2026-09-27T03:19:43Zhttps://mro.massey.ac.nz/server/oai/requestoai:mro.massey.ac.nz:10179/176002025-11-11T14:22:13Zcom_10179_294col_10179_296
DSpace at Massey University
advisor
Biggs, Patrick
author
Collis, Rose
2022-05-22T20:55:02Z2022-09-28T00:37:02Z
2022-05-22T20:55:02Z2022-09-28T00:37:02Z
2022
http://hdl.handle.net/10179/17600
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.
The Author
Dairy farms
Drug resistance in microorganisms
Escherichia coli
New Zealand
Dean's List of Exceptional Theses
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
Thesis
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CollisPhDThesis.pdf
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CollisPhDThesis.pdf.txt