{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T13:59:54Z","timestamp":1787320794678,"version":"build-2736575974"},"reference-count":49,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T00:00:00Z","timestamp":1742860800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T00:00:00Z","timestamp":1742860800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100006668","name":"Fondo para la Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","doi-asserted-by":"publisher","award":["PICT 2020-01275"],"award-info":[{"award-number":["PICT 2020-01275"]}],"id":[{"id":"10.13039\/501100006668","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006668","name":"Fondo para la Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","doi-asserted-by":"publisher","award":["PICT 2021-0490"],"award-info":[{"award-number":["PICT 2021-0490"]}],"id":[{"id":"10.13039\/501100006668","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Curr Microbiol"],"published-print":{"date-parts":[[2025,5]]},"DOI":"10.1007\/s00284-025-04185-2","type":"journal-article","created":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T11:01:31Z","timestamp":1743073291000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Whole-Genome Sequence Reveals Genetic Determinants of the Colonization of Shiga Toxin-Producing Escherichia coli O22:H8 Isolates in Cattle"],"prefix":"10.1007","volume":"82","author":[{"given":"Wanderson","family":"Marques Da Silva","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Libia Yael","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Flavia Figueira","family":"Aburjaile","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariano","family":"Larzabal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandy Ingrid Aguiar","family":"Alves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"Farace","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos Willian","family":"Dantas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mateus Matiuzzi","family":"Costa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bertram","family":"Brenig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rommel Thiago Juc\u00e1","family":"Ramos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasco","family":"Azevedo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angel","family":"Cataldi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,3,25]]},"reference":[{"key":"4185_CR1","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1093\/infdis\/151.5.775","volume":"151","author":"MA Karmali","year":"1985","unstructured":"Karmali MA, Petric M, Lim C, Fleming PC, Arbus GS, Lior H (1985) The association between idiopathic hemolytic uremic syndrome and infection by verotoxin-producing Escherichia coli. J Infect Dis 151:775\u2013782. https:\/\/doi.org\/10.1093\/infdis\/151.5.775","journal-title":"J Infect Dis"},{"key":"4185_CR2","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1016\/j.ijmm.2018.06.011","volume":"308","author":"M N\u00fcesch-Inderbinen","year":"2018","unstructured":"N\u00fcesch-Inderbinen M, Morach M, Cernela N, Althaus D, Jost M, M\u00e4usezahl M, Bloomberg G, Stephan R (2018) Serotypes and virulence profiles of Shiga toxin-producing Escherichia coli strains isolated during 2017 from human infections in Switzerland. Int J Med Microbiol 308:933\u2013939. https:\/\/doi.org\/10.1016\/j.ijmm.2018.06.011","journal-title":"Int J Med Microbiol"},{"key":"4185_CR3","doi-asserted-by":"publisher","first-page":"4461","DOI":"10.1038\/s41598-021-83775-z","volume":"11","author":"HM Blankenship","year":"2021","unstructured":"Blankenship HM, Mosci RE, Dietrich S, Burgess E, Wholehan