WGS of E. faecium isolates

The npmA gene, encoding a 16S rRNA methyltransferase, confers resistance to all clinically available aminoglycosides, posing a significant threat to effective antibiotic therapy. Here, we investigated the distribution and mobilization mechanisms of npmA variants, npmA1 and npmA2, through an exhaustive analysis of 692,646 available bacterial genomes. We identified a worldwide dissemination of the npmA2 in Clostridioides difficile, predominantly carried by C. difficile ST11. We also detected npmA2 in two vancomycin-resistant Enterococcus faecium isolates from a Dutch hospital. Upon sequencing and phenotypic analysis, we determined that E. faecium isolates were pan-resistant to aminoglycosides. Genomic characterization linked npmA2 to a novel composite transposon Tn7734 which, in turn, is integrated within a previously uncharacterized Integrative and Conjugative Element (ICE) Tn7740, present in both npmA2-carrying C. difficile and E. faecium clinical isolates. These findings suggest the role of ICE Tn7740 in enabling cross-species gene mobilization between these gram-positive bacteria and emphasize the risk of mobile genetic elements transferring pan-aminoglycoside resistance between clinically important bacterial pathogens.