A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland

Abstract

Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001-2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree. This confirms that WGS is superior to MLST for evolutionary analyses and is more accurate than current typing methods used during outbreak investigations. E. faecium has been categorized as belonging to three clades (Clades A1, hospital-associated; A2, animal-associated; and B, community-associated). Phylogenetic analysis of our isolates replicated the distinction between Clade A (97% of isolates) and Clade B but did not support the subdivision of Clade A into Clade A1 and A2. Phylogeographic analyses revealed that Clade A had been introduced multiple times into each hospital referral network or country, indicating frequent movement of E. faecium between regions that rarely share hospital patients. Numerous genetic clusters contained highly related vanA-positive and -negative E. faecium, which implies that control of vancomycin-resistant enterococci (VRE) in hospitals also requires consideration of vancomycin-susceptible E. faecium Our findings reveal the evolution and dissemination of hospital-associated E. faecium in the UK&I and provide evidence for WGS as an instrument for infection control.

Figure 1.

Concordance between MLST and WGS data. (A, left) Tanglegram linking isolates in phylogenetic trees based on WGS and concatenated MLST loci. A different color is used to represent each ST present in more than one position in the WGS tree. Bars to the right show the STs indicated on the tree, the genetic basis for discrepancies between MLST and WGS (recombination = purple; point mutation = orange), and BAPS groups (BAPS 2-1 = purple, BAPS 2-3 = pink, BAPS 3-1 = green, BAPS 3-3 = yellow, unknown = white), with the positions on these bars relating to the position of the isolate on the WGS tree. (B) Recombination across the genome. Red indicates a recombination event found in more than one isolate; blue, a recombination event unique to that isolate. MLST genes and reference sequence are indicated at the top.

Figure 2.

Population structure of E. faecium. Maximum likelihood tree based on SNPs in the 1288 genes core to the 506 isolates from this study and 73 isolates reported by Lebreton et al. (2013). Pink branches indicate Clade A; blue branches, Clade B. Inner incomplete red ring denotes the clonal expansion of Clade A. Middle ring shows the isolate source (yellow, animal; purple, clinical; blue, nonhospital; black, hospital-associated feces/surveillance/outbreak/unknown; green, other; white, unknown). Outer ring shows isolates from Lebreton et al. (2013) colored by the clade to which they were originally assigned (pink, Clade A1; brown, Clade A2; blue, Clade B; black, hybrid Clade A1/B). Scale bar, 9593 SNPs.

Figure 3.

Geographic distribution of E. faecium lineages across the UK&I. (A) Maximum likelihood tree based on SNPs in the core genome for national isolates belonging to the clonal expansion of Clade A. Colors shown in the colored circle represent the referral network or country where the isolates were cultured. Scale bar, 90 SNPs. (B) Map of regions and referral networks described previously (Donker et al. 2012). Centers that submitted samples to the BSAC between 2001 and 2011 are represented by gray dots. Reproduced from Reuter et al. (2016).

Figure 4.

Vancomycin resistance in E. faecium from the UK&I. (A) Relationship between VREfm and VSEfm. Maximum likelihood tree of 477 study isolates belonging to the clonal expansion of Clade A. Colored circle denotes presence of vanA (yellow), vanB (purple), vanA and vanB (green), or none (vancomycin susceptible, white). Scale bar, 90 SNPs. (B) Acquisition of vancomycin resistance within hospitals. Maximum likelihood trees of two clusters labeled by year of isolation and colored by hospital: genes present (black) or absent (white) from the vanA transposon. Scale bar, 27 SNPs. (C) Locally prevalent transposons. Maximum likelihood tree of national isolates belonging to the clonal expansion of Clade A. Colored circles denote isolates carrying transposons overrepresented in Ireland (inner) or the East of England (outer) colored by referral network or country (green, Ireland; blue, East of England; brown, London; navy, Yorkshire; pink, West Midlands; red, North East). (Bottom) Genetic content of the vanA transposon for both transposon types. Scale bar, 90 SNPs.