J, McWilliams K, Pietrzen K, Benko S, Gatesy T, Rudrik JT, Soehnlen M, Manning SD (2021) Population structure and genetic diversity of non-O157 Shiga toxin-producing Escherichia coli (STEC) clinical isolates from Michigan. Sci Rep 11:4461. https:\/\/doi.org\/10.1038\/s41598-021-83775-z","journal-title":"Sci Rep"},{"key":"4185_CR4","doi-asserted-by":"publisher","first-page":"S102","DOI":"10.1111\/j.1523-1755.2005.09717.x","volume":"97","author":"HA Repetto","year":"2005","unstructured":"Repetto HA (2005) Long-term course and mechanisms of progression of renal disease in hemolytic uremic syndrome. Kidney Int Suppl 97:S102\u2013S106. https:\/\/doi.org\/10.1111\/j.1523-1755.2005.09717.x","journal-title":"Kidney Int Suppl"},{"key":"4185_CR5","doi-asserted-by":"publisher","first-page":"e0183248","DOI":"10.1371\/journal.pone.0183248","volume":"12","author":"V Brusa","year":"2017","unstructured":"Brusa V, Restovich V, Galli L, Teitelbaum D, Signorini M, Brasesco H, Londero A, Garc\u00eda D, Padola NL, Superno V, Sanz M, Petroli S, Costa M, Bruzzone M, Sucari A, Ferreghini M, Linares L, Suberbie G, Rodr\u00edguez R, Leotta GA (2017) Isolation and characterization of non-O157 Shiga toxin-producing Escherichia coli from beef carcasses, cuts and trimmings of abattoirs in Argentina. PLoS ONE 12:e0183248. https:\/\/doi.org\/10.1371\/journal.pone.0183248","journal-title":"PLoS ONE"},{"key":"4185_CR6","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1007\/s11274-023-03624-1","volume":"28","author":"R Colello","year":"2023","unstructured":"Colello R, Baigorri M, Del Canto F, Gonz\u00e1lez J, Rog\u00e9 A, van der Ploeg C, S\u00e1nchez Chopa F, Sparo M, Etcheverr\u00eda A, Padola NL (2023) Occurrence and genetic characterization of Shiga toxin-producing Escherichia coli on bovine and pork carcasses and the environment from transport trucks. World J Microbiol Biotechnol 28:174. https:\/\/doi.org\/10.1007\/s11274-023-03624-1","journal-title":"World J Microbiol Biotechnol"},{"key":"4185_CR7","doi-asserted-by":"publisher","first-page":"e8","DOI":"10.1111\/zph.12403","volume":"65","author":"L Mughini-Gras","year":"2018","unstructured":"Mughini-Gras L, van Pelt W, van der Voort M, Heck M, Friesema I, Franz E (2018) Attribution of human infections with Shiga toxin-producing Escherichia coli (STEC) to livestock sources and identification of source-specific risk factors, The Netherlands (2010\u20132014). Zoonoses Public Health 65:e8\u2013e22. https:\/\/doi.org\/10.1111\/zph.12403","journal-title":"Zoonoses Public Health"},{"key":"4185_CR8","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1186\/s12864-023-09902-4","volume":"20","author":"N Naidoo","year":"2023","unstructured":"Naidoo N, Zishiri OT (2023) Comparative genomics analysis and characterization of Shiga toxin-producing Escherichia coli O157:H7 strains reveal virulence genes, resistance genes, prophages and plasmids. BMC Genomics 20:791. https:\/\/doi.org\/10.1186\/s12864-023-09902-4","journal-title":"BMC Genomics"},{"key":"4185_CR9","doi-asserted-by":"publisher","first-page":"2951","DOI":"10.1128\/JCM.00860-12","volume":"50","author":"F Scheutz","year":"2012","unstructured":"Scheutz F, Teel LD, Beutin L, Pi\u00e9rard D, Buvens G, Karch H, Mellmann A, Caprioli A, Tozzoli R, Morabito S, Strockbine NA, Melton-Celsa AR, Sanchez M, Persson S, O\u2019Brien AD (2012) Multicenter evaluation of a sequence-based protocol for subtyping Shiga toxins and standardizing Stx nomenclature. J Clin Microbiol 50:2951\u201363. https:\/\/doi.org\/10.1128\/JCM.00860-12","journal-title":"J Clin Microbiol"},{"key":"4185_CR10","doi-asserted-by":"publisher","first-page":"4868","DOI":"10.1073\/pnas.0710834105","volume":"25","author":"SD Manning","year":"2008","unstructured":"Manning SD, Motiwala AS, Springman AC, Qi W, Lacher DW, Ouellette LM, Mladonicky JM, Somsel P, Rudrik JT, Dietrich SE, Zhang W (2008) Swaminathan B, Alland D, Whittam TS. