Genomic characterization of oxacillin-susceptible mecA-positive Staphylococcus aureus ST59

Abstract

Objective. To characterize the genomes of oxacillin-susceptible mecA-positive Staphylococcus aureus ST59 isolated in St. Petersburg. Materials and Methods. Nine oxacillin-susceptible mecA-positive of S. aureus isolates (OS-MRSA) of ST59 were included in the study. The isolates were obtained from children who showed no clinical signs of staphylococcal infections during nasal screening of S. aureus in St. Petersburg in 2018–2019. One isolate was obtained from an adult patient with skin and soft tissue infection (SSTI). The susceptibility to antibiotics and whole genome sequencing were performed. The analysis included 242 genomes of S. aureus ST59 from open access databases. Results. By employing the broth serial dilution and VITEK, the isolates’ phenotypic susceptibility to oxacillin was determined. The cefoxitin inhibition zones ranged from 17 to 22 mm. All isolates showed a penicillinclavulanate MIC ≤ 0.5 µg/mL. Isolates obtained from carriers belonged to the ST59-t1950-SCCmec Vb (seb+) genotype whereas the isolate obtained from SSTI belonged to the ST59-t437-SCCmec Vb (seb/ lukF/lukS+) genotype. Nucleotide position -33 (C/T) of mecA promoter and mutations in PBP2a (S225R + E246G) were present in all isolates. Based on phylogenetic analysis and Bayesian clustering the ST59 genomes were divided into four clusters and all Russian genomes belonged to the East Asian ST59 sublineage. The PVL toxin was present in the genomes of the first cluster of the East Asian ST59 sublineage. Pairwise comparisons of nucleotide substitutions among the genomes of Russian isolates showed a high similarity: median 13, interquartile range 8–18. All ST59 clusters were characterized by the presence of enterotoxin B, as well as mutations in PBP2a (S225R and E246G) and the promoter regions of the mecA gene (-7 G/A or -33 C/T). The genomes of the Russian isolates differed from the globally spread ST59 by specific mutations at the following loci (relative to the reference genome of S. aureus M013TW): lactose catabolism regulator RS03495 (N168D), ribosomal protein L28 (V47A), putative glyoxalase RS07825 (V42A), and the hypothetical protein RS13235 (K32E). Conclusions. Russian MRSA-ST59 isolates belong to the East Asian sublineage and are characterized by the presence of the enterotoxin B gene. Oxacillin susceptibility and borderline resistance to cefoxitin are specific characteristics of MRSA-ST59. OS-MRSA phenotypes have a risk of improper sensitivity testing leading to ineffective antibiotic treatment. Detection of mecA gene is the most accurate method for differentiating between MSSA and MRSA.