Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis

Abstract

In 2015, a marked increase in vancomycin-resistant Enterococcus faecium (VREfm) isolation was detected at the Royal Hobart Hospital, Australia. The primary objective of this work was to examine the dynamics of VREfm transmission using whole genome data mapped to public health surveillance information. Screening and clinical isolates of VREfm from patients were typed for the specific vancomycin-resistance locus present. Of total isolates collected from 2014-2016 (n = 222), 15.3% and 84.7% harboured either the vanA or the vanB vancomycin-resistance locus, respectively. Whole-genome sequencing of 80 isolates was performed in conjunction with single-nucleotide polymorphic (SNP) analysis and in silico multi-locus sequence typing (MLST). Among the isolates sequenced, 5 phylogenetic clades were identified. The largest vanB clade belonged to MLST sequence type ST796 and contained clinical isolates from VREfm infections that clustered closely with isolates from colonised patients. Correlation of VREfm genotypes with spatio-temporal patient movements detected potential points of transmission within the hospital. ST80 emerged as the major vanA sequence type for which the most likely index case of a patient cluster was ascertained from SNP analyses. This work has identified the dominant clones associated with increased VREfm prevalence in a healthcare setting, and their likely direction of transmission.

Figure 1

Number of newly identified vancomycin-resistant enterococcal (VRE) isolates (clinical and/or screening) in Tasmanian healthcare settings, 2008–2016. The number of new VRE isolates reported from Q1, 2008 to Q4, 2016 (columns). Since Q1, 2015, a marked increase in VRE isolates is indicated (red columns). The number of healthcare-associated Staphylococcus aureus bacteraemia cases (HA-SAB) is shown for comparison (black line).

Figure 2

Temporal distribution of vancomycin-resistant Enterococcus faecium (VREfm) isolates (n = 222) collected from patients at the Royal Hobart Hospital from 2014–2016. Each horizontal bar represents the period of time between patient hospital admission and VREfm sample collection. The selection criteria of VREfm isolates for whole-genome sequencing were based on the temporal overlap (vertical silver columns) of clinical isolates (red bars with*) (n = 16) with vanB screening VREfm isolates (blue bars). Also included in this study were VREfm isolates that tested positive for the vanA locus (green bars) (n = 34).

Figure 3

Phylogenetic analysis of vancomycin-resistant Enterococcus faecium (VREfm) isolates collected from patients at the Royal Hobart Hospital from 2014–2016 that underwent whole-genome sequencing (n = 80). A SNP-based maximum-likelihood (PhyML) phylogenetic tree was generated using E. faecium DO TX16 as the reference genome (NC017960) to root the tree. Branches of the phylogenetic tree revealed five major phylogenetic clades (PC). The whole genome data enabled in silico determination of multi-locus sequence types (MLST) and vancomycin resistance loci.

Figure 4

Spatio-temporal location of patients who tested positive for vancomycin-resistant Enterococcus faecium (VREfm) at the Royal Hobart Hospital. (a) Transmission of vanB ST796 VREfm from closely-related screening isolates belonging to Phylogenetic Clade 1 (PC1) to clinical patient 16C_RHH005. (b) Transmission of vanA ST80 VREfm among patients with isolates belonging to Phylogenetic Clade 2 (PC2). The movement of patients following admission to the Royal Hobart Hospital through to date of discharge are indicated with respect to time (x-axis) and hospital location (y-axis). The colour of each line represents each patient (dotted line – screening patient; solid line – clinical patient).

Figure 5

Vancomycin-resistant Enterococcus faecium (VREfm) transmission analysis based on single nucleotide polymorphism (SNP) genotypes of Phylogenetic Clade 1 (PC1). (a) Inferred VREfm transmission directions are represented by line connections between patients. Phylogenetic relationship is measured by differences in unique SNPs (numbers above connecting lines) and patristic distances between the isolates (numbers below connecting lines). (b) Correlation of SNP genotype data with epidemiological data revealed likely direction of transmission and potential points of transmission within the hospital. Potential points of transmission of PC1 vanB ST796 VREfm are indicated (pink areas). The Intensive Care Unit (ICU) was identified as the most likely location where transmission of VREfm occurred to patient 16C_RHH005 who presented with clinical symptoms of a urinary tract infection. Additional hospital units where patients from this cluster were located are indicated (yellow areas). Hospital ward abbreviations: ACW, acute cardiac ward; ED, emergency department; GMW, acute general medicine ward; ICU, intensive care unit; MAU, acute medical admissions unit; MSW, acute medical specialties ward; SSW, acute surgical specialties ward.

Figure 6

Vancomycin-resistant Enterococcus faecium (VREfm) transmission analysis based on single nucleotide polymorphism (SNP) genotypes of Phylogenetic Clade 2 (PC2). (a) Inferred VREfm transmission directions are represented by line connections between patients. Phylogenetic relationship is measured by differences in unique SNPs (numbers above connecting lines) and patristic distances between the isolates (numbers below connecting lines). (b) Correlation of SNP genotype data with epidemiological data revealed likely direction of transmission and potential points of transmission within the hospital. Potential points of transmission of PC2 vanA ST80 VREfm are indicated (pink areas). The acute medical admissions unit (MAU) and the acute general medicine ward (GMW) represented potential points where transmission of VREfm may have occurred from the index patient 16S_RHH014 in the direction of patient 16S_RHH003. Additional hospital units where patients from this cluster were located are indicated (yellow areas). Hospital ward abbreviations: ACW, acute cardiac ward; ED, emergency department; GMW, acute general medicine ward; ICU, intensive care unit; MAU, acute medical admissions unit; MSW, acute medical specialties ward; SSW, acute surgical specialties ward.