Comprehensive whole genome analysis of Staphylococcus aureus isolates from dairy cows with subclinical mastitis

Staphylococcus aureus is one of the major bacteria which is a frequent cause of bovine mastitis. Understanding the frequency of virulence traits and antimicrobial resistance would shed light on the molecular epidemiology of S. aureus strains linked to mastitis. In the current investigation, 38 mastitis-associated S. aureus isolates obtained from the Free State province, South Africa, were subjected to whole-genome sequencing and comparative genomic analysis. The 38 isolates were grouped by the in silico multi-locus sequencing types (MLST) into seven sequence types (STs), that is, (ST 97, 352, 152, 243) and three new STs (ST8495, ST8500 and ST8501). The average GC content of the 2.7 Mbp genome was 32.7%. Thirty-three strains were divided into 7 core SNP clusters. The Spa-types t2883 accounted for the majority of isolates at 12 (31.57%), followed by t416 with 11 (28.94%) and t2844 with 5 (13.15%), among the 9 distinct spatypes that were found. The data also revealed the identification of four (4) plasmids, with Rep_N (rep20) accounting for the majority of isolates with 17 (44.73%), followed by Inc18 (repUS5) with 2 (5.26%). These isolates included 11 distinct antimicrobial resistance (AMR) genes and 23 genes linked to bacterial virulence. Remarkably, no methicillin resistance was predicted in these isolates. Due to the virulence traits of S. aureus that play a role in the mastitis disease process, characterisation is essential for risk assessment. The results of our study on genes associated with virulence and antibiotic resistance are relevant due to the implications for public health.