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Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium Isolates with Full and Truncated vanA Operons from
Anna Slavokhotova1, Andrey Shelenkov1, Yulia Mikhaylova1
1Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia.
Abstract:
Background: Vancomycin-resistant Enterococcus faecium (VREfm), particularly vanA-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 E. faecium as a hospital pathogen. Methods: This study presents the whole genomic characterization of vanA-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. Results: 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 vanY and vanZ genes, representing a potentially emerging variant of the vanA operon in Russian clinical settings. A plasmid carrying a truncated vanA operon was reconstructed using long-read sequencing. Conclusions: 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.
Insights
Vancomycin-resistant Enterococcus faecium (VREfm) in Russian hospitals shows high genomic plasticity and resistance. Genomic surveillance is crucial for tracking VREfm spread and understanding antimicrobial resistance evolution.
Area of Science:
- Microbiology
- Genomics
- Epidemiology
Background:
- Vancomycin-resistant Enterococcus faecium (VREfm) is a significant global hospital threat, especially vanA-positive strains.
- E. faecium's success as a pathogen is linked to its environmental resilience, genome plasticity, and antimicrobial resistance acquisition.
- Understanding VREfm epidemiology in Russia is critical due to its increasing prevalence.
Purpose of the Study:
- To perform whole-genome characterization of vanA-positive VREfm clinical isolates from Moscow hospitals.
- To analyze the genetic relatedness, antimicrobial resistance profiles, virulence factors, and plasmid content of these isolates.
- To provide baseline genomic data for VREfm epidemiological surveillance in Russia.
Main Methods:
- Whole genome sequencing (WGS) of 10 clinical VREfm isolates.
- Multilocus Sequence Typing (MLST) and core genome MLST (cgMLST) for phylogenetic analysis.
- Phenotypic and genomic antimicrobial resistance profiling, virulence factor analysis, and plasmid content determination.
Main Results:
- All isolates belonged to the CC17 lineage (ST80 and ST552).
- Two isolates harbored truncated Tn1546 transposons, indicating a potential emerging vanA operon variant.
- Long-read sequencing enabled reconstruction of a plasmid carrying a truncated vanA operon.
Conclusions:
- Genomic investigation is vital for tracking VREfm resistance mechanisms and dissemination.
- The study provides essential baseline data for VREfm surveillance in Russia.
- Continuous genomic monitoring is necessary to understand antimicrobial resistance evolution in enterococci.
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