Browsing by Author "Zaheer, Rahat"
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- ItemOpen AccessCharacterization 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, KarenEnterococcus 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.
- ItemOpen AccessComparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent(2019-08-27) Zaheer, Rahat; Lakin, Steven M; Polo, Rodrigo O; Cook, Shaun R; Larney, Francis J; Morley, Paul S; Booker, Calvin W; Hannon, Sherry J; Van Domselaar, Gary; Read, Ron R; McAllister, Tim AAbstract Background Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin water, manured agricultural soil and urban sewage. Results Metagenomic DNA from composite fecal samples (FC; n = 12) collected from penned cattle at four feedlots in Alberta, Canada, along with water from adjacent catchment basins (CB; n = 13), soil (n = 4) from fields in the vicinity of one of the feedlots and urban sewage influent (SI; n = 6) from two municipalities were subjected to Illumina HiSeq2000 sequencing. Firmicutes exhibited the highest prevalence (40%) in FC, whereas Proteobacteria were most abundant in CB (64%), soil (60%) and SI (83%). Among sample types, SI had the highest diversity of antimicrobial resistance (AMR), and metal and biocide resistance (MBR) classes (13 & 15) followed by FC (10 & 8), CB (8 & 4), and soil (6 & 1). The highest antimicrobial resistant (AMR) gene (ARG) abundance was harboured by FC, whereas soil samples had a very small, but unique resistome which did not overlap with FC & CB resistomes. In the beef production system, tetracycline resistance predominated followed by macrolide resistance. The SI resistome harboured β-lactam, macrolide, tetracycline, aminoglycoside, fluoroquinolone and fosfomycin resistance determinants. Metal and biocide resistance accounted for 26% of the SI resistome with a predominance of mercury resistance. Conclusions This study demonstrates an increasing divergence in the nature of the microbiome and resistome as the distance from the feedlot increases. Consistent with antimicrobial use, tetracycline and macrolide resistance genes were predominant in the beef production system. One of the feedlots contributed both conventional (raised with antibiotics) and natural (raised without antibiotics) pens samples. Although natural pen samples exhibited a microbiota composition that was similar to samples from conventional pens, their resistome was less complex. Similarly, the SI resistome was indicative of drug classes used in humans and the greater abundance of mercury resistance may be associated with contamination of municipal water with household and industrial products.