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.
Animals
Animals, Wild
/ microbiology
Anti-Bacterial Agents
/ pharmacology
Diagnostic Tests, Routine
/ methods
Drug Resistance, Bacterial
/ genetics
Escherichia coli
/ drug effects
Escherichia coli Infections
/ epidemiology
Livestock
/ microbiology
Manure
/ microbiology
Multilocus Sequence Typing
/ methods
Ontario
Plasmids
/ genetics
Raccoons
/ microbiology
Salmonella
/ drug effects
Salmonella Infections
/ epidemiology
Soil
Swine
/ microbiology
Whole Genome Sequencing
/ methods
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2021
2021
Historique:
received:
17
09
2021
accepted:
04
11
2021
entrez:
18
11
2021
pubmed:
19
11
2021
medline:
8
1
2022
Statut:
epublish
Résumé
To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli 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 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella 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 Salmonella 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.
Identifiants
pubmed: 34793571
doi: 10.1371/journal.pone.0260234
pii: PONE-D-21-30211
pmc: PMC8601536
doi:
Substances chimiques
Anti-Bacterial Agents
0
Manure
0
Soil
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0260234Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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