A Daptomycin Resistance-Conferring cls1 I269T Mutation in Enterococcus faecium and its Global Prevalence.

Daptomycin is widely considered as a ‘last-resort’ antibiotic used for the treatment of antibiotic-resistant Gram-positive bacteria, including vancomycin-resistant Enterococcus. Resistance to this antibiotic can lead to severe consequences, including inability to find a cure for Gram positive infections. Our previous investigations showed that a mutated cls1 gene mediated low-level daptomycin resistance in Enterococcus faecium strain EF332, distinguishing it from previous reports that only linked cls2 mutations to daptomycin resistance. In this study, through additional genetic and microbiological assays, we confirmed that this effect is specifically attributed to the I269T mutation in cls1 gene, and further identified that this mutation endows E. faecium with a heteroresistant phenotype. The prevalence of cls1 I269T mutation was further investigated by downloading and investigating all 17,388 E. faecium genomes from Genbank. This heteroresistance-associated mutation was detected in 71.97% of all genomes carrying cls1, suggesting the wide presence of this mutation. Further sequence type (ST) analysis showed that the I269T mutation was selectively enriched in 12 STs that are part of the hospital-associated CC17 lineage, implicating that the heteroresistant phenotype mediated by this mutation may facilitate bacterial adaptation in clinical settings. Geographical location analysis suggested that the I269T mutation was found in 42 countries around the world. This study identifies a globally prevalent I269T mutation in cls1 that confers low-level daptomycin resistance via a heteroresistant phenotype, and suggests this mutation contributes to the global prevalence of daptomycin resistance in E. faecium.