{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T15:49:20Z","timestamp":1778341760474,"version":"3.51.4"},"reference-count":55,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T00:00:00Z","timestamp":1637193600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000094","name":"Ontario Ministry of Agriculture, Food and Rural Affairs","doi-asserted-by":"publisher","award":["UofG2016-2642"],"award-info":[{"award-number":["UofG2016-2642"]}],"id":[{"id":"10.13039\/501100000094","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>To better understand the contribution of wildlife to the dissemination of<jats:italic>Salmonella<\/jats:italic>and antimicrobial resistance in<jats:italic>Salmonella<\/jats:italic>and<jats:italic>Escherichia coli<\/jats:italic>, we examined whole-genome sequence data from<jats:italic>Salmonella<\/jats:italic>and<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>isolates collected from raccoons<jats:italic>(Procyon lotor<\/jats:italic>) and environmental sources on farms in southern Ontario. All<jats:italic>Salmonella<\/jats:italic>and phenotypically resistant<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159<jats:italic>Salmonella<\/jats:italic>and 96 resistant<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>isolates were included. A diversity of<jats:italic>Salmonella<\/jats:italic>serovars and sequence types were identified, and, in some cases, we found similar or identical<jats:italic>Salmonella<\/jats:italic>isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of<jats:italic>Salmonella<\/jats:italic>and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.<\/jats:p>","DOI":"10.1371\/journal.pone.0260234","type":"journal-article","created":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T18:47:04Z","timestamp":1637261224000},"page":"e0260234","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":11,"title":["Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0156-4206","authenticated-orcid":true,"given":"Nadine A.","family":"Vogt","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin M.","family":"Hetman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David L.","family":"Pearl","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam A.","family":"Vogt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard J.","family":"Reid-Smith","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E. 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