Metagenomic analysis and culture-based methods to examine the prevalence and distribution of antimicrobial resistance on two New Zealand dairy farms : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand

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Antimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, antimicrobial usage on NZ dairy farms and its potential for driving the spread of AMR within the dairy farm environment is under-researched. This research addresses the hypothesis that antimicrobial use on NZ dairy farms influences the prevalence of AMR in dairy farm environments, taking into consideration seasonality and contrasting farm management practices. The aims of this study, focused on two NZ dairy farm environments over an 15 month period, were to (i) determine the prevalence and distribution of AmpC- and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, utilising culture-based methods, and (ii) to determine the abundance and diversity of antimicrobial resistance genes (ARGs), utilising a metagenomic approach, and lastly (iii), to assess the impact of systemic antimicrobial treatment on the bovine faecal microbiome. Overall, the research presented in this thesis has shown a low sample level prevalence of ESBL-producing E. coli from two NZ dairy farms (faeces 0%, 1.7%; farm dairy effluent (FDE) 0%, 6.7% from Dairy 1 and Dairy 4, respectively) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3%, 8.3%; FDE 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). AmpC- and ESBL-producing E. coli were isolated in spring and summer, during months with varying levels of antimicrobial use. Analysis at the individual animal level showed a decrease in bacterial diversity and richness during systemic antimicrobial treatment and in many cases the microbiome diversity recovered post-treatment when the cow re-entered the milking herd. Compared to overseas data in a similar context, NZ dairy farm environments had a low abundance of ARGs, with the highest abundance detected in soil (0.20 - 0.63 copies of ARG per 16S rRNA gene). However, many of the ARGs identified in soil are not frequently found in human pathogens or acquired genes. FDE had a lower ARG abundance but the ARGs were more diverse (0.03 - 0.37 copies of ARG per 16S rRNA gene). There was no association between the normalised ARG abundance and antimicrobial use or collection date, however the low ARG abundance in the farm samples may have made any associations difficult to detect. AMR is a burden for human, animal and environmental health and requires a holistic "One Health" approach to address. The outcomes from this research improve our understanding of the current levels of AMR on two NZ dairy farms and identifies areas for future research. Prevention is better than a cure and urgent action is required to slow the development and dissemination of AMR and to improve antimicrobial stewardship in humans and animals.
Listed in 2022 Dean's List of Exceptional Theses
Dairy farms, Drug resistance in microorganisms, Escherichia coli, New Zealand, Dean's List of Exceptional Theses