Characterization and Comparison of Antimicrobial Resistance Phenotypes and Genotypes in Enterococcus spp. Isolated from Cattle Feces, Poultry Feces, and Beef and Poultry Retail Meats in Alberta, Canada, Related to Surveillance
Date
2020-12-15
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Abstract
Enterococcus spp. are ubiquitous in the gastrointestinal tracts of animals and the environment and are important nosocomial pathogens. The use of antimicrobials in food producing animals along with the ability of enterococci to acquire antimicrobial resistance leads to concern about the contamination of retail meat products with antimicrobial resistant Enterococcus spp. from food production animals. The concern is that the antimicrobial resistant enterococci from retail meats may transfer to the human population and cause disease. In addition, increased resistant enterococci and genes in the environment may increase overall risk their transfer to humans. The objective of this thesis was to contribute to the surveillance of Enterococcus spp. from food animal production through a scoping review and the characterization of enterococcal isolates from surveillance in Alberta, Canada using whole genome sequencing. The scoping review followed PRISMA and JBI guidelines and included 57 articles, of which 87.7% identified E. faecium and the majority included isolates from human clinical or commensal samples. Significant findings from the articles included the increasing prevalence of vancomycin-resistant enterococci in hospitals and the importance of surveillance for enterococci in humans, animals, and the environment. E. faecium (n=107) and E. faecalis (n=132) were isolated from research and surveillance samples previously collected from beef cattle feces, broiler poultry feces, and beef and poultry retail meats in Alberta, Canada. Antimicrobial susceptibility and whole genome sequencing with comparative genomics were performed on the isolates. The odds of multiclass resistance in E. faecium was about 3 times that of E. faecalis after adjusting for sample source and clustering (OR 3.09; 95% CI: 1.48, 6.48). In contrast, a higher number of virulence genes were found in E. faecalis as compared to E. faecium. Generally antimicrobial resistance genotype showed good sensitivity and specificity for use as a presumptive predictor of the corresponding phenotype. Comparative genomic analyses showed distinct clustering within sample source for E. faecium, but not for E. faecalis. Overall, this work supports the usefulness of whole genome sequencing for surveillance of Enterococcus spp. and further characterizes a population of E. faecium and E. faecalis isolates from surveillance programs in Alberta, Canada.
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Keywords
Enterococcus spp., Beef Cattle, Broiler Poultry, Comparative Genomics, Bioinformatics
Citation
Rogers, L. A. (2020). Characterization and Comparison of Antimicrobial Resistance Phenotypes and Genotypes in Enterococcus spp. Isolated from Cattle Feces, Poultry Feces, and Beef and Poultry Retail Meats in Alberta, Canada, Related to Surveillance (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.