","author":"TJ Johnson","year":"2007","journal-title":"J Bacteriol"},{"issue":"11","key":"pone.0342894.ref045","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0112048","article-title":"Comparative genomic analysis shows that avian pathogenic Escherichia coli isolate IMT5155 (O2:K1:H5; ST complex 95, ST140) shares close relationship with ST95 APEC O1:K1 and human ExPEC O18:K1 strains","volume":"9","author":"X Zhu Ge","year":"2014","journal-title":"PLoS One"},{"issue":"3","key":"pone.0342894.ref046","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1128\/IAI.00585-12","article-title":"Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms","volume":"81","author":"F Dziva","year":"2013","journal-title":"Infect Immun"},{"issue":"4","key":"pone.0342894.ref047","article-title":"Complete Genome Sequence of Escherichia coli Strain RS218 (O18:H7:K1), Associated with Neonatal Meningitis","volume":"3","author":"DSS Wijetunge","year":"2015","journal-title":"Genome Announc"},{"issue":"20","key":"pone.0342894.ref048","doi-asserted-by":"crossref","first-page":"9072","DOI":"10.1073\/pnas.0915077107","article-title":"Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli","volume":"107","author":"DG Moriel","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"15","key":"pone.0342894.ref049","doi-asserted-by":"crossref","first-page":"5977","DOI":"10.1073\/pnas.0600938103","article-title":"Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach","volume":"103","author":"SL Chen","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"26","key":"pone.0342894.ref050","doi-asserted-by":"crossref","first-page":"17020","DOI":"10.1073\/pnas.252529799","article-title":"Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli","volume":"99","author":"RA Welch","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pone.0342894.ref051","doi-asserted-by":"crossref","first-page":"5968","DOI":"10.1038\/s41467-020-19714-9","article-title":"Horizontally acquired papGII-containing pathogenicity islands underlie the emergence of invasive uropathogenic Escherichia coli lineages","volume":"11","author":"M Biggel","year":"2020","journal-title":"Nat Commun"},{"key":"pone.0342894.ref052","doi-asserted-by":"crossref","first-page":"14145","DOI":"10.1038\/srep14145","article-title":"Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association","volume":"5","author":"NJC Strachan","year":"2015","journal-title":"Sci Rep"},{"issue":"26","key":"pone.0342894.ref053","doi-asserted-by":"crossref","first-page":"17043","DOI":"10.1073\/pnas.262441699","article-title":"Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning","volume":"99","author":"M Ohnishi","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0342894.ref054","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.3389\/fmicb.2017.01625","article-title":"The mobilome; a major contributor to Escherichia coli stx2-Positive O26:H11 Strains Intra-Serotype Diversity","volume":"8","author":"S Delannoy","year":"2017","journal-title":"Front Microbiol"},{"issue":"42","key":"pone.0342894.ref055","doi-asserted-by":"crossref","first-page":"17939","DOI":"10.1073\/pnas.0903585106","article-title":"Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli","volume":"106","author":"Y Ogura","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pone.0342894.ref056","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0008801","article-title":"Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042","volume":"5","author":"RR Chaudhuri","year":"2010","journal-title":"PLoS One"},{"issue":"11","key":"pone.0342894.ref057","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0048228","article-title":"Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2","volume":"7","author":"SA Ahmed","year":"2012","journal-title":"PLoS One"},{"issue":"3","key":"pone.0342894.ref058","doi-asserted-by":"crossref","first-page":"473","DOI":"10.3201\/eid1803.111281","article-title":"Escherichia coli O104:H4 infections and international travel","volume":"18","author":"DC Alexander","year":"2012","journal-title":"Emerg Infect Dis"},{"issue":"21","key":"pone.0342894.ref059","doi-asserted-by":"crossref","first-page":"5822","DOI":"10.1128\/JB.00710-10","article-title":"A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407","volume":"192","author":"LC Crossman","year":"2010","journal-title":"J Bacteriol"},{"issue":"20","key":"pone.0342894.ref060","doi-asserted-by":"crossref","first-page":"6881","DOI":"10.1128\/JB.00619-08","article-title":"The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates","volume":"190","author":"DA Rasko","year":"2008","journal-title":"J