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

Background: <i>Enterococcus faecium</i> is a major nosocomial pathogen causing significant morbidity and mortality worldwide. Assessment of <i>E. faecium</i> 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 <i>E. faecium</i> surveillance. Objectives: To use WGS to characterize recently identified vancomycin-resistant <i>E. faecium</i> (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 <i>E. faecium</i> (NTEfm) isolates. Phylogenetic and bioinformatics analyses were subsequently performed using a number of in silico tools. Results: Sixty-six <i>E. faecium</i> isolates were identified by WGS from multiple health jurisdictions in Australia that could not be typed by MLST due to a missing <i>pstS</i> allele. SMRT sequencing and complete genome assembly revealed a large chromosomal rearrangement in representative strain DMG1500801, which likely facilitated the deletion of the <i>pstS</i> region. Phylogenomic analysis of this population suggests that deletion of <i>pstS</i> within <i>E. faecium</i> 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 <i>E. faecium