Identification of Novel Staphylococcus aureus Core and Accessory Virulence Patterns in Chronic Rhinosinusitis

<i>Staphylococcus aureus</i> (<i>S. aureus</i>) colonizes the nasal cavities of both healthy individuals and patients with chronic rhinosinusitis (CRS) with (CRSwNP) and without (CRSsNP) nasal polyps. Treatment-resistant <i>S. aureus</i> biofilms and intracellular persistence are common in CRS patients, requiring the expression of specific virulence factor genes to transition into these forms. We hypothesized that <i>S. aureus</i> isolates from non-diseased controls, CRSsNP patients, and CRSwNP patients would exhibit distinct virulence factor patterns contributing to persistence and intracellular survival in CRS patients. Nasal swabs from seventy-seven individuals yielded <i>S. aureus</i> cultures in eight non-diseased controls, eight CRSsNP patients, and five CRSwNP patients. Whole-genome sequencing analyzed stress, antimicrobial resistance, and virulence genes, including plasmids and prophages. Four virulence factor gene patterns emerged: a core set (<i>hlgA</i>, <i>icaC</i>, <i>hlgB</i>, <i>hlgC</i>, <i>hld</i>, and <i>aur</i>) present in all isolates, and accessory sets, including the enterotoxin gene cluster (<i>seo</i>, <i>sem</i>, <i>seu</i>, <i>sei</i>, and <i>sen</i>) and a partial/complete invasive virulence factor set (<i>splE</i>, <i>splA</i>, <i>splB</i>, <i>lukE</i>, and <i>lukD</i>) (<i>p</i> = 0.001). CRSwNP isolates exhibited incomplete carriage of the core set, with frequent loss of <i>scn</i>, <i>icaC</i>, and <i>hlgA</i> (<i>p</i> < 0.05). These findings suggest that <i>S. aureus</i> has clusters of virulence factors that may act in concert to support the survival and persistence of the bacteria, resulting in enhanced pathogenicity. This may manifest clinically with resistant disease and refractoriness to antibiotics.