Characterization of the virulence shaping and adaptability in the methicillin-resistant <i>Staphylococcus aureus</i> ST9 lineage

<i>Staphylococcus aureus</i> is a major pathogen responsible for hospital- and community-acquired infections, with the accessory gene regulator (<i>agr</i>) system playing a central role in virulence control. The ST9 lineage commonly associated with livestock exhibits multidrug resistance but remains understudied in terms of virulence. In this work, we examined nine clinical ST9 methicillin-resistant <i>S. aureus</i> isolates and identified two strains carrying spontaneous frameshift mutations in the <i>agr</i> locus, resulting in the loss of RNAIII and α-toxin expression. These <i>agr</i>-deficient strains exhibited reduced hemolytic activity, enhanced biofilm formation, and attenuated virulence in a <i>Galleria mellonella</i> infection model. These preliminary pieces of evidence suggested a critical role of the <i>agr</i> system in ST9 virulence. Comparative genomic analyses revealed distinct pathogenicity islands in ST9, differing from those in other common clinical lineages. Notably, we identified three novel prophage islands (φST9-A, φST9-B, and φST9-C), with φST9-B carrying the recently characterized <i>tarP</i> virulence gene, suggesting that recombination events within livestock-associated MRSA could contribute to the genetic diversification of ST9. These findings demonstrate the significant virulence potential of the ST9 lineage and the importance of <i>agr</i>-mediated regulation. Moreover, the presence of new prophages highlights the evolutionary adaptability of this lineage. Collectively, our results underscore the clinical threat posed by ST9 MRSA and the necessity for vigilant monitoring to control its spread.IMPORTANCEMethicillin-resistant <i>Staphylococcus aureus</i> (MRSA) ST9 commonly associated with livestock remains understudied in terms of virulence mechanisms. This study identifies key insights into ST9 MRSA virulence, focusing on the accessory gene regulator (<i>agr</i>) system, which regulates virulence in <i>S. aureus</i>. We show that <i>agr</i>-deficient ST9 strains exhibit altered virulence phenotypes, including reduced hemolysis and increased biofilm formation. Additionally, our genomic analysis reveals novel prophage islands in ST9, highlighting the lineage's genetic adaptability and potential for increased virulence. These findings emphasize the need for continued surveillance and targeted strategies to control the spread of ST9 MRSA, with important implications for diagnostic and therapeutic approaches.