Complete genome and plasmid sequences of Staphylococcus aureus strain COL52-A5 isolated from a persistent nasal carrier

Abstract

Persistent colonization with Staphylococcus aureus is associated with a higher risk of invasive infections. With increasing rates of colonization, especially with antibiotic-resistant strains, it may be useful to identify specific characteristics of colonization that confer a greater infection risk. Therefore, whole-genome sequencing (WGS) of an S. aureus strain isolated from a medical student identified as a persistent carrier in Cartagena, Colombia, was performed to better characterize the strain and to identify genetic components associated with virulence and antimicrobial resistance. Antimicrobial susceptibility testing was performed for several antibiotics. Total genomic DNA was extracted and WGS was performed on a PacBio RS II sequencing platform. Whole-genome assembly was generated using PacBio SMRT Analysis v.2.3.0 and HGAP v.1.2. In silico analysis of the chromosomal and plasmid components of this strain was performed using tools available online. Strain COL52-A5 was identified as a Panton-Valentine leukocidin (PVL)-positive methicillin-resistant S. aureus (MRSA) carrying staphylococcal cassette chromosome mec (SCCmec) type IVa and was resistant to cefoxitin, erythromycin, clindamycin and tetracycline. The completely closed genome of strain COL52-A5 was 2 820 086 bp with a GC content of 32.84% and it harboured one large plasmid, two active prophages, five antimicrobial resistance determinants and several virulence factors. The allelic profile was consistent with sequence type ST923 (CC8). Genome analysis of strain COL52-A5 found numerous virulence and resistance factors. Further comparison of genomic sequences from persistent and intermittent strains is required to gain insights into the genomic features that favour persistent carriage in healthy individuals.