Genomic diversity of antibiotic multi-resistant Staphylococcus epidermidis isolated from a tertiary care hospital in México City

Staphylococcus epidermidis is a human commensal and opportunistic pathogen worldwide distributed. To ascertain which pathogenic S. epidermidis clones are circulating in a local tertiary hospital setting, we sequenced the complete genomes of 17 S. epidermidis isolates obtained from neonatal infections at a Hospital Care Unit in México City. Genomic comparisons between S. epidermidis isolates revealed high pairwise whole genome nucleotide identities of about 97% to 99% and essentially a clonal structure. We inferred eight Multilocus Sequence Types (MLST´s), six of them of worldwide distribution, and two showing allelic variants, not in MLST databases. The profile of virulence includes genes involved in biofilm and modulin formation; most of the strains are multi-resistant to methicillin and several other beta-lactams, fluoroquinolones, and macrolides. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more frequent than the mutation rate and affected the whole genome. Therefore, recombination properties shape the population structure of local nosocomial S. epidermidis strains, formed by pathogenic and probably, non-pathogenic clones.