Genomic diversity of prevalentStaphylococcus epidermidismultidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey

Abstract

Staphylococcus epidermidisis a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistantS. epidermidisstrains in eight years at a children’s health-care unit in México City. Multidrug-resistantS. epidermidiswere present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17S. epidermidisisolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in theS. epidermidissequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of theS. epidermidisanalyzed lacked the ica operon for biofilm formation. Likely, they are commensalS. epidermidisstrains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination betweenS. epidermidisstrains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adaptedS. epidermidisclonal lineages in nosocomial settings.