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc Natl Acad Sci U S A 25:4868\u201373. https:\/\/doi.org\/10.1073\/pnas.0710834105","journal-title":"Proc Natl Acad Sci U S A"},{"key":"4185_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1046\/j.1365-2958.1998.00783.x","volume":"28","author":"SJ Elliott","year":"1998","unstructured":"Elliott SJ, Wainwright LA, McDaniel TK, Jarvis KG, Deng YK, Lai LC, McNamara BP, Donnenberg MS, Kaper JB (1998) The complete sequence of the locus of enterocyte effacement (LEE) from enteropathogenic Escherichia coli E2348\/69. Mol Microbiol 28:1\u20134. https:\/\/doi.org\/10.1046\/j.1365-2958.1998.00783.x","journal-title":"Mol Microbiol"},{"key":"4185_CR12","doi-asserted-by":"publisher","first-page":"7011","DOI":"10.1038\/s41598-017-06999-y","volume":"7","author":"DA Montero","year":"2017","unstructured":"Montero DA, Velasco J, Del Canto F, Puente JL, Padola NL, Rasko DA, Farf\u00e1n M, Salazar JC, Vidal R (2017) Locus of Adhesion and Autoaggregation (LAA), a pathogenicity island present in emerging Shiga Toxin-producing Escherichia coli strains. Sci Rep 7:7011. https:\/\/doi.org\/10.1038\/s41598-017-06999-y","journal-title":"Sci Rep"},{"key":"4185_CR13","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1016\/j.vetmic.2017.06.021","volume":"208","author":"L Martorelli","year":"2017","unstructured":"Martorelli L, Albanese A, Vilte D, Cantet R, Bentancor A, Zolezzi G, Chinen I, Ibarra C, Rivas M, Mercado EC, Cataldi A (2017) Shiga toxin-producing Escherichia coli (STEC) O22:H8 isolated from cattle reduces E. coli O157:H7 adherence in vitro and in vivo. Vet Microbiol 208:8\u201317. https:\/\/doi.org\/10.1016\/j.vetmic.2017.06.021","journal-title":"Vet Microbiol"},{"key":"4185_CR14","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1007\/s12275-022-1616-z","volume":"60","author":"WM Da Silva","year":"2022","unstructured":"Da Silva WM, Larzabal M, Aburjaile FF, Riviere N, Martorelli L, Bono J, Amadio A, Cataldi A (2022) Whole-genome sequencing analysis of Shiga toxin-producing Escherichia coli O22:H8 isolated from cattle prediction pathogenesis and colonization factors and position in STEC universe phylogeny. J Microbiol 60:689\u2013704. https:\/\/doi.org\/10.1007\/s12275-022-1616-z","journal-title":"J Microbiol"},{"key":"4185_CR15","doi-asserted-by":"publisher","first-page":"e000376","DOI":"10.1099\/mgen.0.000376","volume":"6","author":"LYR Wang","year":"2020","unstructured":"Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ (2020) Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenicEscherichia coli serotypes within a closed beef herd in Canada. Microb Genom 6:e000376. https:\/\/doi.org\/10.1099\/mgen.0.000376","journal-title":"Microb Genom"},{"key":"4185_CR16","doi-asserted-by":"publisher","first-page":"e0258753","DOI":"10.1371\/journal.pone.0258753","volume":"16","author":"A Amadio","year":"2021","unstructured":"Amadio A, Bono JL, Irazoqui M, Larz\u00e1bal M, Marques da Silva W, Eberhardt MF, Riviere NA, Gally D, Manning SD, Cataldi A (2021) Genomic analysis of shiga toxin-containing Escherichia coli O157:H7 isolated from Argentinean cattle. PLoS ONE 16:e0258753. https:\/\/doi.org\/10.1371\/journal.pone.0258753","journal-title":"PLoS