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

Abstract

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.

Genomic Analysis of Antibiotic-Resistant Staphylococcus epidermidis Isolates From Clinical Sources in the Kwazulu-Natal Province, South Africa

“…As well, erm(C) , msr(A) , dfrG , and mph(C) genes were distributed across the regional hospital but were not ward specific, while dfrG , tet(K) , and erm(B) were frequently found in the district hospital. The detection of blaZ in all isolates and the regulator genes blaR and blaI may explain the resistance against penicillin and cephalosporins observed in antibiotic susceptibility tests, which is in agreement with a previous study ( Cabrera-Contreras et al, 2019 ). S. epidermidis isolates carrying similar resistance gene profiles have been previously reported ( Xu et al, 2018 ; Cabrera-Contreras et al, 2019 ; Raue et al, 2020 ).…”

“…S. epidermidis is commonly recovered from bacterial bloodstream infections from neonatal units as a probable causative agent ( Asante et al, 2020 ). Children are particularly susceptible to acquiring S. epidermidis in perinatal hospitals ( Cabrera-Contreras et al, 2019 ).…”

“…Staphylococcus epidermidis are coagulase-negative staphylococci (CoNS) that are commensals of the skin microbiome. Among the CoNS, S. epidermidis and Staphylococcus haemolyticus , together referred to as the S. epidermidis group, are the most prevalent in clinical settings ( Azih and Enabulele, 2013 ) and can behave as pathogens by colonizing medical devices, infecting surgical wounds, and causing bacteremia ( Cabrera-Contreras et al, 2019 ). CoNS infection is commonly associated with device-associated healthcare infection.…”

“…According to recent phylogenetic studies, the ACME most likely originated from S. epidermidis and transmitted to S. aureus through horizontal transfer ( Onishi et al, 2013 ; Planet et al, 2013 ). Other factors that have been associated with pathogenicity in S. epidermidis include the metabolic state of the bacterial cell, genomic rearrangements in pathogenic isolates facilitated by IS256, and the conjugative transfer of antibiotic resistance ( Cabrera-Contreras et al, 2019 ).…”

Development of Staphylococcus Enzybiotics: The Ph28 Gene of Staphylococcus epidermidis Phage PH15 Is a Two-Domain Endolysin

“…Some S. epidermidis strains behave as pathogens colonizing surgery wounds and in some circumstances, they reach the human bloodstream causing severe bacteremia and potential mortality [17,18]. Children are especially prone to acquire methicillin-resistant S. epidermidis strains in perinatal hospitals [18,19]. In addition, S. epidermidis is thought to be associated with periodontitis, acute and chronic pulpitis, pericoronitis, dry socket and angular stomatitis [20].…”