J Bacteriol 2019 11 21;201(22). Epub 2019 Oct 21.
Food Microbial Systems, Agroscope, Bern, Switzerland
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. harbors up to three genomic islands, Saα, Saβ, and Saγ. The Saβ region of can encode a number of virulence-associated factors, such as serine proteases, leukocidins, enterotoxins, bacteriocins, or a hyaluronate lyase. In this study, the Saβ regions of 103 clinically relevant strains were characterized and compared to the three predefined Saβ types. We here suggest a superordinate system of 15 different Saβ types, of which 12 were newly defined. Each Saβ 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 Saβ type is strongly coupled with its clonal complex, suggesting that Saβ was acquired in an ancestral 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 Saβ region. With the rapid increase of available sequencing data on clinically relevant bacterial species such as , 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 genomic island Saβ and defined a superordinate system to categorize strains based on their Saβ type, providing information about the strains' virulence-associated genes and clinical potential.