Predicted and inducible prophages display contrasting virulence gene profiles within the prophage–SaPI mobilome of <i>Staphylococcus aureus</i>

Prophages play a significant role in bacterial evolution by shaping genomic diversity, virulence, and host adaptation. This study investigated the prophage composition of 109 clinical <i>Staphylococcus aureus</i> isolates obtained from four tertiary care hospitals in Mexico City and compared these results with data from 993 global genomes. Prophages were present in 97% of local isolates. Consistently, analysis of the global genome collection revealed a 99% prevalence, supporting the near ubiquity of prophages in <i>S. aureus</i>. Analysis identified 216 genomic regions corresponding to the predicted prophages within the Mexican <i>S. aureus</i> isolates. A substantial fraction (19%) of the predicted prophages was identified as phage-inducible chromosomal islands (PICIs), such as SaPI1, SaPI2, and SaPIpt1028-like elements. These PICIs encoded anti-phage defense systems (63%) and virulence genes (27%). Experimental treatment with mitomycin C induced 17 temperate phages, of which 12 demonstrated functional activity and the ability to undergo lysogenic-lytic switching and reinfection. No virulence or antibiotic resistance genes were identified in these temperate phages. Conversely, several uninduced prophages coincided with the virulence determinants. These findings highlight the complexity of the <i>S. aureus</i> mobilome, characterized by distinct functional profiles and heterogeneous mobilization capabilities, which may influence the dissemination of virulence factors.IMPORTANCE<i>Staphylococcus aureus</i> is a significant hospital-associated pathogen whose evolutionary processes are shaped by mobile genetic elements, including prophages and phage-inducible chromosomal islands (PICIs). While computational analyses suggest that nearly all <i>S. aureus</i> genomes contain prophages, our findings indicate that only a subset is inducible following mitomycin C treatment. These temperate phages do not possess virulence genes; however, other predicted prophages are associated with virulence factors. Additionally, we identified numerous predicted prophages as PICIs, which harbored anti-phage defense mechanisms and toxins. This study highlights the intricate mobilome of <i>S. aureus</i> and the various strategies that contribute to its horizontal gene transfer and pathogenic evolution.