First report of regional spreading and long-term inhabitation of VanD-type vancomycin-resistant Enterococcus faecalis clinical strains: A proposal of new classification of vanD gene subtypes.

OBJECTIVE

VanD-type vancomycin resistance is rarely reported in Enterococcus faecalis. This study aimed to characterise five VanD-type vancomycin-resistant E. faecalis strains isolated over 8 years from three hospitals in a local city in Japan, with a focus on resistance mechanisms, genetic background, and phylogenetic classification.

METHODS

Five E. faecalis strains (SVR2085, SVR2281, SVR2330, SVR2331, and SVR2332) were analysed using antimicrobial susceptibility testing, plasmid profiling, and whole-genome sequencing. Genomic islands (GIs) containing vanD gene clusters were characterised. Core GI gene and core genome phylogenies were compared, and vanD homologues were classified using public database sequences.

RESULTS

All strains exhibited high-level resistance to vancomycin (MIC >1024-64 mg/L), multiple drug resistance, and carried pheromone-responsive plasmids encoding bacteriocin 41 as a colonisation factor. Four strains shared nearly identical GIs (126-185 kbp), while SVR2330 had a structurally distinct GI. Phylogenetic analysis showed that the four similar strains formed a single cluster, suggesting a common ancestor, whereas SVR2330 was divergent. Comparative analysis of 37 vanD homologues revealed high genetic diversity, allowing classification into three subgroups - vanD(I), vanD(II), and vanD(III). The vanD of SVR2330 was assigned as vanD(III)-4, and the others as vanD(II)-6, -11, -15, and -17.

CONCLUSIONS

This study proposes a new classification scheme for diverse vanD genes and provides the first evidence of the regional spread and long-term persistence of VanD-type vancomycin-resistant E. faecalis in Japan.