Investigation of antimicrobial use on Irish pig farms and effects on antimicrobial resistance in Escherichia coli and the faecal resistome throughout the production cycle

Antimicrobial resistance (AMR) is a current and future threat to human and animal health. Although not precisely quantified, antimicrobial use (AMU) in agriculture may contribute to the emergence of AMR bacteria of importance to human health. Pig farming is known as one of the largest consumers of veterinary antimicrobials worldwide. However, little is known about the quantities and patterns of AMU in the Irish pig sector or the drivers for this use. Furthermore, there are significant gaps in knowledge of how AMR evolves during the entire pig lifecycle on commercial farms. The objectives of this thesis were to characterise and quantify AMU on Irish pig farms, explore the risk factors for use and to explore the dynamics and evolution of AMR in the commensal Escherichia coli population and in the faecal microbiome during the pig lifecycle. A cross-sectional study of 67 farms was conducted to determine the quantities and patterns of AMU. The findings showed that the majority of antimicrobials are used prophylactically and administered via medicated feed, that the pig sector accounts for c. 40% of veterinary AMU in Ireland and that, while well within international industry norms, the amounts used are much higher than countries with well-established antimicrobial stewardship programmes. Metadata pertaining to management, biosecurity practices and respiratory health were used to evaluate the risk factors for AMU. Prophylactic use practices and factors related to respiratory disease were associated with total AMU indicating that measures to promote behavioural change and measures to improve pig health are required to achieve reductions in AMU. A longitudinal study was carried out on 12 farms with different levels of AMU to investigate how AMR evolves in the faecal microbiota during the pig lifecycle. The study had a phenotypic component investigating AMR in E. coli and a molecular component that used metagenomic sequencing to investigate AMR in the whole bacterial community, i.e., the ‘resistome’. There were parallel findings in both components: resistance peaked after weaning regardless of the level of AMU or the choice of antimicrobial but was higher on farms that used medicated feed compared to those that did not. The main exception was for resistance to fluoroquinolones and cephalosporins which was highest in suckling piglets. Age related changes in the microbial population had a greater influence on the resistome than AMU. The findings of this thesis provide much needed data to guide policy makers and researchers in the ongoing efforts to reduce AMU. They improve our understanding of the epidemiology of AMR on pig farms and offer encouragement that reducing AMU will ultimately result in reduced AMR. The link between animal health and AMU and between AMU and AMR bacteria and or genes of relevance to human health reinforces the value of a One Health approach to combatting AMR.