Genetic diversity, virulence factors and antimicrobial resistance profiles of S. aureus isolated from raw meat, meat products and veterinary samples of food-producing animals in South African provinces

S. aureus is an important pathogen responsible for a wide range of infections in humans and animals. Its pathogenicity arises from diverse virulence factors (VFs), while its ability to acquire resistance to multiple antimicrobial agents further complicates treatment and contributes to its public health significance. The aim of this study was to investigate the presence of VFs, staphylococcal cassette chromosome mec elements (SCCmec) and the antimicrobial resistance profiles of S. aureus isolated from raw meat, meat products, and veterinary samples of food-producing animals, and to assess its genetic diversity. Whole-genome sequencing (WGS) was employed to analyse S. aureus (n = 27) isolates. The WGS-based MLST analysis identified 14 distinct sequence types (STs), with ST30, ST699, ST8 and ST96 being the most prevalent. Spa typing revealed 15 different spa types, including three novel ones: t76, t1029 and t12450, indicating a high genetic diversity. The results further revealed that the isolates harbored a broad spectrum of VFs and associated genes. The SCCmec typing did not identify the mec gene in all our isolates. Tetracycline resistance was widespread, with tet detected in all isolates and tetA (14.81%) and tetK (11.11%) identified in smaller subsets. Additionally, antimicrobial resistance genes such as blaZ (37.04%; 10/27), tet (38) (100%; 27/27), were detected in the isolates. Several ST, spa types and virulence genes identified in this study were linked to infections with high genetic relatedness, indicating the potential risk of S. aureus infections in South Africa.