ABSTRACT
Staphylococcus aureus is a widespread opportunistic pathogen to humans and animals. Of its genome, 20 to 25% varies between strains and consists of phages, pathogenicity islands, transposons, and genomic islands. S. aureus harbors up to three genomic islands, vSaα, vSaß, and vSaγ. The vSaß region of S. aureus can encode a number of virulence-associated factors, such as serine proteases, leukocidins, enterotoxins, bacteriocins, or a hyaluronate lyase. In this study, the vSaß regions of 103 clinically relevant S. aureus strains were characterized in silico and compared to the three predefined vSaß types. We here suggest a superordinate system of 15 different vSaß types, of which 12 were newly defined. Each vSaß type has a distinct structure with a distinct set of genes, which are both highly conserved. Between the different types, gene content and composition vary substantially. Based on our data, a strain's vSaß type is strongly coupled with its clonal complex, suggesting that vSaß was acquired in an ancestral S. aureus strain, arguably by phage mediation, before differentiation into clonal complexes. In addition, we addressed the issue of ambiguous nomenclature in the serine protease gene cluster and propose a novel, phylogeny-based nomenclature of the cluster contained in the vSaß region.IMPORTANCE With the rapid increase of available sequencing data on clinically relevant bacterial species such as S. aureus, the genomic basis of clinical phenotypes can be investigated in much more detail, allowing a much deeper understanding of the mechanisms involved in disease. We characterized in detail the S. aureus genomic island vSaß and defined a superordinate system to categorize S. aureus strains based on their vSaß type, providing information about the strains' virulence-associated genes and clinical potential.
