Genomic and phenotypic adaptations of methicillin resistant Staphylococcus aureus during vancomycin therapy

Methicillin-resistant Staphylococcus aureus (MRSA) poses a significant global health challenge, particularly associated with serious infections such as bacteremia. Lipoglycopeptide antibiotics, including vancomycin, dalbavancin, and daptomycin, are critical in MRSA treatment. In this study, we analyzed two MRSA isolates (XF1 and XF2) from a bacteremia patient treated with vancomycin. Antimicrobial susceptibility testing revealed that XF1 was sensitive to vancomycin, dalbavancin, and daptomycin, whereas XF2 exhibited 8- to 16-fold higher minimum inhibitory concentrations for these antibiotics, alongside a 4- to 8-fold reduction in resistance to β-lactam antibiotics, demonstrating the "β-lactam seesaw effect". Whole-genome sequencing confirmed their isogenic nature (ST59-SCCmecIV-t172), identifying seven mutations in XF2, including those in walK (G223S), vraR (D88Y), clpX (P64L), and ltaS (L62P), as well as a frameshift mutation in mgt (S39fs), likely contributing to resistance. Transmission electron microscopy and autolysis assays demonstrated that XF2 had a thicker cell wall and a slower autolysis rate compared to XF1. Phenotypic analysis showed that XF2 exhibited reduced growth rate, diminished virulence, and enhanced biofilm formation compared to XF1. Gene expression analysis supported these findings, revealing significant alterations in pathways related to cell wall metabolism, autolysis, and virulence regulation. These adaptations highlight the genomic and phenotypic plasticity of MRSA under antibiotic pressure, enabling resistance and persistence. This study underscores the urgent need for enhanced surveillance and alternative therapeutic strategies, including exploiting the β-lactam seesaw effect, to combat lipoglycopeptide-nonsusceptible MRSA.