Timely excision of prophage Φ13 is essential for the infectious process.

Mobile genetic elements play an essential part in the infectious process of major pathogens, yet the role of prophage dynamics in pathogenesis is still not well understood. Here, we studied the impact of the Φ13 converting prophage, whose integration inactivates the β-toxin gene, on staphylococcal pathogenesis. We showed that prophage Φ13 is lost in approximately half the bacterial population during the course of infection. Inactivation of the Φ13 recombinase gene, essential for insertion/excision, locked the prophage in the bacterial chromosome, leading to a significant loss of virulence in a murine systemic infection model. In contrast, the non-lysogen strain (ΔΦ13), where the beta-hemolysin gene is reconstituted, displayed strongly increased virulence. Accordingly, histopathological analyses revealed more severe nephritis in mice infected with bacteria lacking prophage Φ13 (ΔΦ13), compared to infection with the parental strain. Infection with the ∆ mutant, where beta-hemolysin production is abolished, led to the least severe renal lesions. Cytokine induction in a human neutrophil model showed significantly increased IL-6 expression following infection with the beta-hemolysin producing strain (ΔΦ13). Our results indicate that timely excision of the Φ13 prophage is essential for progression of the infectious process: early excision leads to rapid host death, whereas the inability to excise the prophage significantly reduces staphylococcal virulence.IMPORTANCEThis study highlights prophage Φ13 excision as a critical factor in pathogenesis, influencing infection outcomes by balancing rapid host killing with reduced bacterial virulence. This mechanism may represent a bet-hedging strategy in genetic regulation, resulting in a mixed bacterial population capable of rapidly switching between two processes: bacterial colonization and host damage. Unraveling this dynamic opens new possibilities for developing targeted therapies to disrupt or modulate prophage activity, offering a novel approach to mitigating infections.