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Published on: December 23, 2022
Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium
Glen P Carter1,2, Andrew H Buultjens3,2, Susan A Ballard4
1Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia glen.carter@unimelb.edu.au.
Background:
Enterococcus faecium is a major nosocomial pathogen causing significant morbidity and mortality worldwide. Assessment of E. faecium using MLST to understand the spread of this organism is an important component of hospital infection control measures. Recent studies, however, suggest that MLST might be inadequate for E. faecium surveillance.
Objectives:
To use WGS to characterize recently identified vancomycin-resistant E. faecium (VREfm) isolates non-typeable by MLST that appear to be causing a multi-jurisdictional outbreak in Australia.
Methods:
Illumina NextSeq and Pacific Biosciences SMRT sequencing platforms were used to determine the genome sequences of 66 non-typeable E. faecium (NTEfm) isolates. Phylogenetic and bioinformatics analyses were subsequently performed using a number of in silico tools.
Results:
Sixty-six E. faecium isolates were identified by WGS from multiple health jurisdictions in Australia that could not be typed by MLST due to a missing pstS allele. SMRT sequencing and complete genome assembly revealed a large chromosomal rearrangement in representative strain DMG1500801, which likely facilitated the deletion of the pstS region. Phylogenomic analysis of this population suggests that deletion of pstS within E. faecium has arisen independently on at least three occasions. Importantly, the majority of these isolates displayed a vancomycin-resistant genotype.
Conclusions:
We have identified NTEfm isolates that appear to be causing a multi-jurisdictional outbreak in Australia. Identification of these isolates has important implications for MLST-based typing activities designed to monitor the spread of VREfm and provides further evidence supporting the use of WGS for hospital surveillance of E. faecium.
Insights
Whole genome sequencing identified novel vancomycin-resistant Enterococcus faecium strains non-typeable by MLST, highlighting limitations in current hospital surveillance methods for this major nosocomial pathogen.
Area of Science:
- Microbiology
- Genomics
- Infectious Diseases
Background:
- Enterococcus faecium is a significant cause of hospital-acquired infections globally.
- Multilocus sequence typing (MLST) is commonly used for E. faecium surveillance but may be insufficient.
- Recent findings suggest MLST inadequacy for accurate E. faecium epidemiological tracking.
Purpose of the Study:
- To employ whole genome sequencing (WGS) for characterizing vancomycin-resistant E. faecium (VREfm) isolates.
- To investigate VREfm isolates non-typeable by MLST causing a multi-jurisdictional outbreak in Australia.
Main Methods:
- Genome sequencing of 66 non-typeable E. faecium (NTEfm) isolates using Illumina NextSeq and Pacific Biosciences SMRT platforms.
- Phylogenetic and bioinformatics analyses were conducted using in silico tools.
- Complete genome assembly and identification of genetic features.
Main Results:
- WGS identified 66 NTEfm isolates from Australian health jurisdictions, untypeable by MLST due to a missing pstS allele.
- A large chromosomal rearrangement in a representative strain facilitated pstS deletion.
- Phylogenomic analysis indicated independent pstS deletion events on at least three occasions; most isolates were vancomycin-resistant.
Conclusions:
- Identified NTEfm isolates are implicated in a multi-jurisdictional Australian outbreak.
- Findings underscore the limitations of MLST for VREfm spread monitoring.
- Whole genome sequencing is crucial for effective hospital surveillance of E. faecium.
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