A φSa3int (NM3) Prophage Domestication in <i>Staphylococcus aureus</i> Leads to Increased Virulence Through Human Immune Evasion

<i>Staphylococcus aureus</i> with varying virulence is often isolated from chronic rhinosinusitis (CRS) patients and impacts disease severity. Prophage-mediated virulence, particularly encoded by φSa3int (NM3) prophages, which often encodes human immune-evasion cluster genes is well known, but how a new prophage domestication impacts overall expression of core bacterial genes, and the expression of resident prophages is understudied. To understand this, we transduced a φSa3int prophage recovered from hyper-biofilm forming mucoid <i>S. aureus</i> (SA333) into a high-biofilm forming non-mucoid <i>S. aureus</i> (SA222) recovered from same CRS patient but at different time points. Upon φSa3int prophage domestication, we observed a significant upregulation of 21 exoproteins including human immune-evasion toxins and an intercellular adhesion protein B (IcaB). Further, φSa3int prophage domestication led to reduced phagocytosis implying φSa3int prophage mediates escape of <i>S. aureus</i> from human innate immunity. Our data further show that in addition to adding novel prophage-encoded virulence, φSa3int prophage domestication also affects the expression of non-prophage (bacterial) genes and suppresses expression of structural proteins of resident prophages. Since strains without prophage or with specific prophages have varying virulence and pathogenicity, targeted identification virulence factors associated with mobile genetic elements (MGEs) in addition to species identification may lead to better personalized therapy, particularly in chronic infections.