Staphylococcus epidermidis Genome sequencing and assembly. Staphylococcus epidermidis

Staphylococcus epidermidis is a significant cause of nosocomial bloodstream infections worldwide and the fact that it is difficult to treat, represents a major burden for global public health. Recent study by analyzing a representative collection of the isolates from diverse geographic locations using whole genome sequencing (WGS) demonstrated global predominance in the hospital setting of three multidrug-resistant lineages of S. epidermidis (two ST2 and one ST23) (Lee et al., 2018). These lineages are resistant to rifampicin through acquisition of dual D471E and I527M mutations in the rpoB gene. Moreover, the D471E and I527M RpoB substitutions are also responsible for reduced susceptibility to the glycopeptide antibiotics, vancomycin and teicoplanin, and are almost exclusively found in isolates representing the ST2 and ST23 lineages. Since no data from the Netherlands was used in this study, we assessed all S. epidermidis isolates detected in blood cultures in our hospital, University Medical Center Groningen (UMCG), the Netherlands. All S. epidermidis isolates detected in blood cultures in UMCG from 2013-2018 were assessed. The isolates with co-resistance to both rifampicin and fusidic acid (n=63; 56 available for DNA sequencing) were selected for molecular evaluation based on next-generation sequencing approach (MiSeq Illumina).