Bacteriol"},{"issue":"1","key":"pone.0342894.ref061","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1128\/JB.01238-08","article-title":"Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348\/69","volume":"191","author":"A Iguchi","year":"2009","journal-title":"J Bacteriol"},{"issue":"5331","key":"pone.0342894.ref062","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1126\/science.277.5331.1453","article-title":"The complete genome sequence of Escherichia coli K-12","volume":"277","author":"FR Blattner","year":"1997","journal-title":"Science"},{"issue":"4","key":"pone.0342894.ref063","doi-asserted-by":"crossref","DOI":"10.1128\/msphere.00709-20","article-title":"F plasmids are the major carriers of antibiotic resistance genes in human-associated commensal Escherichia coli","volume":"5","author":"C Stephens","year":"2020","journal-title":"mSphere"},{"issue":"1","key":"pone.0342894.ref064","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1101\/gr.251678.119","article-title":"The EnteroBase user\u2019s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity","volume":"30","author":"Agama Study Group","year":"2020","journal-title":"Genome Res"},{"issue":"7","key":"pone.0342894.ref065","article-title":"ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping","volume":"4","author":"J Beghain","year":"2018","journal-title":"Microb Genom"},{"issue":"8","key":"pone.0342894.ref066","doi-asserted-by":"crossref","first-page":"2410","DOI":"10.1128\/JCM.00008-15","article-title":"Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data","volume":"53","author":"KG Joensen","year":"2015","journal-title":"J Clin Microbiol"},{"key":"pone.0342894.ref067","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"pone.0342894.ref068","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"MV Larsen","year":"2012","journal-title":"J Clin Microbiol"},{"issue":"8","key":"pone.0342894.ref069","doi-asserted-by":"crossref","first-page":"2538","DOI":"10.1128\/JCM.00737-17","article-title":"Development of a Web Tool for Escherichia coli Subtyping Based on fimH Alleles","volume":"55","author":"L Roer","year":"2017","journal-title":"J Clin Microbiol"},{"key":"pone.0342894.ref070","article-title":"VFDB 2022: a general classification scheme for bacterial virulence factors","volume":"50","author":"B Liu","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"pone.0342894.ref071","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1089\/crispr.2020.0059","article-title":"CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci","volume":"3","author":"J Russel","year":"2020","journal-title":"CRISPR J"},{"key":"pone.0342894.ref072","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1186\/1471-2105-8-209","article-title":"CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats","volume":"8","author":"C Bland","year":"2007","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"pone.0342894.ref073","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1007\/s11427-022-2172-x","article-title":"SecReT6 update: a comprehensive resource of bacterial Type VI Secretion Systems","volume":"66","author":"J Zhang","year":"2023","journal-title":"Sci China Life Sci"},{"key":"pone.0342894.ref074","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkad382","article-title":"PHASTEST: faster than PHASTER, better than PHAST","volume":"51","author":"DS Wishart","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"22","key":"pone.0342894.ref075","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"AJ Page","year":"2015","journal-title":"Bioinformatics"},{"key":"pone.0342894.ref076","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae909","article-title":"KEGG: biological systems database as a model of the real world","volume":"53","author":"M Kanehisa","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"pone.0342894.ref077","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1007\/978-1-62703-646-7_10","article-title":"Phylogeny-aware alignment with PRANK","volume":"1079","author":"A L\u00f6ytynoja","year":"2014","journal-title":"Methods Mol Biol"},{"issue":"1","key":"pone.0342894.ref078","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"DM Emms","year":"2019","journal-title":"Genome Biol"},{"issue":"5","key":"pone.0342894.ref079","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"RC Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"pone.0342894.ref080","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"S Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"issue":"9","key":"pone.0342894.ref081","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"A Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"pone.0342894.ref082","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"I Letunic","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"pone.0342894.ref083","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1007\/s12275-021-1154-0","article-title":"Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity","volume":"59","author":"D Kim","year":"2021","journal-title":"J Microbiol"},{"key":"pone.0342894.ref084","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1186\/1471-2164-12-402","article-title":"BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons","volume":"12","author":"N-F Alikhan","year":"2011","journal-title":"BMC Genomics"},{"issue":"4","key":"pone.0342894.ref085","article-title":"Escherichia coli ST131-H22 as a Foodborne Uropathogen","volume":"9","author":"CM Liu","year":"2018","journal-title":"mBio"},{"issue":"12","key":"pone.0342894.ref086","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1086\/375347","article-title":"Molecular analysis and experimental virulence of French and North American Escherichia coli neonatal meningitis isolates: identification of a new virulent clone","volume":"187","author":"S Bonacorsi","year":"2003","journal-title":"J Infect Dis"},{"issue":"5","key":"pone.0342894.ref087","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0010877","article-title":"The GimA locus of extraintestinal pathogenic E. coli: does reductive evolution correlate with habitat and pathotype?","volume":"5","author":"T Homeier","year":"2010","journal-title":"PLoS One"},{"key":"pone.0342894.ref088","article-title":"CDD\/SPARCLE: the conserved domain database in 2020","volume":"48","author":"S Lu","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"pone.0342894.ref089","article-title":"The conserved domain database in 2023","volume":"51","author":"J Wang","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"pone.0342894.ref090","doi-asserted-by":"crossref","first-page":"2304","DOI":"10.1021\/acschembio.6b00279","article-title":"Members of a novel kinase family (DUF1537) can recycle toxic intermediates into an essential metabolite","volume":"11","author":"JJ Thiaville","year":"2016","journal-title":"ACS Chem Biol"},{"key":"pone.0342894.ref091","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1016\/j.gene.2004.11.005","article-title":"Identification of the gene for the monomeric alkaline phosphatase of Vibrio cholerae serogroup O1 strain","volume":"344","author":"A Majumdar","year":"2005","journal-title":"Gene"},{"key":"pone.0342894.ref092","doi-asserted-by":"crossref","DOI":"10.21307\/jofnem-2021-021","article-title":"The grazing activity of Acrobeloides sp. drives phytate mineralisation within its trophic relationship with bacteria","volume":"53","author":"M Garc\u00eda-S\u00e1nchez","year":"2021","journal-title":"J Nematol"},{"issue":"3","key":"pone.0342894.ref093","doi-asserted-by":"crossref","first-page":"200","DOI":"10.4167\/jbv.2015.45.3.200","article-title":"Transcriptional profiling of an attenuated Salmonella Typhimurium ptsI mutant strain under low-oxygen conditions using microarray analysis","volume":"45","author":"S Lim","year":"2015","journal-title":"J Bacteriol Virol"},{"issue":"1","key":"pone.0342894.ref094","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003141","article-title":"Point mutations in FimH adhesin of Crohn\u2019s disease-associated adherent-invasive Escherichia coli enhance intestinal inflammatory response","volume":"9","author":"N Dreux","year":"2013","journal-title":"PLoS Pathog"},{"issue":"39","key":"pone.0342894.ref095","doi-asserted-by":"crossref","first-page":"15530","DOI":"10.1073\/pnas.1315203110","article-title":"Positively selected FimH residues enhance virulence during urinary tract infection by altering FimH conformation","volume":"110","author":"DJ Schwartz","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1772","key":"pone.0342894.ref096","doi-asserted-by":"crossref","first-page":"20180087","DOI":"10.1098\/rstb.2018.0087","article-title":"Origins and evolution of CRISPR-Cas systems","volume":"374","author":"EV Koonin","year":"2019","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"pone.0342894.ref097","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1016\/j.meegid.2013.09.031","article-title":"Genetic diversity and features analysis of type VI secretion systems loci in avian pathogenic Escherichia coli by wide genomic scanning","volume":"20","author":"J Ma","year":"2013","journal-title":"Infect Genet Evol"},{"issue":"12","key":"pone.0342894.ref098","doi-asserted-by":"crossref","first-page":"3159","DOI":"10.1128\/JB.184.12.3159-3166.2002","article-title":"SitABCD is the alkaline Mn(2+) transporter of Salmonella enterica serovar Typhimurium","volume":"184","author":"DG Kehres","year":"2002","journal-title":"J