Using genomics to investigate the epidemiology of Vancomycin-resistant Enterococcus faecium ST78 at a primary care hospital in Queensland

Abstract
Objective: To investigate an outbreak of vancomycin-resistant Enterococcus faecium (VREfm) sequence type 78 (ST78) in a large tertiary Australian hospital.

Methods: A collection of 63 VREfm ST78 isolates, identified during a routine genomic surveillance program, were subjected to genomic epidemiological analysis based on whole genome sequencing (WGS) data. The population structure was reconstructed using phylogenetic analysis and a collection of publicly available VREfm ST78 genomes were used to provide global context. Core genome SNP distances and available clinical metadata were used to characterize outbreak clusters and reconstruct transmission events.

Results: In silico genotyping confirmed all study isolates were vanB-type VREfm carrying virulence characteristics of the hospital-associated E. faecium. Phylogenetic analysis identified two distinct phylogenetic clades, only one of which was responsible for a hospital outbreak. Four outbreak subtypes could be defined with examples of recent transmissions. Inference on transmission trees suggested complex transmission routes with unknown environmental reservoirs mediating the outbreak. WGS-based cluster analysis with publicly available genomes identified closely related Australian ST78 and ST203 isolates, highlighting the capacity for WGS to resolve complex clonal relationships between the VREfm lineages.

Conclusions: Whole-genome based analysis has provided a high-resolution description of an outbreak of vanB-type VREfm ST78 in a Queensland hospital. Combined routine genomic surveillance and epidemiological analysis have facilitated better understanding of the local epidemiology of this endemic strain, providing valuable insight for better targeted control of VREfm.

Poster: