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Using whole-genome sequencing and a One Health approach to understand the epidemiology of zoonotic pathogens and antimicrobial resistance at the human, wildlife, environmental, and livestock interface in southern Ontario

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Title: Using whole-genome sequencing and a One Health approach to understand the epidemiology of zoonotic pathogens and antimicrobial resistance at the human, wildlife, environmental, and livestock interface in southern Ontario
Author: Vogt, Nadine Anna
Department: Department of Population Medicine
Program: Population Medicine
Advisor: Pearl, David
Abstract: This thesis examines the role of racoons in the ecology of Campylobacter, Salmonella, E. coli and associated antimicrobial resistance, using wildlife and environmental samples from a previous repeated cross-sectional study of wildlife on swine farms and conservation areas in southern Ontario, along with isolates collected through public health surveillance for Salmonella and E. coli. Using whole-genome sequencing data from Salmonella and E. coli isolates, microbial population structure was assessed using core-genome multi-locus sequence types (cgMLST; 3002- and 2513-loci Enterobase schemes, respectively), and antimicrobial resistance (AMR) genes and plasmid replicons were identified using in silico tools. Outputs from bioinformatics analyses were used in logistic regression analyses to assess associations with source type, location type, and farm location. Potential transmission of Salmonella and E. coli was assessed based on similarities between cgMLST types, as well as examination of extensively multi-drug resistant isolates. Based on results from mixed multivariable logistic regression, Campylobacter carriage among raccoons was associated with climatic variables such as season, temperature, and rainfall, but not with demographic factors (age, sex), or location type (swine farm vs. conservation area). Assessment of Salmonella from human, livestock, wildlife, soil, and water samples revealed that Salmonella obtained from raccoons and soil on farm sites were more similar, and, on average, demonstrated fewer allelic differences than water, human, and livestock isolates obtained from the broader geographic region. Apart from one Salmonella Heidelberg isolate that differed at 4 cgMLST loci, no raccoon Salmonella isolates clustered together with human Salmonella isolates. Comparisons of Salmonella and E. coli isolates from raccoons, soil and swine manure pits suggest that on- and between-farm transmission may be occurring. Results from statistical analyses revealed associations between certain genes and plasmid replicons with source; in many cases, livestock and water samples were significantly more likely to harbour resistance genes and plasmid types compared to wildlife. Overall, our findings underscore the complexity of AMR and pathogen transmission in the ecosystem, and suggest that anthropogenic sources such as conservation areas, swine farms, and contaminated water represent potential sources of these organisms for wildlife in this region.
URI: https://hdl.handle.net/10214/25921
Date: 2021-06-10
Rights: Attribution-NonCommercial-NoDerivatives 4.0 International
Terms of Use: All items in the Atrium are protected by copyright with all rights reserved unless otherwise indicated.
Related Publications: Vogt, N. A., Pearl, D. L., Taboada, E. N., Mutschall, S. K., Bondo, K. J., & Jardine, C. M. (2021). Epidemiology of Campylobacter jejuni in raccoons (Procyon lotor) on swine farms and in conservation areas in southern Ontario. Zoonoses and Public Health, 68(1), 19–28. https://doi.org/10.1111/zph.12786


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Attribution-NonCommercial-NoDerivatives 4.0 International Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivatives 4.0 International