Bacteriol"},{"issue":"9","key":"pone.0342894.ref099","doi-asserted-by":"crossref","first-page":"3532","DOI":"10.1128\/JB.01744-06","article-title":"Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli","volume":"189","author":"AL Lloyd","year":"2007","journal-title":"J Bacteriol"},{"key":"pone.0342894.ref100","first-page":"1040","article-title":"Sur un remarquable exemple d\u2019antagonisme entre deux souches de colibacille","volume":"93","author":"A Gratia","year":"1925","journal-title":"C R Soc Biol"},{"issue":"8","key":"pone.0342894.ref101","doi-asserted-by":"crossref","first-page":"3539","DOI":"10.1128\/IAI.00455-08","article-title":"Specific roles of the iroBCDEN genes in virulence of an avian pathogenic Escherichia coli O78 strain and in production of salmochelins","volume":"76","author":"M Caza","year":"2008","journal-title":"Infect Immun"},{"issue":"11","key":"pone.0342894.ref102","doi-asserted-by":"crossref","DOI":"10.1016\/j.cmi.2023.07.024","article-title":"HlyF, an underestimated virulence factor of uropathogenic Escherichia coli","volume":"29","author":"CV Chagneau","year":"2023","journal-title":"Clin Microbiol Infect"},{"issue":"5","key":"pone.0342894.ref103","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1093\/infdis\/jiv506","article-title":"HlyF produced by extraintestinal pathogenic Escherichia coli Is a virulence factor that regulates outer membrane vesicle biogenesis","volume":"213","author":"K Murase","year":"2016","journal-title":"J Infect Dis"},{"issue":"2","key":"pone.0342894.ref104","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1128\/iai.24.2.562-564.1979","article-title":"Relationship between colicin V activity and virulence in Escherichia coli","volume":"24","author":"RL Quackenbush","year":"1979","journal-title":"Infect Immun"},{"issue":"1","key":"pone.0342894.ref105","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1038\/s41467-022-28342-4","article-title":"A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58","volume":"13","author":"CJ Reid","year":"2022","journal-title":"Nat Commun"},{"issue":"4","key":"pone.0342894.ref106","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1128\/IAI.00981-09","article-title":"Characterization of the contribution to virulence of three large plasmids of avian pathogenic Escherichia coli chi7122 (O78:K80:H9)","volume":"78","author":"M Mellata","year":"2010","journal-title":"Infect Immun"},{"issue":"2","key":"pone.0342894.ref107","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1023\/A:1022854902700","article-title":"Resistance to serum complement, iss, and virulence of avian Escherichia coli","volume":"27","author":"LK Nolan","year":"2003","journal-title":"Vet Res Commun"},{"issue":"3","key":"pone.0342894.ref108","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/S0147-619X(02)00013-6","article-title":"Characterisation and distribution of a cryptic Salmonella typhi plasmid pHCM2","volume":"47","author":"C Kidgell","year":"2002","journal-title":"Plasmid"},{"issue":"1","key":"pone.0342894.ref109","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1038\/s41579-020-0416-x","article-title":"The population genetics of pathogenic Escherichia coli","volume":"19","author":"E Denamur","year":"2021","journal-title":"Nat Rev Microbiol"},{"issue":"5","key":"pone.0342894.ref110","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1128\/JCM.05057-11","article-title":"Diagnostic strategy for identifying avian pathogenic Escherichia coli based on four patterns of virulence genes","volume":"50","author":"C Schouler","year":"2012","journal-title":"J Clin Microbiol"},{"issue":"6","key":"pone.0342894.ref111","doi-asserted-by":"crossref","first-page":"2300","DOI":"10.1128\/JCM.39.6.2300-2305.2001","article-title":"Prevalence of iron transport gene on pathogenicity-associated island of uropathogenic Escherichia coli in E. coli O157:H7 containing Shiga toxin gene","volume":"39","author":"C Ye","year":"2001","journal-title":"J Clin Microbiol"},{"issue":"12","key":"pone.0342894.ref112","doi-asserted-by":"crossref","first-page":"6949","DOI":"10.1128\/IAI.00866-06","article-title":"Identification and characterization of a novel ABC iron transport system, fit, in Escherichia coli","volume":"74","author":"Z Ouyang","year":"2006","journal-title":"Infect Immun"},{"issue":"4","key":"pone.0342894.ref113","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1002\/pro.84","article-title":"Structure and heme binding properties of Escherichia coli O157:H7 ChuX","volume":"18","author":"MDL Suits","year":"2009","journal-title":"Protein Sci"},{"issue":"2","key":"pone.0342894.ref114","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00010-12","article-title":"FdeC, a novel broadly conserved Escherichia coli adhesin eliciting protection against urinary tract infections","volume":"3","author":"B Nesta","year":"2012","journal-title":"mBio"},{"key":"pone.0342894.ref115","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1099\/mic.0.066472-0","article-title":"The type 1 pili regulator gene fimX and pathogenicity island PAI-X as molecular markers of uropathogenic Escherichia coli","volume":"159","author":"SL Bateman","year":"2013","journal-title":"Microbiology (Reading)"},{"issue":"2","key":"pone.0342894.ref116","article-title":"Loss of an intimin-like protein encoded on a uropathogenic E. coli pathogenicity island reduces inflammation and affects interactions with the urothelium","volume":"90","author":"AE Shea","year":"2022","journal-title":"Infect Immun"},{"issue":"7","key":"pone.0342894.ref117","doi-asserted-by":"crossref","first-page":"3890","DOI":"10.1128\/IAI.72.7.3890-3901.2004","article-title":"Identification and characterization of a novel uropathogenic Escherichia coli-associated fimbrial gene cluster","volume":"72","author":"EL Buckles","year":"2004","journal-title":"Infect Immun"},{"issue":"3","key":"pone.0342894.ref118","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1128\/jb.173.3.1335-1338.1991","article-title":"Map position and genomic organization of the kps cluster for polysialic acid synthesis in Escherichia coli K1","volume":"173","author":"ER Vimr","year":"1991","journal-title":"J Bacteriol"},{"key":"pone.0342894.ref119","doi-asserted-by":"crossref","first-page":"622725","DOI":"10.3389\/fvets.2021.622725","article-title":"Insight into the virulence related secretion systems, fimbriae, and toxins in O2:K1 Escherichia coli Isolated From Bovine Mastitis","volume":"8","author":"M Sun","year":"2021","journal-title":"Front Vet Sci"},{"issue":"39","key":"pone.0342894.ref120","doi-asserted-by":"crossref","first-page":"15508","DOI":"10.1073\/pnas.0706532104","article-title":"Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin","volume":"104","author":"S Pukatzki","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0342894.ref121","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/1471-2180-12-51","article-title":"tkt1, located on a novel pathogenicity island, is prevalent in avian and human extraintestinal pathogenic Escherichia coli","volume":"12","author":"G Li","year":"2012","journal-title":"BMC Microbiol"},{"issue":"1","key":"pone.0342894.ref122","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/S0021-9258(17)43626-X","article-title":"Nucleotide sequence of dnaB and the primary structure of the dnaB protein from Escherichia coli","volume":"259","author":"N Nakayama","year":"1984","journal-title":"J Biol Chem"},{"issue":"6","key":"pone.0342894.ref123","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1110\/ps.083495908","article-title":"Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis","volume":"17","author":"D Wu","year":"2008","journal-title":"Protein Sci"},{"issue":"1","key":"pone.0342894.ref124","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/0006-291X(85)91851-0","article-title":"Aromatic amino acid aminotransferase of Escherichia coli: nucleotide sequence of the tyrB gene","volume":"133","author":"S Kuramitsu","year":"1985","journal-title":"Biochem Biophys Res Commun"},{"issue":"4","key":"pone.0342894.ref125","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0121830","article-title":"Alanine aminotransferase variants conferring diverse NUE phenotypes in Arabidopsis thaliana","volume":"10","author":"CH McAllister","year":"2015","journal-title":"PLoS One"},{"issue":"17","key":"pone.0342894.ref126","doi-asserted-by":"crossref","first-page":"5035","DOI":"10.1128\/jb.177.17.5035-5039.1995","article-title":"MalY of Escherichia coli is an enzyme with the activity of a beta C-S lyase (cystathionase)","volume":"177","author":"E Zdych","year":"1995","journal-title":"J Bacteriol"},{"issue":"23","key":"pone.0342894.ref127","doi-asserted-by":"crossref","first-page":"6790","DOI":"10.1128\/jb.178.23.6790-6795.1996","article-title":"Molecular analysis of the gat genes from Escherichia coli and of their roles in galactitol transport and metabolism","volume":"178","author":"B Nobelmann","year":"1996","journal-title":"J Bacteriol"},{"issue":"7","key":"pone.0342894.ref128","doi-asserted-by":"crossref","first-page":"1829","DOI":"10.1007\/s12010-014-0969-0","article-title":"The yjjN of E. coli codes for an L-galactonate dehydrogenase and can be used for quantification of L-galactonate and L-gulonate","volume":"173","author":"J Kuivanen","year":"2014","journal-title":"Appl Biochem Biotechnol"},{"issue":"1","key":"pone.0342894.ref129","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1128\/jb.145.1.211-220.1981","article-title":"Regulation of hexuronate system genes in