ONE"},{"key":"4185_CR17","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068\u20132069. https:\/\/doi.org\/10.1093\/bioinformatics\/btu153","journal-title":"Bioinformatics"},{"key":"4185_CR18","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691\u20133693. https:\/\/doi.org\/10.1093\/bioinformatics\/btv421","journal-title":"Bioinformatics"},{"key":"4185_CR19","doi-asserted-by":"publisher","first-page":"e000056","DOI":"10.1099\/mgen.0.000056","volume":"29","author":"AJ Page","year":"2016","unstructured":"Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, Harris SR (2016) SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom. 29:e000056. https:\/\/doi.org\/10.1099\/mgen.0.000056","journal-title":"Microb Genom."},{"key":"4185_CR20","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312\u20131313. https:\/\/doi.org\/10.1093\/bioinformatics\/btu033","journal-title":"Bioinformatics"},{"key":"4185_CR21","doi-asserted-by":"publisher","first-page":"W242","DOI":"10.1093\/nar\/gkw290","volume":"8","author":"I Letunic","year":"2016","unstructured":"Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 8:W242-5. https:\/\/doi.org\/10.1093\/nar\/gkw290","journal-title":"Nucleic Acids Res"},{"key":"4185_CR22","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-016-1108-8","volume":"25","author":"O Brynildsrud","year":"2016","unstructured":"Brynildsrud O, Bohlin J, Scheffer L, Eldholm V (2016) Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol 25:238. https:\/\/doi.org\/10.1186\/s13059-016-1108-8","journal-title":"Genome Biol"},{"key":"4185_CR23","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1016\/j.jbiotec.2015.09","volume":"20","author":"SC Soares","year":"2016","unstructured":"Soares SC, Geyik H, Ramos RT, de S\u00e1 PH, Barbosa EG, Baumbach J, Figueiredo HC, Miyoshi A, Tauch A, Silva A, Azevedo V (2016) GIPSy: Genomic Island prediction software. J Biotechnol 20:2\u201311. https:\/\/doi.org\/10.1016\/j.jbiotec.2015.09","journal-title":"J Biotechnol"},{"key":"4185_CR24","doi-asserted-by":"publisher","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","volume":"4","author":"B Jia","year":"2017","unstructured":"Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FS, Wright GD, McArthur AG (2017) CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 4:D566\u2013D573. https:\/\/doi.org\/10.1093\/nar\/gkw1004","journal-title":"Nucleic Acids Res"},{"key":"4185_CR25","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","volume":"75","author":"V Bortolaia","year":"2020","unstructured":"Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nyk\u00e4senoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75:3491\u20133500. https:\/\/doi.org\/10.1093\/jac\/dkaa345","journal-title":"J Antimicrob Chemother"},{"key":"4185_CR26","doi-asserted-by":"publisher","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","volume":"50","author":"B Liu","year":"2022","unstructured":"Liu B, Zheng D, Zhou S, Chen L, Yang J (2022) VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res 50:D912\u2013D917. https:\/\/doi.org\/10.1093\/nar\/gkab1107","journal-title":"Nucleic Acids Res"},{"key":"4185_CR27","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1128\/JCM.03617-13","volume":"52","author":"KG Joensen","year":"2014","unstructured":"Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM (2014) Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 52:1501\u201310. https:\/\/doi.org\/10.1128\/JCM.03617-13","journal-title":"J Clin Microbiol"},{"key":"4185_CR28","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1002\/pmic.201700071","volume":"17","author":"CS Casimiro-Soriguer","year":"2017","unstructured":"Casimiro-Soriguer CS, Mu\u00f1oz-M\u00e9rida A, P\u00e9rez-Pulido AJ (2017) Sma3s: