Abstract
Primary production has been the backbone of the New Zealand economy, with dairy being the largest export earner. One challenge for the dairy sector is disease burden, with bovine mastitis costs estimated to be $180 million/year. Mastitis is a multifactorial complex disease predominantly caused by pathogen invasion. Genomics has revolutionised the way mastitis pathogens can be studied. Staphylococcus aureus (S. aureus) is a contagious mastitis-causing bacteria and has been the focus of research due to its contagious nature and zoonotic tendencies. Two published studies built a crucial foundation for understanding the genomic landscape of New Zealand bovine S. aureus, providing an opportunity for deeper insights into its genetic makeup. In this thesis, I aimed to understand the national, regional, and farm population structure of New Zealand bovine S. aureus using whole genome sequencing (WGS). In this body of work, I generated 11 bovine S. aureus reference genomes for the mastitis and veterinary research fields and unveiled insights into regional sequence type (ST) and antimicrobial resistance gene (AMR) trends. In addition, I evaluated genomic differences between ST1 S. aureus human and bovine genomes and discovered coagulase-negative S. aureus variants circulating in the dairy sector. The finding of two ST97 plasmids carrying quaternary ammonium compound (qac) genes and 55% of ST97 carrying blaZ highlighted the need for plasmid surveillance and the need to link sequence type to on-farm mastitis outcomes. ST1 was the dominant sequence type in the New Zealand bovine population. However, regional trends were discovered, with ST97 increasing in prevalence in the South Island. Climate and management could be key contributing factors to why this is. ST1 is uniquely dominant in the human and bovine populations, and the detection of the φSabovST1 carrying lukF-like/lukM genes were indicative of bovine host adaptation; what this means in terms of clinical significance in mastitis cases is yet to be established. Accurate diagnostics are crucial in the dairy sector; due to the contagious nature of S. aureus, my finding of coagulase-negative variants circulating reinforced the need for a combination of testing methods for the identification of mastitis pathogens to avoid costly mismanagement and additional diagnostic expenses. This thesis lays the groundwork for understanding S. aureus mastitis within New Zealand. The S. aureus population dynamics uncovered in this thesis can provide valuable genomic and epidemiological insights for the mastitis research field and veterinary medicine.