Escherichia coli K-12: multiple regulation of the uxu operon by exuR and uxuR gene products","volume":"145","author":"J Robert-Baudouy","year":"1981","journal-title":"J Bacteriol"},{"key":"pone.0342894.ref130","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1146\/annurev.micro.54.1.881","article-title":"Iron metabolism in pathogenic bacteria","volume":"54","author":"C Ratledge","year":"2000","journal-title":"Annu Rev Microbiol"},{"key":"pone.0342894.ref131","doi-asserted-by":"crossref","first-page":"90","DOI":"10.3389\/fcimb.2013.00090","article-title":"Iron, copper, zinc, and manganese transport and regulation in pathogenic Enterobacteria: correlations between strains, site of infection and the relative importance of the different metal transport systems for virulence","volume":"3","author":"G Porcheron","year":"2013","journal-title":"Front Cell Infect Microbiol"},{"issue":"10","key":"pone.0342894.ref132","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1016\/j.micinf.2011.04.008","article-title":"Yersiniabactin iron uptake: mechanisms and role in Yersinia pestis pathogenesis","volume":"13","author":"RD Perry","year":"2011","journal-title":"Microbes Infect"},{"issue":"1","key":"pone.0342894.ref133","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1111\/j.1365-2958.2011.07570.x","article-title":"Secretion, but not overall synthesis, of catecholate siderophores contributes to virulence of extraintestinal pathogenic Escherichia coli","volume":"80","author":"M Caza","year":"2011","journal-title":"Mol Microbiol"},{"issue":"5","key":"pone.0342894.ref134","doi-asserted-by":"crossref","first-page":"2818","DOI":"10.1128\/IAI.73.5.2818-2827.2005","article-title":"Identification of genes required for avian Escherichia coli septicemia by signature-tagged mutagenesis","volume":"73","author":"G Li","year":"2005","journal-title":"Infect Immun"},{"issue":"4","key":"pone.0342894.ref135","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.2307\/1590278","article-title":"Adhesive properties and iron uptake ability in Escherichia coli lethal and nonlethal for chicks","volume":"28","author":"M Dho","year":"1984","journal-title":"Avian Dis"},{"issue":"5","key":"pone.0342894.ref136","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1128\/IAI.01230-10","article-title":"Transcriptome analysis of avian pathogenic Escherichia coli O1 in chicken serum reveals adaptive responses to systemic infection","volume":"79","author":"G Li","year":"2011","journal-title":"Infect Immun"},{"issue":"6","key":"pone.0342894.ref137","doi-asserted-by":"crossref","first-page":"1389","DOI":"10.1002\/j.1460-2075.1986.tb04372.x","article-title":"Two regulatory fim genes, fimB and fimE, control the phase variation of type 1 fimbriae in Escherichia coli","volume":"5","author":"P Klemm","year":"1986","journal-title":"EMBO J"},{"issue":"7","key":"pone.0342894.ref138","doi-asserted-by":"crossref","first-page":"3325","DOI":"10.1128\/IAI.01989-06","article-title":"Regulation of P-fimbrial phase variation frequencies in Escherichia coli CFT073","volume":"75","author":"N Holden","year":"2007","journal-title":"Infect Immun"},{"issue":"1","key":"pone.0342894.ref139","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1111\/j.1365-2958.2007.06025.x","article-title":"LeuX tRNA-dependent and -independent mechanisms of Escherichia coli pathogenesis in acute cystitis","volume":"67","author":"TJ Hannan","year":"2008","journal-title":"Mol Microbiol"},{"issue":"1","key":"pone.0342894.ref140","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/s12223-019-00719-x","article-title":"Classical chaperone-usher (CU) adhesive fimbriome: uropathogenic Escherichia coli (UPEC) and urinary tract infections (UTIs)","volume":"65","author":"P Behzadi","year":"2020","journal-title":"Folia Microbiol (Praha)"},{"issue":"3","key":"pone.0342894.ref141","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1590\/S1517-838246320140621","article-title":"Invasin gimB found in a bovine intestinal Escherichia coli with an adherent and invasive profile","volume":"46","author":"LB Matter","year":"2015","journal-title":"Braz J Microbiol"},{"issue":"9","key":"pone.0342894.ref142","doi-asserted-by":"crossref","first-page":"3657","DOI":"10.1128\/IAI.01890-14","article-title":"Contribution of the highly conserved EaeH surface protein to enterotoxigenic Escherichia coli pathogenesis","volume":"82","author":"A Sheikh","year":"2014","journal-title":"Infect Immun"},{"key":"pone.0342894.ref143","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1146\/annurev.biochem.75.103004.142545","article-title":"Biosynthesis and assembly of capsular polysaccharides in Escherichia coli","volume":"75","author":"C Whitfield","year":"2006","journal-title":"Annu