Comparative Genomics Study of Staphylococcus epidermidis Isolates from Orthopedic-Device-Related Infections Correlated with Patient Outcome

Staphylococcus epidermidis has emerged as an important opportunistic pathogen causing orthopedic device-related infections (ODRIs). This study investigated the association of genome variation and phenotypic features of the infecting S. epidermidis isolate with the clinical outcome of the infected patient. S. epidermidis isolates were collected from 104 patients with ODRI. Their clinical outcome was evaluated, after an average of 26 months, as either "cured" or "not cured". The isolates were tested for antibiotic susceptibility and biofilm formation. Whole genome sequencing was performed on all isolates and genomic variation was related to features associated with "cured" and "not cured". Strong biofilm formation and aminoglycoside resistance were associated with a "not cured" outcome (p = 0.031 and p < 0.001, respectively). Based on gene-by-gene analysis, some accessory genes were more prevalent in isolates from the "not cured" group. These included: the biofilm-associated bhp gene; the antiseptic resistance qacA gene, the cassette chromosome recombinase encoding genes ccrA and ccrB and IS256-like transposase. This study identifies biofilm formation and antibiotic resistance as associated with poor outcome in S. epidermidis ODRI. Whole genome sequencing identified specific genes associated with a "not cured" outcome that should be validated in future studies.