A universal tool for easy functional annotation of proteomes and transcriptomes. Proteomics 17:12. https:\/\/doi.org\/10.1002\/pmic.201700071","journal-title":"Proteomics"},{"key":"4185_CR29","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"9","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra CP, Hern\u00e1ndez-Plaza A, Letunic I, Bork P, Huerta-Cepas J (2021) eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the Metagenomic scale. Mol Biol Evol 9:5825\u20135829. https:\/\/doi.org\/10.1093\/molbev\/msab293","journal-title":"Mol Biol Evol"},{"key":"4185_CR30","doi-asserted-by":"publisher","first-page":"W317","DOI":"10.1093\/nar\/gkab447","volume":"2","author":"D Bu","year":"2021","unstructured":"Bu D, Luo H, Huo P, Wang Z, Zhang S, He Z, Wu Y, Zhao L, Liu J, Guo J, Fang S, Cao W, Yi L, Zhao Y, Kong L (2021) KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. Nucleic Acids Res 2:W317\u2013W325. https:\/\/doi.org\/10.1093\/nar\/gkab447","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"4185_CR31","doi-asserted-by":"publisher","first-page":"e1319","DOI":"10.7717\/peerj.1319","volume":"8","author":"AM Eren","year":"2015","unstructured":"Eren AM, Esen \u00d6C, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO (2015) Anvi\u2019o: an advanced analysis and visualization platform for \u2019omics data. PeerJ 8(3):e1319. https:\/\/doi.org\/10.7717\/peerj.1319","journal-title":"PeerJ"},{"key":"4185_CR32","doi-asserted-by":"publisher","first-page":"e0066022","DOI":"10.1128\/spectrum.00660-22","volume":"31","author":"X Bai","year":"2022","unstructured":"Bai X, Ylinen E, Zhang J, Salmenlinna S, Halkilahti J, Saxen H, Narayanan A, Jahnukainen T, Matussek A (2022) Comparative genomics of Shiga toxin-producing Escherichia coli strains isolated from pediatric patients with and without Hemolytic uremic syndrome from 2000 to 2016 in Finland. Microbiol Spectr 31:e0066022. https:\/\/doi.org\/10.1128\/spectrum.00660-22","journal-title":"Microbiol Spectr"},{"key":"4185_CR33","doi-asserted-by":"publisher","first-page":"772574","DOI":"10.3389\/fcimb.2021.772574","volume":"11","author":"X Zhang","year":"2022","unstructured":"Zhang X, Payne M, Kaur S, Lan R (2022) Improved genomic identification, clustering, and serotyping of Shiga toxin-producing Escherichia coli using cluster\/serotype-specific gene markers. Front Cell Infect Microbiol 11:772574. https:\/\/doi.org\/10.3389\/fcimb.2021.772574","journal-title":"Front Cell Infect Microbiol"},{"key":"4185_CR34","doi-asserted-by":"publisher","first-page":"000499","DOI":"10.1099\/mgen.0.000499","volume":"7","author":"G Horesh","year":"2021","unstructured":"Horesh G, Blackwell GA, Tonkin-Hill G, Corander J, Heinz E, Thomson NR (2021) A comprehensive and high-quality collection of Escherichia coli genomes and their genes. Microb Genom. 7:000499. https:\/\/doi.org\/10.1099\/mgen.0.000499","journal-title":"Microb Genom."},{"key":"4185_CR35","doi-asserted-by":"publisher","first-page":"771","DOI":"10.1007\/s10096-023-04600-1","volume":"42","author":"A Matussek","year":"2023","unstructured":"Matussek A, Mernelius S, Chromek M, Zhang J, Frykman A, Hansson S, Georgieva V, Xiong Y, Bai X (2023) Genome-wide association study of hemolytic uremic syndrome causing Shiga toxin-producing Escherichia coli from Sweden, 1994\u20132018. Eur J Clin Microbiol Infect Dis 42:771\u2013779. https:\/\/doi.org\/10.1007\/s10096-023-04600-1","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"4185_CR36","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1590\/s1517-83822014000400003","volume":"45","author":"D Harwani","year":"2015","unstructured":"Harwani D (2015) Regulation of gene expression: cryptic \u03b2-glucoside (bgl) operon of Escherichia coli as a paradigm. Braz J Microbiol 45:1139\u20131144. https:\/\/doi.org\/10.1590\/s1517-83822014000400003","journal-title":"Braz J Microbiol"},{"key":"4185_CR37","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1128\/IAI.01386-07","volume":"76","author":"AJ Fabich","year":"2008","unstructured":"Fabich AJ, Jones SA, Chowdhury FZ, Cernosek A, Anderson A, Smalley D, McHargue JW, Hightower GA, Smith JT, Autieri SM, Leatham MP, Lins JJ, Allen RL, Laux DC, Cohen PS, Conway T (2008) Comparison of carbon nutrition for pathogenic and commensal Escherichia coli strains in the mouse intestine. Infect Immun 76:1143\u20131152. https:\/\/doi.org\/10.1128\/IAI.01386-07","journal-title":"Infect Immun"},{"key":"4185_CR38","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1038\/nature18849","volume":"7","author":"AJ B\u00e4umler","year":"2016","unstructured":"B\u00e4umler AJ, Sperandio V (2016) Interactions between the microbiota and pathogenic bacteria in the gut. Nature 7:85\u201393. https:\/\/doi.org\/10.1038\/nature18849","journal-title":"Nature"},{"key":"4185_CR39","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1038\/ismej.2016","volume":"11","author":"LM Solden","year":"2017","unstructured":"Solden LM, Hoyt DW, Collins WB, Plank JE, Daly RA, Hildebrand E, Beavers TJ, Wolfe R, Nicora CD, Purvine SO, Carstensen M, Lipton MS, Spalinger DE, Firkins JL, Wolfe BA, Wrighton KC (2017) New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11. ISME J 11:691\u2013703. https:\/\/doi.org\/10.1038\/ismej.2016","journal-title":"ISME J"},{"key":"4185_CR40","doi-asserted-by":"publisher","first-page":"1020","DOI":"10.1099\/mic.0.078105-0","volume":"160","author":"L Staib","year":"2014","unstructured":"Staib L, Fuchs TM (2014) From food to cell: nutrient exploitation strategies of enteropathogens. Microbiology 160:1020\u20131039. https:\/\/doi.org\/10.1099\/mic.0.078105-0","journal-title":"Microbiology"},{"key":"4185_CR41","doi-asserted-by":"publisher","first-page":"e1006129","DOI":"10.1371\/journal.ppat.1006129","volume":"13","author":"F Faber","year":"2017","unstructured":"Faber F, Thiennimitr P, Spiga L, Byndloss MX, Litvak Y, Lawhon S, Andrews-Polymenis HL, Winter SE, B\u00e4umler AJ (2017) Respiration of microbiota-derived 1,2-propanediol drives Salmonella expansion during colitis. PloS Pathog 13:e1006129. https:\/\/doi.org\/10.1371\/journal.ppat.1006129","journal-title":"PloS Pathog"},{"key":"4185_CR42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/ecosalplus","volume":"7","author":"L Journet","year":"2016","unstructured":"Journet L, Cascales E (2016) The Type VI secretion system in Escherichia coli and related species. EcoSal Plus 7:1. https:\/\/doi.org\/10.1128\/ecosalplus","journal-title":"EcoSal Plus"},{"key":"4185_CR43","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1126\/science.aap8775","volume":"12","author":"W Zhao","year":"2018","unstructured":"Zhao W, Caro F, Robins W, Mekalanos JJ (2018) Antagonism toward the intestinal microbiota and its effect on Vibrio cholerae virulence. Science 12:210\u2013213. https:\/\/doi.org\/10.1126\/science.aap8775","journal-title":"Science"},{"key":"4185_CR44","doi-asserted-by":"publisher","first-page":"110731","DOI":"10.1016\/j.celrep.2022","volume":"26","author":"A Serapio-Palacios","year":"2022","unstructured":"Serapio-Palacios A, Woodward SE, Vogt SL, Deng W, Creus-Cuadros A, Huus KE, Cirstea M, Gerrie M, Barcik W, Yu H, Finlay BB (2022) Type VI secretion systems of pathogenic and commensal bacteria mediate niche occupancy in the gut. Cell