Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium.

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.