Examining antibiotic resistance in the feedlot cattle industry using real-time, quantitative PCR (qPCR) and enterococci as an indicator bacterium

Antibiotics are administered to livestock at subtherapeutic levels to maintain animal health. Many of the antibiotics used are analogues or the same as those used in human medicine, raising the possibility that genes conferring resistance arise within agricultural production systems. This thesis examined antibiotic resistance in the Canadian beef feedlot industry. Real-time, quantitative PCR was used to examine differences in the relative abundance of eighteen resistance genes across five antibiotic families from feedlot cattle faeces and urban environments. The effect of infeed administration and withdrawal of tylosin phosphate on macrolide resistance was examined using enterococci as an indicator bacterium. Resistant enterococci (n=21) were selected for whole-genome sequencing and comparative genomics. Results presented here show that the relative abundance of resistance genes differs between cattle feedlots and urban environments, likely a reflection of differences in antibiotic use. Sulfonamide, fluoroquinolone and β-lactam resistance genes predominated in urban wastewater, whilst tetracycline resistance genes were more prevalent in cattle faeces. Macrolide use in cattle production increased the proportion of erythromycinand tylosin-resistant enterococci. However, withdrawal of tylosin from the diet appeared to contribute to reduced macrolide resistance in enterococci. Comparative genomics revealed resistance to macrolides was present on mobile genetic elements, specifically the Tn917 transposon harbouring erm(B). This transposon was identified in both Enterococcus hirae and Enterococcus faecium suggesting inter-species transfer of resistance genes may occur in the bovine gastrointestinal tract. Furthermore, the integrative conjugative elements (ICEs) Tn916 and Tn5801, both conferring tetracycline resistance, were identified in E. faecium. As the cost of genomic sequencing continues to decrease, further investigation of ICEs using whole genome sequencing will help determine if there are linkages between enterococci isolates from bovine environmental and human clinical sources and whether bovine enterococci represent a source to the dissemination and spread of antibiotic resistance