Antibiotic Susceptibility Profiling of Human Pathogenic Staphylococcus aureus Strains Using Whole Genome Sequencing and Genome-Scale Annotation Approaches

Abstract

Staphylococcus species are major pathogens with increasing importance due to the rise in antibiotic resistance. Whole genome sequencing and genome-scale annotation are promising approaches to study the pathogenicity and dissemination of virulence factors in nosocomial methicillin-resistant and multidrug-resistant bacteria in intensive care units. Draft genome sequences of eight clinical S. aureus strains were assembled and annotated for the prediction of antimicrobial resistance genes, virulence factors, and phylogenetic analysis. Most of the studied S. aureus strains displayed multi-resistance toward the tested drugs, reaching more than seven drugs up to 12 in isolate S22. The mecA gene was detected in three isolates (S14, S21, and S23), mecC was identified in S8 and S9, and blaZ was commonly identified in all isolates except strain S23. Additionally, two complete mobile genomic islands coding for methicillin resistance SCCmec Iva (2B) were identified in strains S21 and S23. Numerous antimicrobial resistance genes (norA, norC, MgrA, tet(45), APH(3′)-IIIa, and AAC(6′)-APH(2″)) were identified in chromosomes of different strains. Plasmid analysis revealed the presence of blaZ, tetK, and ermC in different plasmid types, located in gene cassettes containing plasmid replicons (rep) and insertion sequences (IS). Additionally, the aminoglycoside-resistant determinants were identified in S1 (APH(3′)-IIIa), while AAC(6)-APH(2″) was detected in strains S8 and S14. The trimethoprim (dfrC) resistance gene was detected in S. aureus S21, and the fosfomycin (fosB) resistance gene was detected only in S. aureus S14. We also noted that S. aureus S1 belongs to ST1-t127, which has been reported as one of the most frequent human pathogen types. Additionally, we noted the presence of rare plasmid-mediated mecC-MRSA in some of our isolates.

Comparative genomic analysis of antibiotic resistance and virulence genes in Staphylococcus aureus isolates from patients and retail meat

“…The distribution of antibiotic resistance genes among MRSA strains in a tertiary care facility in Riyadh was as follows: ermC (28.8%), msrA (10.4%), aphA3 and sat (18.4%), fusC (43.2%), tetK (17.6%), tetM (7.2%), and fosB (56.8%) (Senok et al, 2019). According to Snoussi et al (2023), the genes associated with antimicrobial resistance in S. aureus isolates included fusC (50%), fosB, tetK, tet45, sat-4, aph(3′)-IIIa (12%), aac(6′)-aph(2″), and ermC (25%). In the present study, resistance genes in meat isolates included aph(3')-IIIa (15%), gyrA (23%), tetK (7%), tetM (2%), ermC (9%), fosB (62%), msrA, fusC, and sat-4 (13%), whereas those in patient isolates included aph(3')-IIIa (7%), gyrA (40%), msrA (8%), ermC (20%), fusC (51%), fosB (71%), tetK, and sat-4 (6%).…”