Genomic characterization of a vancomycin-intermediate Staphylococcus aureus (VISA) small colony variant after long-term antibiotic therapy

OBJECTIVES: Vancomycin (VCM)-intermediate Staphylococcus aureus (VISA) and small-colony variants (SCVs) are clinically important phenotypes that are frequently difficult to treat and commonly encountered in persistent or recurrent infections. We previously reported a VISA strain, HV2019-1, isolated during a relapse episode of pacemaker-associated bloodstream infection. In the present study, we further investigated its phenotypic characteristics and genomic background. METHODS: Colony size, hemolytic activity, and pigmentation were quantitatively evaluated. To elucidate the genetic basis underlying the observed phenotype, whole-genome sequencing was performed and compared with that of a VCM-susceptible MRSA strain exhibiting a normal phenotype. RESULTS: HV2019-1 formed small colonies on agar plates and displayed reduced hemolysis and pigmentation, consistent with characteristic features of S. aureus SCVs. Genome analysis identified multiple mutations, including 25 disrupted open reading frames and five missense variants affecting regulatory functions and surface-associated factors. Among these, six genes previously implicated in VISA-related traits were detected. In contrast, no high-impact mutations were observed in metabolic pathways classically linked to SCVs, such as fatty acid, hemin, menadione, or thymidylate biosynthesis. CONCLUSION: The absence of canonical metabolic defects characteristic of SCVs, together with widespread alterations in regulatory and surface genes, is aligned with the concept that SCVs represent heterogeneous adaptive phenotypes rather than phenotypes defined primarily by specific metabolic deficiencies. The strain described here provides an example of a bacterial response that may contribute to both resistance and persistence under prolonged antibiotic pressure.