Study on Genomic Diversity, Prophage Distribution of Bovine-Derived Staphylococcus aureus and Their Association with Antimicrobial Resistance

<i>Staphylococcus aureus</i> is the core pathogen causing bovine mastitis, and its antimicrobial resistance evolution is closely linked to prophage-mediated genetic material transfer, but their systematic association remains unclear. This study focused on 101 bovine-derived <i>S. aureus</i> strains isolated from large-scale dairy farms in Shihezi, Xinjiang, from September 2024 to January 2025, to explore their genomic diversity, prophage distribution characteristics, and intrinsic links to resistance. Results showed that the strains had resistance rates of 0.00-80.20% to 18 antibiotics across 12 classes, with ceftiofur having the highest resistance rate (80.20%) and 10 antibiotics including amoxicillin showing 0.00% resistance. Multidrug-resistant (MDR) strains accounted for 9.9% (10 strains), among which 2 had a resistance spectrum covering 7 antibiotic classes. The average genome size was 2.57 Mb with a GC content of 33.44%, cloud genes accounted for 85.00% of the pan-genome, and MLST identified 14 ST types, with ST5404 as the dominant type (36.6%). A total of 398 prophages were detected: 82.18% of strains carried resistance genes via prophages (Type I), while this proportion was 50.00% in MDR strains (Type II). This study confirms that prophages synergize with the ST5404 clonal group to promote clustered resistance gene transmission, providing a scientific basis for regional control of mastitis-causing drug-resistant strains and precise drug use.