Abstract
BackgroundBacterial whole-genome sequencing (WGS) has the potential to identify reservoirs of multidrug-resistant organisms and transmission of these pathogens across healthcare networks. We used WGS to define transmission of vancomycin-resistant enterococci (VRE) within a long-term care facility (LTCF), and between this and an acute hospital in the United Kingdom (UK).MethodsA longitudinal prospective observational study of faecal VRE carriage was conducted in a LTCF in Cambridge, UK. Stool samples were collected at recruitment, and then repeatedly until the end of the study period, discharge or death. Selective culture media were used to isolate VRE, which were subsequently sequenced and analysed. We also analysed the genomes of 45 Enterococcus faecium bloodstream isolates collected at Cambridge University Hospitals NHS Foundation Trust (CUH).ResultsForty-five residents were recruited during a 6-month period in 2014, and 693 stools were collected at a frequency of at least 1 week apart. Fifty-one stool samples from 3/45 participants (7 %) were positive for vancomycin-resistant E. faecium. Two residents carried multiple VRE lineages, and one carried a single VRE lineage. Genome analyses based on single nucleotide polymorphisms (SNPs) in the core genome indicated that VRE carried by each of the three residents were unrelated. Participants had extensive contact with the local healthcare network. We found that VRE genomes from LTCF residents and hospital-associated bloodstream infection were interspersed throughout the phylogenetic tree, with several instances of closely related VRE strains from the two settings.ConclusionsA proportion of LTCF residents are long-term carriers of VRE. Evidence for genetic relatedness between these and VRE associated with bloodstream infection in a nearby acute NHS Trust indicate a shared bacterial population.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0259-7) contains supplementary material, which is available to authorized users.
Highlights
Bacterial whole-genome sequencing (WGS) has the potential to identify reservoirs of multidrugresistant organisms and transmission of these pathogens across healthcare networks
The aim of this study was to define vancomycin-resistant enterococci (VRE) carriage by residents of a long-term care facility (LTCF) over a 6-month period, and to use WGS to describe the genetic relatedness of isolates within and between residents, document whether VRE was transmitted in the LTCF over time, and compare these data with the genomes of bloodstream isolates in patients in the nearby acute hospital
We focused on carriage and transmission of VRE, a nosocomial pathogen that has remained a persistent problem despite the raft of infection control measures introduced into United Kingdom (UK) hospitals to reduce the prevalence of methicillinresistant Staphylococcus aureus (MRSA) and C. difficile
Summary
Bacterial whole-genome sequencing (WGS) has the potential to identify reservoirs of multidrugresistant organisms and transmission of these pathogens across healthcare networks. We used WGS to define transmission of vancomycin-resistant enterococci (VRE) within a long-term care facility (LTCF), and between this and an acute hospital in the United Kingdom (UK). Individuals in long-term care facilities (LTCF) frequently move through healthcare networks and are potential reservoirs for VRE [6, 7]. Pathogen transmission between people in long-term residential and acute care facilities is likely to be common [8], but investigation is hampered by the low resolution of current typing methods, which cannot distinguish between isolates belonging to the same clone [9, 10]. The aim of this study was to define VRE carriage by residents of a LTCF over a 6-month period, and to use WGS to describe the genetic relatedness of isolates within and between residents, document whether VRE was transmitted in the LTCF over time, and compare these data with the genomes of bloodstream isolates in patients in the nearby acute hospital
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