Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates

Abstract

BackgroundWhile Staphylococcus epidermidis is commonly isolated from healthy human skin, it is also the most frequent cause of nosocomial infections on indwelling medical devices. Despite its importance, few genome sequences existed and the most frequent hospital-associated lineage, ST2, had not been fully sequenced.ResultsWe cultivated 71 commensal S. epidermidis isolates from 15 skin sites and compared them with 28 nosocomial isolates from venous catheters and blood cultures. We produced 21 commensal and 9 nosocomial draft genomes, and annotated and compared their gene content, phylogenetic relatedness and biochemical functions. The commensal strains had an open pan-genome with 80% core genes and 20% variable genes. The variable genome was characterized by an overabundance of transposable elements, transcription factors and transporters. Biochemical diversity, as assayed by antibiotic resistance and in vitro biofilm formation, demonstrated the varied phenotypic consequences of this genomic diversity. The nosocomial isolates exhibited both large-scale rearrangements and single-nucleotide variation. We showed that S. epidermidis genomes separate into two phylogenetic groups, one consisting only of commensals. The formate dehydrogenase gene, present only in commensals, is a discriminatory marker between the two groups.ConclusionsCommensal skin S. epidermidis have an open pan-genome and show considerable diversity between isolates, even when derived from a single individual or body site. For ST2, the most common nosocomial lineage, we detect variation between three independent isolates sequenced. Finally, phylogenetic analyses revealed a previously unrecognized group of S. epidermidis strains characterized by reduced virulence and formate dehydrogenase, which we propose as a clinical molecular marker.

Deciphering Genomic Virulence Traits of a Staphylococcus epidermidis Strain Causing Native-Valve Endocarditis

“…The capABCD operon is involved in resistance to neutrophil phagocytosis (8). Finally, in a pangenomic study of S. epidermidis, it was suggested that isolates having a formate dehydrogenase-encoding gene (fdh) were characterized by a reduced virulence and that this gene was lost in virulent strains (21). This is consistent with our study, as strain CSUR P278 lacked the fdh gene.…”

Do Staphylococcus epidermidis Genetic Clusters Predict Isolation Sources?

“…Such markers may promote a hospital lifestyle and thus provide increased opportunities to cause infections. In contrast, the genetic markers fdh and arginine catabolic mobile element (ACME) have been reported to be more common in contaminant or commensal isolates than in true infection isolates (14)(15)(16).…”

Bypassing the Restriction System To Improve Transformation of Staphylococcus epidermidis

“…In addition, we assessed the role of the clonal complex-specific hsdS genes in the restriction barrier of S. epidermidis. For this purpose, we engineered DC10B cells, which can bypass the type IV restriction system, to encode a plasmid artificial modification (PAM) system (18) for type I HsdMS complexes of S. epidermidis strains, including NIH04008 (19), RP62A (20), NIH051475 (19), and VCU036 (21). NIH04008 belongs to CC2, the most common CC among clinical isolates, while RP62A is a CC10 laboratory-passaged strain, and the remaining two strains are clinical isolates belonging to CC89.…”