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Staphylococcus capitis  is an opportunistic pathogen of the coagulase negative staphylococci (CoNS). Functional genomic studies of  S. capitis  have thus far been limited by a lack of available complete genome sequences. Here, we determined the closed  S. capitis  genome and methylome using Single Molecule Real Time (SMRT) sequencing. The strain, AYP1020, harbors a single circular chromosome of 2.44 Mb encoding 2304 predicted proteins, which is the smallest of all complete staphylococcal genomes sequenced to date. AYP1020 harbors two large mobile genetic elements; a plasmid designated pAYP1020 (59.6 Kb) and a prophage, ΦAYP1020 (48.5 Kb). Methylome analysis identified significant adenine methylation across the genome involving two distinct methylation motifs (1972 putative 6-methyladenine (m6A) residues identified). Putative adenine methyltransferases were also identified. Comparative analysis of AYP1020 and the closely related CoNS,  S. epidermidis  RP62a, revealed a host of virulence factors that likely contribute to  S. capitis  pathogenicity, most notably genes important for biofilm formation and a suite of phenol soluble modulins (PSMs); the expression/production of these factors were corroborated by functional assays. The complete  S. capitis  genome will aid future studies on the evolution and pathogenesis of the coagulase negative staphylococci.

Insights on virulence from the complete genome of Staphylococcus capitis