Browsing by Author "McAllister, Tim A."

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    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
    (2020-12-15) Rogers, Lindsay A; Checkley, Sylvia L.; Cork, Susan C.; McAllister, Tim A.; Zaheer, Rahat; Liljebjelke, Karen
    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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    Comparative genomic analysis of mobile genetic elements in Histophilus somni isolates from feedlot cattle
    (2020-08-25) Mostafa Nazari Zanjani, Mohammad; Liljebjelke, Karen A.; McAllister, Tim A.; Schryvers, Anthony Bernard
    Organisms, including bacteria, are defined by the genes they possess. This genomic pool determines whether a bacterial species can survive or compete in a changing environment. Bacteria can acquire new genomic content through de novo mutations or through external genomic reservoirs via horizontal gene transfer. Horizontal gene transfer (HGT) is the exchange of genetic material through mobile genetic elements (MGE) between cells which have no parent-offspring relationship. The conjugation pathway is one of the main routes of HGT in bacteria and is in part mediated by plasmids or integrative and conjugative elements (ICE). ICEs can provide new genes through HGT which confer new phenotypic traits such as resistance to antibiotics and heavy metals, biofilm-formation and metabolic alterations. In this study, an ICE was identified in Histophilus somni, a Gram-negative bacterium that is one of the major bacteria involved in bovine respiratory disease (BRD). The ICE and other mobile genetic elements were identified through analysis of whole-genome sequences (WGS) of H. somni isolates collected from tissue samples from Canadian and American feedlot cattle mortalities. A variety of antimicrobial resistance genes were located within ICE sequences. AMR genes tet(H), Sul2/folP, APH(3”)-Ib, APH(6)-Id, and APH(3’’)-Ia, were identified. These genes may provide phenotypic resistance for the antimicrobial classes: tetracyclines, sulfonamides, phenicols and aminoglycosides. Plasmids were not identified in WGS files. No AMR genes were found on the chromosome other than those within ICE sequences. The ICEs in Canadian and American H. somni isolates exhibited similar genome assembly and genome content. The similarity of the ICE in Canadian and American H. somni isolates indicates that they may have moved between the two countries during import and export of cattle. The ICEs of H. somni were identified as members of the ICEHin1056 ICE-family. ICEs of the ICEHin1056 ICE-family have been identified in four bacterial species; two human-specific species, Haemophilus influenzae, and Haemophilus parainfluenzae, and the animal pathogens, H. somni, Actinobacillus pleuropneumoniae, M. haemolytica, and P. multocida.