Unnoticed spread of linear VanA-plasmids in vancomycin-variable <i>Enterococcus faecium</i> strains across different regions: a diagnostics challenge

BACKGROUND: Vancomycin-variable enterococci (VVE) are van-positive Enterococcus faecium strains with a vancomycin-susceptible phenotype that can revert to resistance upon exposure to vancomycin, posing an emerging diagnostic challenge. METHODS: We screened VVE within a large collection of E. faecium from hospitalised patients (n = 319) and healthy human volunteers (n = 60) during 2009-2022. VVE prevalence, antimicrobial resistance, plasmid replicases, virulence factors and bacteriocins were investigated using culture-based methods and WGS. vanA-carrying clusters and plasmids were analysed and compared with similar sequences available in GenBank. Reversion to a resistant phenotype was also evaluated. RESULTS: Seven VVE (2%) were identified, six from hospitalized patients (isolated in 2009 and 2011) and one from a healthy individual (2022). All isolates belonged to ST78 (5-CT230; 2-CT330) and carried a unique vanA-Tn1546 arrangement with truncated vanX, vanS, and transposase genes, located on large linear plasmids carrying a putative novel rep_pZY2 replicase from the Rep3 family. Such plasmids are spread across different countries representing a threat as drivers of silent van gene clusters. VVE reverted to a vancomycin-resistant phenotype after 48-72 hours (MIC > 32 mg/L) with high reversion rates (0.36-0.79); however, no underlying genetic mechanism could be identified to explain this shift. CONCLUSIONS: This study marks the first identification of VVE strains outside hospital settings, emphasizing the need for broader surveillance. The identification of unique Tn1546-type transposons on linear, broad-host-range plasmids in genetically related E. faecium strains from both hospital and community sources, alongside the detection of similar plasmids in international VVE strains, highlights the importance of routine van gene screening in phenotypically susceptible isolates to improve diagnostic accuracy, support antibiotic stewardship, and prevent future outbreaks.