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Staphylococcus epidermidis  is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant  S. epidermidis  strains in eight years at a children’s health-care unit in México City. Multidrug-resistant  S. epidermidis  were 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 17  S. epidermidis  isolates. 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 the  S. epidermidis  sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the  S. epidermidis  analyzed lacked the ica operon for biofilm formation. Likely, they are commensal  S. epidermidis  strains but multi-antibiotic resistant. 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 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 adapted  S. epidermidis  clonal lineages in nosocomial settings.

peerj

Genomic diversity of prevalent<i>Staphylococcus epidermidis</i>multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey

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