Whole genome investigation of multi-drug resistant Staphylococcus aureus strain

The emergence of multidrug-resistant (MDR) Staphylococcus aureus strains poses significant challenges for effective management and treatment, often harboring genes associated with antimicrobial resistance (AMR) and virulence factors contributing to their pathogenicity, establishing them as a global health threat. This study aims to perform a comprehensive genomic investigation of a Libyan MDR S. aureus strain to assess its resistance profile and virulence mechanisms. Whole genome sequencing and bioinformatics analyses, including comparative genome analysis, phylogenetics and the screening of key genetic elements involved in pathogenicity and AMR, were conducted to explore the genomic features of this strain. Several resistance detection tools and databases were applied to evaluate variations in genomic annotation and prediction. Our strain presented a 2.77 Mb genome with 2,650 coding sequences, sharing 94.04% orthologous genes with the CC239-MRSA-III strain. Key resistance and virulence factors, such as mecA, blaZ, and efflux pumps, were identified, along with point mutations in metabolic and replication enzymes. Additionally, an alanine racemase gene (alr) homologous to the vanT in vanG cluster was identified, suggesting a potential evolving resistance variant and pointing to a potential undercharacterized gene related to early stages of resistance development. Variations among resistance prediction tools also highlighted the need for integrating multiple analysis approaches. This study provides a detailed genomic analysis of a Libyan MDR S. aureus strain, revealing an extensive array of resistance and virulence factors. The discrepancies across resistance detection tools underscore the importance of standardized genomic investigation approaches for improved management of resistant infections.