Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium Isolates with Full and Truncated vanA Operons from Russian Hospitals

<b>Background</b>: Vancomycin-resistant <i>Enterococcus faecium</i> (VREfm), particularly <i>vanA</i>-positive strains, represents a growing threat in hospital settings worldwide. These bacteria are able to survive under severe environmental conditions, including high temperatures and saline concentrations. High genome plasticity and advanced ability of inheriting antimicrobial resistance determinants defined the success of <i>E. faecium</i> as a hospital pathogen. <b>Methods</b>: This study presents the whole genomic characterization of <i>vanA</i>-positive VREfm isolates, analyzing 10 clinical isolates collected from three tertiary care hospitals in Moscow, Russia. Several typing approaches, including two MLST schemes and cgMLST profiles, were used to elucidate the relationship between the isolates. Phylogenetic analysis placed the isolates in context with global VREfm populations, demonstrating both local clonal expansion and possible international connections. Phenotypic and genomic antimicrobial resistance profiles were obtained, as well as data regarding the repertoire of virulence factors and plasmid content. <b>Results</b>: Whole genome sequencing revealed that all isolates belonged to the clinically significant CC17 lineage, specifically sequence types ST80 and ST552. Notably, two isolates possessed truncated Tn1546-type transposons lacking <i>vanY</i> and <i>vanZ</i> genes, representing a potentially emerging variant of the <i>vanA</i> operon in Russian clinical settings. A plasmid carrying a truncated <i>vanA</i> operon was reconstructed using long-read sequencing. <b>Conclusions</b>: The study highlights the utility of genomic investigation for tracking resistance mechanisms and strain dissemination, providing crucial baseline data for epidemiological surveillance of infections caused by VREfm in Russia. These findings emphasize the need for continued genomic monitoring to understand the evolution and spread of antimicrobial resistance in clinically important enterococcal lineages.