Rep 26:110731. https:\/\/doi.org\/10.1016\/j.celrep.2022","journal-title":"Cell Rep"},{"key":"4185_CR45","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1111\/mmi.13292","volume":"99","author":"N Flaugnatti","year":"2016","unstructured":"Flaugnatti N, Le TT, Canaan S, Aschtgen MS, Nguyen VS, Blangy S, Kellenberger C, Roussel A, Cambillau C, Cascales E, Journet L (2016) A phospholipase A1 antibacterial Type VI secretion effector interacts directly with the C-terminal domain of the VgrG spike protein for delivery. Mol Microbiol 99:1099\u2013118. https:\/\/doi.org\/10.1111\/mmi.13292","journal-title":"Mol Microbiol"},{"key":"4185_CR46","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1080\/22221751.2019.1595985","volume":"8","author":"DA Montero","year":"2019","unstructured":"Montero DA, Canto FD, Velasco J, Colello R, Padola NL, Salazar JC, Martin CS, O\u00f1ate A, Blanco J, Rasko DA, Contreras C, Puente JL, Scheutz F, Franz E, Vidal RM (2019) Cumulative acquisition of pathogenicity islands has shaped virulence potential and contributed to the emergence of LEE-negative Shiga toxin-producing Escherichia coli strains. Emerg Microbes Infect 8:486\u2013502. https:\/\/doi.org\/10.1080\/22221751.2019.1595985","journal-title":"Emerg Microbes Infect"},{"key":"4185_CR47","doi-asserted-by":"publisher","first-page":"E149","DOI":"10.1111\/1469-0691.12122","volume":"19","author":"V Michelacci","year":"2013","unstructured":"Michelacci V, Tozzoli R, Caprioli A, Mart\u00ednez R, Scheutz F, Grande L, S\u00e1nchez S, Morabito SA (2013) New pathogenicity island carrying an allelic variant of the Subtilase cytotoxin is common among Shiga toxin producing Escherichia coli of human and ovine origin. Clin Microbiol Infect 19:E149-156. https:\/\/doi.org\/10.1111\/1469-0691.12122","journal-title":"Clin Microbiol Infect"},{"key":"4185_CR48","doi-asserted-by":"publisher","first-page":"1707","DOI":"10.1111\/j.1462-5822.2006.00794.x","volume":"8","author":"O Gal-Mor","year":"2006","unstructured":"Gal-Mor O, Finlay BB (2006) Pathogenicity islands: a molecular toolbox for bacterial virulence. Cell Microbiol 8:1707\u20131719. https:\/\/doi.org\/10.1111\/j.1462-5822.2006.00794.x","journal-title":"Cell Microbiol"},{"key":"4185_CR49","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1186\/1471-2164-13-202","volume":"13","author":"JR Grant","year":"2012","unstructured":"Grant JR, Arantes AS, Stothard P (2012) Comparing thousands of circular genomes using the CGView comparison tool. BMC Genomics 13:202. https:\/\/doi.org\/10.1186\/1471-2164-13-202","journal-title":"BMC Genomics"}],"container-title":["Current Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00284-025-04185-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00284-025-04185-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00284-025-04185-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T23:54:52Z","timestamp":1744242892000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00284-025-04185-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,25]]},"references-count":49,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2025,5]]}},"alternative-id":["4185"],"URL":"https:\/\/doi.org\/10.1007\/s00284-025-04185-2","relation":{},"ISSN":["0343-8651","1432-0991"],"issn-type":[{"value":"0343-8651","type":"print"},{"value":"1432-0991","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,25]]},"assertion":[{"value":"28 May 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 March 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 March 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical Approval"}}],"article-number":"207"}}