Genomic characterization and genomic epidemiology of Staphylococcus aureus in chicken farms in Sichuan, China

Staphylococcus aureus (S. aureus) is an important zoonotic opportunistic pathogen, and its transmission risks in poultry production systems have attracted increasing attention in recent years. In this study, 126 S. aureus isolates recovered from clinical and farm environmental samples were subjected to whole-genome sequencing and comparative genomic analysis to characterize their genotypes, antimicrobial resistance, virulence, and transmission patterns. The spa typing identified t2582 as the predominant type, whereas multi-locus sequence typing identified ST398 as the dominant sequence type. Overall, 35 antimicrobial resistance genes (ARGs) and 41 virulence-associated genes were detected. Only five isolates carried mecA , indicating the emergence of methicillin-resistant S. aureus (MRSA) isolates on chicken farms in Sichuan Province, China. Aminoglycoside- and tetracycline-resistance genes were significantly enriched in environmental isolates, whereas the number of virulence genes did not differ significantly between clinical and environmental isolates. Core-genome single-nucleotide polymorphism (SNP) analysis grouped the isolates into two major lineages, with clinical and environmental isolates interspersed throughout the phylogeny. Some clinical and environmental isolates showed extremely small pairwise SNP differences, suggesting potential transmission of S. aureus across difference sources. These findings demonstrate close epidemiological links between clinical and environmental isolates, highlighting the farm environment as a potential reservoir and transmission interface for S. aureus . Continuous genomic surveillance, improved environmental sanitation and enhanced biosecurity are therefore essential for controlling its spread in chicken farms.