{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T19:40:17Z","timestamp":1790883617420,"version":"4.1.0"},"reference-count":80,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2022,3,17]],"date-time":"2022-03-17T00:00:00Z","timestamp":1647475200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","award":["This project was supported by internal USDA\/ARS research funding."],"award-info":[{"award-number":["This project was supported by internal USDA\/ARS research funding."]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Food animals are known reservoirs of multidrug-resistant (MDR)<jats:italic>Escherichia coli<\/jats:italic>, but information regarding the factors influencing colonization by these organisms is lacking. Here we report the genomic analysis of 66 MDR<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>isolates from non-redundant veal calf fecal samples. Genes conferring resistance to aminoglycosides, \u03b2-lactams, sulfonamides, and tetracyclines were the most frequent antimicrobial resistance genes (ARGs) detected and included those that confer resistance to clinically significant antibiotics (<jats:italic>bla<\/jats:italic><jats:sub>CMY-2<\/jats:sub>,<jats:italic>bla<\/jats:italic><jats:sub>CTX-M<\/jats:sub>,<jats:italic>mph(A)<\/jats:italic>,<jats:italic>erm(B)<\/jats:italic>,<jats:italic>aac(6\u2019)Ib-cr<\/jats:italic>, and<jats:italic>qnrS1<\/jats:italic>). Co-occurrence analyses indicated that multiple ARGs significantly co-occurred with each other, and with metal and biocide resistance genes (MRGs and BRGs). Genomic analysis also indicated that the MDR<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>isolated from veal calves were highly diverse. The most frequently detected genotype was phylogroup A-ST Cplx 10. A high percentage of isolates (50%) were identified as sequence types that are the causative agents of extra-intestinal infections (ExPECs), such as ST69, ST410, ST117, ST88, ST617, ST648, ST10, ST58, and ST167, and an appreciable number of these isolates encoded virulence factors involved in the colonization and infection of the human urinary tract. There was a significant difference in the presence of multiple accessory virulence factors (VFs) between MDR and susceptible strains. VFs associated with enterohemorrhagic infections, such as<jats:italic>stx<\/jats:italic>,<jats:italic>tir<\/jats:italic>, and<jats:italic>eae<\/jats:italic>, were more likely to be harbored by antimicrobial-susceptible strains, while factors associated with extraintestinal infections such as the<jats:italic>sit<\/jats:italic>system, aerobactin, and<jats:italic>pap<\/jats:italic>fimbriae genes were more likely to be encoded in resistant strains. A comparative analysis of SNPs between strains indicated that several closely related strains were recovered from animals on different farms indicating the potential for resistant strains to circulate among farms. These results indicate that veal calves are a reservoir for a diverse group of MDR<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>that harbor various resistance genes and virulence factors associated with human infections. Evidence of co-occurrence of ARGs with MRGs, BRGs, and iron-scavenging genes (<jats:italic>sit<\/jats:italic>and aerobactin) may lead to management strategies for reducing colonization of resistant bacteria in the calf gut.<\/jats:p>","DOI":"10.1371\/journal.pone.0265445","type":"journal-article","created":{"date-parts":[[2022,3,17]],"date-time":"2022-03-17T18:42:20Z","timestamp":1647542540000},"page":"e0265445","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":27,"title":["Virulome and genome analyses identify associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7996-1143","authenticated-orcid":true,"given":"Bradd J.","family":"Haley","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seon Woo","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serajus","family":"Salaheen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ernest","family":"Hovingh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo Ann S.","family":"Van Kessel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,3,17]]},"reference":[{"issue":"1","key":"pone.0265445.ref001","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3201\/eid1701.P11101","article-title":"Foodborne illness acquired in the United States\u2014major pathogens","volume":"17","author":"E Scallan","year":"2011","journal-title":"Emerg Infect Dis"},{"issue":"5","key":"pone.0265445.ref002","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1007\/s11934-013-0354-5","article-title":"From physiology to pharmacy: developments in the pathogenesis and treatment of recurrent urinary tract infections.","volume":"14","author":"JA Silverman","year":"2013","journal-title":"Curr Urol Rep"},{"issue":"1","key":"pone.0265445.ref003","doi-asserted-by":"crossref","first-page":"2803","DOI":"10.1038\/s41467-020-16627-5","article-title":"Invasion of vaginal epithelial cells by uropathogenic Escherichia coli.","volume":"11","author":"JR Brannon","year":"2020","journal-title":"Nat Commun."},{"issue":"22","key":"pone.0265445.ref004","doi-asserted-by":"crossref","first-page":"e01903","DOI":"10.1128\/AEM.01903-19","article-title":"Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following In Vitro Incubation in Broiler Ceca","volume":"85","author":"A Oladeinde","year":"2019","journal-title":"Appl Environ Microbiol"},{"issue":"6","key":"pone.0265445.ref005","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1007\/s00284-019-01676-x","article-title":"Horizontal Transfer of Antimicrobial Resistance Determinants Among Enteric Pathogens Through Bacterial Conjugation","volume":"76","author":"NK Devanga Ragupathi","year":"2019","journal-title":"Curr Microbiol"},{"issue":"8","key":"pone.0265445.ref006","doi-asserted-by":"crossref","first-page":"324","DOI":"10.3390\/biom9080324","article-title":"Nutrition Related Stress Factors Reduce the Transfer of Extended-Spectrum Beta-Lactamase Resistance Genes between an Escherichia coli Donor and a Salmonella Typhimurium Recipient In Vitro.","volume":"9","author":"EM Saliu","year":"2019","journal-title":"Biomolecules"},{"issue":"1","key":"pone.0265445.ref007","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/S1473-3099(18)30605-4","article-title":"Burden of AMR Collaborative Group. 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