Whole-Genome Molecular Characterization and Typing of Staphylococcus aureus Isolated from Lebanon

Abstract

Staphylococcus aureus is one of the major causes of nosocomial and community-acquired infections. The rising prevalence of multidrug resistant (MDR) S. aureus in both community and hospital settings is a significant public health concern. In this study, whole-genome sequencing was used for the molecular characterization of 31 S. aureus clinical isolates. Genetic relatedness of the isolates was studied using different typing approaches, including Multilocus Sequence Typing (MLST), S. aureus protein A (spa) typing, and Staphylococcal Chromosomal Cassette (SCCmec) typing of the Methicillin-Resistant S. aureus (MRSA) isolates. The antimicrobial susceptibility patterns were determined, and virulence determinants were detected in silico. Most of the studied isolates carried the blaZ gene, 45% were MRSA, and 32% were MDR. Fifteen distinct MLST allelic profiles were identified with the most common STs being ST80 (22.58%), ST6 (12.9%), and ST1 (12.9%). Nineteen different spa types were detected, with the major ones being t044 (19.35%), t127 (12.9%), and t304 (9.67%). SCCmec typing of MRSA revealed the prevalence the type IV, and the most common strain was MRSA ST80-t044-IV. The worldwide dissemination of the MRSA-ST80 clone decreased over the past few years, but it was still the most common strain in Lebanon. For the first time, we detected an untypeable SCCmec cassette harboring multiple ccr complexes or missing some of the conserved genes. Using the SCCmecFinder, we were able to predict the mec cassettes and showed that the SSA11 harbored a pseudo-SCCmec element resembling the one detected SCCmec type IV(2B). This study provided a high-resolution view of the molecular characteristics of S. aureus clinical isolates. It confirmed that diverse isolates of MSSA and MRSA are circulating in the country differing in antimicrobial susceptibility and virulence determinants. Our results should be further investigated in multiple-center settings to address the high incidence and burden of S. aureus infections in Lebanon.