Vancomycin-resistant Enterococcus faecium: a national wide genomic snapshot in Switzerland

Vancomycin-resistant Enterococcus faecium (VREfm) remains an antibiotic challenge to healthcare systems. In Switzerland, VREfm remains rare but appears to be on the rise. We aimed to conduct a national genomic study of VREfm, identify major circulating clones, and explore evidence of clonal dissemination using genomic epidemiology. All Swiss diagnostic laboratories were invited to submit VREfm isolates collected during February–March 2024 since strains with reduced susceptibility to daptomycin had been identified. Isolates underwent species confirmation, antimicrobial susceptibility testing, and whole genome sequencing. Sequence types (STs), core genome multilocus sequence typing (cgMLST), and resistance gene profiles were determined. Clusters were defined based on allele distances. We analysed 78 VREfm isolates from 17 cantons. Most carried the vanA gene (94%) and exhibited high-level resistance to vancomycin and teicoplanin; the remaining isolates carried vanB . Two clones dominated: ST80 ( n = 43) and ST612 ( n = 14), both within clonal complex 17. Eight cgMLST-defined clusters were identified. The ST80-Q cluster was confined to a single canton and linked to an outbreak. In contrast, ST612-C was found in 7 cantons, suggesting cryptic inter-cantonal dissemination. All ST612 isolates harboured mutations in liaR and liaS associated with reduced daptomycin susceptibility, although phenotypic resistance was not observed. This first nationwide genomic survey reveals the emergence and dissemination of dominant VREfm clones in Switzerland, particularly ST80 and ST612. The results highlight the need for national genomic surveillance and coordinated infection prevention strategies to detect and contain high-risk VREfm clones.