Objectives: This study reports what is, to our knowledge, the first vancomycin-variable Enterococcus faecium (VVEfm) isolate identified and genomically characterized in Switzerland.

Methods: A vancomycin-susceptible, vanA -positive E. faecium isolate recovered from a urine culture was characterized using antimicrobial susceptibility testing (AST), vanA/vanB real-time PCR, population analysis profiling (PAP), spontaneous reversion assays on selective media, and whole-genome sequencing (WGS). Comparative genomic analyses were performed with five vancomycin-resistant E. faecium (VREfm) isolates recovered from the same patient, and three VREfm outbreak isolates from Geneva University Hospitals.

Results: The VVEfm isolate exhibited vancomycin and teicoplanin minimum inhibitory concentrations (MICs) of 1.5 mg/L despite harboring the vanA resistance determinant. PAP showed a progressive reduction in viable counts with increasing vancomycin concentrations, although low-frequency surviving populations remained detectable at intermediate concentrations. This pattern did not demonstrate a clearly separated stable resistant subpopulation. Exposure to selective media containing vancomycin or teicoplanin induced spontaneous reversion to a resistant phenotype, with revertants displaying high-level resistance to vancomycin (MIC ≥ 256 mg/L) and teicoplanin (MIC 64 mg/L). The highest reversion frequency was observed on Brain Heart Infusion agar supplemented with 6 μg/mL vancomycin (9.5 ± 5.6 × 10^-8 ). Genomic analyses demonstrated that the VVEfm isolate, its revertant, and the five VREfm isolates belonged to sequence type ST80 and formed a closely related clonal lineage differing by a maximum of four cgMLST alleles. Structural genomic analysis suggested that resistance reversion was associated with chromosomal integration of a vanHAX -containing mobile element adjacent to an rRNA operon, potentially restoring constitutive resistance gene expression.

Conclusion: This study reports the first identification of VVEfm at Geneva University Hospitals and highlights the limitations of routine phenotypic screening methods for detecting VVE isolates. The rapid emergence of high-level glycopeptide resistance under selective pressure suggests that these isolates may act as silent reservoirs of antimicrobial resistance. Integration of molecular diagnostics with phenotypic testing and genomic surveillance is essential to improve detection, infection control, and antimicrobial stewardship strategies.