Long-term carriage and evolution of vancomycin-resistant Enterococcus faecium: a genomic study on consecutive isolates

Abstract

Abstract Objectives To determine if vancomycin-resistant Enterococcus faecium (VREfm) carriers carry the same VREfm clone after a minimum follow-up of 365 days. For those carrying the same clone, we investigated the genomic evolution per year per genome. Methods We used WGS results to assign VREfm clones to each isolate and determine clone shifts. Finally, we calculated distance in core-genome MLST alleles, and the number of SNPs between consecutive VREfm isolates from patients carrying the same VREfm clone. Results In total, 44.2% of patients carried the same VREfm clone, and the genomic evolution was 1.8 alleles and 2.6 SNPs per genome per year. Conclusions In our population of long-term carriers, we calculated a molecular clock of 2.6 SNPs.