Virulence signature of the endemic vancomycin-resistant Enterococcus faecium clones in Denmark, 2015-2023

Since 2012, Denmark has seen a significant rise in vancomycin-resistant Enterococcus faecium (VREfm) cases, mirroring trends in other countries, though exceptions occurred during the coronavirus disease 2019 (COVID-19) lockdown and between 2022 and 2023. This rise has been accompanied by ongoing changes in the endemic VREfm clones, reflecting the species' high genetic plasticity. VREfm rapidly acquires plasmids and mobile genetic elements, enriching it with putative virulence markers (PVMs), including surface proteins, pili, and factors encoding biofilm production and adhesion. L. Roer, H. Kaya, A.P. Tedim, C. Novias, et al. (Microbiol Spectr 12:e0372423, 2024, https://doi.org/10.1128/spectrum.03724-23) released a database of 27 PVMs for Enterococcus faecium and Enterococcus lactis. In this study, we examined 516 VREfm bloodstream isolates from 2015 to 2023, identifying eight new putative virulence genes added to the database, bringing the total to 35 PVMs. Using whole-genome sequencing (WGS) and single linkage clustering, we identified six dominant VREfm clusters: ST80-CT14 vanA, ST117-CT24 vanA, ST203-CT859 vanA, ST1421-CT1134 vanA, ST117-CT36 vanB, and ST80-CT2406 vanB. We observed significant differences in the distribution of PVMs, particularly in pilin, gene clusters (PGC-1, PGC-2, and PGC-4), genes involved in carbohydrate metabolism (e.g., orf1481, ccpA), and biofilm production (e.g., hylEfm, capD, lysM3). These differences could explain variability in pathogenicity, metabolism, and adaptation to stress, contributing to shifts in endemic clones.IMPORTANCEThe newly developed and now updated database, VirulenceFinder, features 35 potential virulence markers for E. faecium and E. lactis, is highly scalable and provides a valuable tool for the in-depth analysis of closely related species using whole-genome sequencing (WGS) data. It holds considerable promise for a range of public health applications, such as hospital outbreak investigations, surveillance, and assessment of pathogenicity of bacterial species.