A genomic analysis of methicillin resistant Staphylococcus aureus from bovine milk and the discovery of a novel streptococcus species

Staphylococcus aureus and methicillin resistant Staphylococcus aureus (MRSA) are important pathogens of humans and livestock, including dairy cows. In livestock it represents a concern for public health as it may act as a reservoir that can infect humans and provide a source of transferrable resistance genes. The divergent mecA gene, mecC, was first identified in dairy cows in the UK, and has since been detected in many species in continental Europe. However, limited data exists on the epidemiological characteristics or the transmission dynamics of bovine mecC MRSA in the UK. S. aureus Mobile Genetic Elements (MGEs) often encode virulence and antimicrobial resistance genes that can contribute to the pathogenicity of the strain. Acquisition or loss of MGEs and variations within the core genome are reported to play an important role in S. aureus host adaptation although the mechanisms underlying S. aureus host specificity are not fully understood. This study was undertaken to determine the antimicrobial resistance and bovine associated virulence features of S. aureus isolated from bovine milk. The first two chapters of this thesis comprise of an introduction and a description of the methods used. Chapter 3 describes bovine associated features in bulk tank milk S. aureus isolates. SaPI borne-vwb and sec_bovine were widespread. Further, genome analysis detected six new SaPIs harbouring these genes and a class of site-specific integrases that appear to be associated with ruminant derived isolates. Examination of the fnbpA gene identified host specific variations that may be used to distinguish bovine from human isolates. Chapter 4 presents data on the epidemiological characteristics of mecC MRSA at the cow level within a dairy herd. Data from a longitudinal study undertaken suggested that mecC MRSA infections were transient and may not be associated with clinical disease. The prevalence varied between 1.14%-5.07% during the one-year study period, while SNP based whole genome phylogeny revealed four possible chains of transmission. Chapter 5 details a survey conducted to detect the prevalence of MRSA in UK retail meat. No mecC MRSA were found however CC398 were found and compared to CC398 isolates from the bulk tank milk study. A phylogenetic study provided no evidence of a common lineage of livestock association MRSA colonising both cattle and pigs in the UK. Chapter 6 describes the characterisation of a novel Streptococcus species isolated from a mastitic cow from New Zealand. Genome sequencing and phenotypic studies revealed this isolate, originally thought to be Streptococcus uberis to be most closely related to Streptococcus pseudoporcinus.Personal Funding for tuition and other related expenses MRC funding for laboratory expense