Genome-Based Analysis of Enterococcus faecium Bacteremia Associated with Recurrent and Mixed-Strain Infection

Abstract

Vancomycin-resistant Enterococcus faecium (VREfm) bloodstream infections are associated with high recurrence rates. This study used genome sequencing to accurately distinguish the frequency of relapse and reinfection in patients with recurrent E. faecium bacteremia and to investigate strain relatedness in patients with apparent VREfm and vancomycin-susceptible E. faecium (VSEfm) mixed infection. A retrospective study was performed at the Cambridge University Hospitals NHS Foundation Trust (CUH) between November 2006 and December 2012. We analyzed the genomes of 44 E. faecium isolates from 21 patients (26 VREfm isolates from 12 patients with recurrent bacteremia and 18 isolates from 9 patients with putative VREfm/VSEfm mixed infection). Phenotypic antibiotic susceptibility was determined using a Vitek2 instrument. Genomes were compared with those of a further 263 E. faecium isolates associated with bacteremia in patients at CUH over the same time period. Pairwise comparison of core genomes indicated that 10 (71%) episodes of recurrent VREfm bacteremia were due to reinfection with a new strain, with reinfection being more likely with increasing time between the two positive cultures. The majority (78%) of patients with a mixed VREfm and VSEfm infection had unrelated strains. More than half (59%) of study isolates were closely related to another isolate associated with bacteremia from CUH. This included 60% of isolates associated with reinfection, indicating acquisition in the hospital. This study provides the first high-resolution insights into recurrence and mixed infection by E. faecium and demonstrates that reinfection with a new strain, often acquired from the hospital, is a driver of recurrence.

Keywords: VRE; mixed infection; recurrence.

FIG 1

Genetic relatedness of isolates from the same patient with recurrent bacteremia or with mixed infection with VREfm and VSEfm. (A) The right-hand graph shows the pairwise core genome SNP difference between E. faecium isolates cultured from the same patient with recurrent bacteremia more than 30 days apart and the timing of the episodes. Red indicates isolate pairs that were closely related (1 to 7 SNPs) based on genome sequence data. The left-hand graph represents an expansion of the boxed area (under 100 SNPs) of the graph on the right. (B) Graph showing the pairwise core genome SNP difference between VREfm and VSEfm isolates cultured from the same patient with mixed infection within 48 h.

FIG 2

Comparison of strain similarities based on genome sequence data and antibiograms. Two patients with both relapse and reinfection occur twice in the list. Changes in antibiotic resistance between isolates from the same patient are shown (red, change from susceptible to resistant; green, change from resistant to susceptible; white, no change).