Rev Biochem"},{"issue":"1","key":"pone.0342894.ref144","doi-asserted-by":"crossref","DOI":"10.1128\/ecosalplus.esp-0001-2018","article-title":"Function and biogenesis of lipopolysaccharides","volume":"8","author":"B Bertani","year":"2018","journal-title":"EcoSal Plus"},{"issue":"2","key":"pone.0342894.ref145","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/j.bbrc.2009.07.154","article-title":"Structure prediction and functional analysis of KdsD, an enzyme involved in lipopolysaccharide biosynthesis","volume":"388","author":"S Sommaruga","year":"2009","journal-title":"Biochem Biophys Res Commun"},{"issue":"2","key":"pone.0342894.ref146","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/nrmicro3185","article-title":"Type VI secretion system effectors: poisons with a purpose","volume":"12","author":"AB Russell","year":"2014","journal-title":"Nat Rev Microbiol"},{"issue":"7","key":"pone.0342894.ref147","doi-asserted-by":"crossref","first-page":"2196","DOI":"10.1111\/1462-2920.12794","article-title":"SecReT6: a web-based resource for type VI secretion systems found in bacteria","volume":"17","author":"J Li","year":"2015","journal-title":"Environ Microbiol"},{"issue":"1","key":"pone.0342894.ref148","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1111\/j.1758-2229.2012.00394.x","article-title":"Distribution and diversity of bacterial secretion systems across metagenomic datasets","volume":"5","author":"M Barret","year":"2013","journal-title":"Environ Microbiol Rep"},{"key":"pone.0342894.ref149","doi-asserted-by":"crossref","first-page":"588","DOI":"10.3389\/fmicb.2014.00588","article-title":"DotU expression is highly induced during in vivo infection and responsible for virulence and Hcp1 secretion in avian pathogenic Escherichia coli","volume":"5","author":"S Wang","year":"2014","journal-title":"Front Microbiol"},{"issue":"14","key":"pone.0342894.ref150","doi-asserted-by":"crossref","first-page":"12317","DOI":"10.1074\/jbc.M110.193045","article-title":"Type VI secretion system in Pseudomonas aeruginosa: secretion and multimerization of VgrG proteins","volume":"286","author":"A Hachani","year":"2011","journal-title":"J Biol Chem"},{"issue":"16","key":"pone.0342894.ref151","doi-asserted-by":"crossref","first-page":"4089","DOI":"10.1128\/JB.00201-10","article-title":"The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems","volume":"192","author":"K-S Kim","year":"2010","journal-title":"J Bacteriol"},{"issue":"10","key":"pone.0342894.ref152","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1111\/j.1365-2958.1992.tb00854.x","article-title":"Characterization of the Escherichia coli codBA operon encoding cytosine permease and cytosine deaminase","volume":"6","author":"S Danielsen","year":"1992","journal-title":"Mol Microbiol"},{"issue":"12","key":"pone.0342894.ref153","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.4014\/jmb.2210.10037","article-title":"The ybcF Gene of Escherichia coli encodes a local orphan enzyme, catabolic carbamate kinase","volume":"32","author":"NY Kim","year":"2022","journal-title":"J Microbiol Biotechnol"},{"key":"pone.0342894.ref154","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.enzmictec.2014.03.003","article-title":"Identification of UshA as a major enzyme for NAD degradation in Escherichia coli","author":"L Wang","year":"2014","journal-title":"Enzyme Microb Technol"},{"key":"pone.0342894.ref155","doi-asserted-by":"crossref","first-page":"3055","DOI":"10.3389\/fimmu.2019.03055","article-title":"Avian Pathogenic Escherichia coli (APEC) strain-dependent immunomodulation of respiratory granulocytes and mononuclear phagocytes in CSF1R-reporter transgenic chickens","volume":"10","author":"A Alber","year":"2020","journal-title":"Front Immunol"},{"issue":"5","key":"pone.0342894.ref156","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1007\/s00424-005-1487-2","article-title":"Molecular properties of the SLC13 family of dicarboxylate and sulfate transporters","volume":"451","author":"AM Pajor","year":"2006","journal-title":"Pflugers Arch"},{"issue":"16","key":"pone.0342894.ref157","doi-asserted-by":"crossref","first-page":"4160","DOI":"10.1128\/JB.180.16.4160-4165.1998","article-title":"The Escherichia coli citrate carrier CitT: a member of a novel eubacterial transporter family related to the 2-oxoglutarate\/malate translocator from spinach chloroplasts","volume":"180","author":"KM Pos","year":"1998","journal-title":"J Bacteriol"},{"key":"pone.0342894.ref158","doi-asserted-by":"crossref","first-page":"3431","DOI":"10.1099\/00221287-145-12-3431","article-title":"TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters","author":"R Rabus","year":"1999","journal-title":"Microbiology (Reading)"},{"issue":"17","key":"pone.0342894.ref159","doi-asserted-by":"crossref","first-page":"4307","DOI":"10.1128\/JB.05074-11","article-title":"Identification of C(4)-dicarboxylate transport systems in Pseudomonas aeruginosa PAO1","volume":"193","author":"M Valentini","year":"2011","journal-title":"J Bacteriol"},{"issue":"7","key":"pone.0342894.ref160","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1093\/molbev\/msv072","article-title":"High Recombinant Frequency in Extraintestinal Pathogenic Escherichia coli Strains","volume":"32","author":"J Rodr\u00edguez-Beltr\u00e1n","year":"2015","journal-title":"Mol Biol Evol"},{"key":"pone.0342894.ref161","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1186\/1471-2164-13-256","article-title":"Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli","volume":"13","author":"X Didelot","year":"2012","journal-title":"BMC Genomics"},{"issue":"7","key":"pone.0342894.ref162","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1111\/febs.15185","article-title":"How enzyme promiscuity and horizontal gene transfer contribute to metabolic innovation","volume":"287","author":"ME Glasner","year":"2020","journal-title":"FEBS J"},{"issue":"12","key":"pone.0342894.ref163","doi-asserted-by":"crossref","first-page":"5613","DOI":"10.1073\/pnas.1815994116","article-title":"Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes","volume":"116","author":"DS Milner","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"pone.0342894.ref164","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0096953","article-title":"Ecotype diversity and conversion in Photobacterium profundum strains","volume":"9","author":"FM Lauro","year":"2014","journal-title":"PLoS One"},{"key":"pone.0342894.ref165","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/1471-2164-6-122","article-title":"Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains","volume":"6","author":"S Campanaro","year":"2005","journal-title":"BMC Genomics"},{"key":"pone.0342894.ref166","doi-asserted-by":"crossref","first-page":"186","DOI":"10.3389\/fmicb.2019.00186","article-title":"Comparative genomic analysis reveals the potential risk of Vibrio parahaemolyticus Isolated From Ready-To-Eat Foods in China","volume":"10","author":"R Pang","year":"2019","journal-title":"Front Microbiol"},{"key":"pone.0342894.ref167","doi-asserted-by":"crossref","first-page":"126410","DOI":"10.1016\/j.micres.2020.126410","article-title":"Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15","volume":"233","author":"NN Roslan","year":"2020","journal-title":"Microbiol Res"},{"issue":"10","key":"pone.0342894.ref168","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1016\/j.jcma.2011.08.013","article-title":"Chromobacterium violaceum infection: a clinical review of an important but neglected infection","volume":"74","author":"C-H Yang","year":"2011","journal-title":"J Chin Med Assoc"},{"issue":"6","key":"pone.0342894.ref169","doi-asserted-by":"crossref","first-page":"3088","DOI":"10.1128\/IAI.71.6.3088-3096.2003","article-title":"DegS is necessary for virulence and is among extraintestinal Escherichia coli genes induced in murine peritonitis","volume":"71","author":"P Redford","year":"2003","journal-title":"Infect Immun"},{"issue":"3","key":"pone.0342894.ref170","doi-asserted-by":"crossref","DOI":"10.1016\/j.chom.2017.07.018","article-title":"An oxidative central metabolism enables Salmonella to utilize microbiota-derived succinate","volume":"22","author":"L Spiga","year":"2017","journal-title":"Cell Host Microbe"},{"issue":"8","key":"pone.0342894.ref171","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.00635-19","article-title":"The arginine deiminase operon is responsible for a fitness trade-off in extended-spectrum-\u03b2-lactamase-producing strains of Escherichia coli","volume":"63","author":"T Billard-Pomares","year":"2019","journal-title":"Antimicrob Agents Chemother"},{"issue":"3","key":"pone.0342894.ref172","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1111\/jfd.13571","article-title":"The role of dctP gene in regulating colonization, adhesion and pathogenicity of Vibrio alginolyticus strain HY9901","volume":"45","author":"Y Zhang","year":"2022","journal-title":"J Fish Dis"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0342894","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T18:27:55Z","timestamp":1771871275000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0342894"}},"subtitle":[],"editor":[{"given":"Feng","family":"Gao","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,2,23]]},"references-count":172,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0342894","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,23]]}}}