Whole-genome sequencing of Staphylococcus aureus L401, a mecA-negative community-associated methicillin-resistant strain isolated from a healthy carrier.

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a human pathogen of great concern owing to its antimicrobial resistance and virulence properties. Here we report the first draft genome sequence of a mecA-negative community-associated MRSA strain isolated from a healthy young Mexican paediatric carrier in order to reveal the genomic structure underlying the multidrug-resistant phenotype and to discover the virulence properties of this strain. The draft genome sequence of S. aureus L401 was obtained using an Ion Torrent™ PGM platform. De novo assembled contigs were annotated, and antimicrobial resistance genes and virulence factors were identified using ResFinder and VirulenceFinder, respectively. In addition, a mutational survey of native pbp, gdpP and yjbH genes was performed. In silico multilocus sequence typing (MLST) and spa typing were also performed. S. aureus L401 has a genome size of 2 831 587 bp with 2799 protein-coding sequences. Various antimicrobial resistance genes conferring resistance to aminoglycosides, β-lactams, fluoroquinolones and macrolide-lincosamide-streptogramin B antimicrobials were found. Although both mecA and staphylococcal cassette chromosome mec (SCCmec) elements were absent, a missense mutation in PBP3 was identified. Moreover, genes encoding exfoliative toxin A, γ- and β-haemolysin, and several enterotoxins were also identified. S. aureus L401 belongs to ST109 and spa type t209. The availability of this genome will allow an insight into S. aureus resistance and virulence determinants as well as its epidemiology, lineage, evolution and genomic features involved in the paediatric commensal carriage.