title: Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates.
abstract: BACKGROUND
  While 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  Commensal 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.
authors: Sean
authors: S
authors: Conlan
authors: Lilia A
authors: LA
authors: Mijares
authors: Jesse
authors: J
authors: Becker
authors: Robert W
authors: RW
authors: Blakesley
authors: Gerard G
authors: GG
authors: Bouffard
authors: Shelise
authors: S
authors: Brooks
authors: Holly
authors: H
authors: Coleman
authors: Jyoti
authors: J
authors: Gupta
authors: Natalie
authors: N
authors: Gurson
authors: Morgan
authors: M
authors: Park
authors: Brian
authors: B
authors: Schmidt
authors: Pamela J
authors: PJ
authors: Thomas
authors: Michael
authors: M
authors: Otto
authors: Heidi H
authors: HH
authors: Kong
authors: Patrick R
authors: PR
authors: Murray
authors: Julia A
authors: JA
authors: Segre
mesh_terms: D055499:Catheter-Related Infections / Q000382:microbiology*; D003428:Cross Infection / Q000382:microbiology*; D024881:Drug Resistance, Bacterial; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D008969:Molecular Sequence Data; D058889:Molecular Typing; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012867:Skin / Q000382:microbiology*; D013212:Staphylococcus epidermidis / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification