Genome Analysis of Staphylococcus aureus Isolated From the Feces of Diarrheal Patients in the Region of East China, 2019–2024

Staphylococcus aureus is a leading cause of foodborne diarrhea, primarily due to staphylococcal enterotoxins (SEs). This study employed whole‐genome sequencing to characterize 106 S. aureus isolates from diarrheal patients in East China (2019–2024). We identified 23 sequence types, with ST398 (22.6%) and ST5 (7.5%) among the most prevalent. Clonal complex analysis revealed the codominance of CC398 and CC5 (22.6% each), with CC5 exhibiting higher virulence and antimicrobial resistance (AMR) gene diversity. A significant 18.9% of isolates were methicillin‐resistant S. aureus (MRSA). While the tetracycline resistance gene tet38 was ubiquitous, 23.6% of isolates were multidrug‐resistant. Plasmid profiling showed rep16 (53.8%) and rep5a (51.9%) as the most common replicons. Crucially, SEs were detected in 51.9% of isolates, with a high prevalence in CC5 (83.3%) and a complete absence in CC398. A key temporal trend was the decline in virulence factors, coinciding with the rise of CC398. These findings reveal a dynamic genomic landscape and underscore the need for continued surveillance of diarrheagenic S. aureus .