Vancomycin-resistant Enterococcus faecalis (VREfs) is an important nosocomial pathogen1,2. We undertook whole genome sequencing of E. faecalis associated with bloodstream infection in the UK and Ireland over more than a decade to determine the population structure and genetic associations with hospital adaptation. Three lineages predominated in the population, two of which (L1 and L2) were nationally distributed, and one (L3) geographically restricted. Genome comparison with a global collection identified that L1 and L3 were also present in the USA, but were genetically distinct. Over 90% of VREfs belonged to L1–L3, with resistance acquired and lost multiple times in L1 and L2, but only once followed by clonal expansion in L3. Putative virulence and antibiotic resistance genes were over-represented in L1, L2 and L3 isolates combined, versus the remainder. Each of the three main lineages contained a mixture of vancomycin-resistant and -susceptible E. faecalis (VSEfs), which has important implications for infection control and antibiotic stewardship.
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The authors thank the Wellcome Trust Sanger Institute library construction, sequence and core informatics teams, the staff at BSAC and the Cambridge Public Health England Microbiology and Public Health Laboratory, and H. Brodrick, A. Cain, D. Pickard, K. Judge and E. Blane for their technical support. The authors acknowledge BSAC for allowing the use of isolates from the BSAC Resistance Surveillance Project. This publication presents independent research supported by the Health Innovation Challenge Fund (HICF-T5-342 and WT098600), a parallel funding partnership between the UK Department of Health and the Wellcome Trust. The views expressed in this publication are those of the authors and not necessarily those of the Department of Health or the Wellcome Trust. This project was also funded by a grant awarded to the Wellcome Trust Sanger Institute (098051). M.E.T. is a Clinical Scientist Fellow supported by the Academy of Medical Sciences, the Health Foundation and the NIHR Cambridge Biomedical Research Centre.
The authors declare no competing financial interests.
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Raven, K., Reuter, S., Gouliouris, T. et al. Genome-based characterization of hospital-adapted Enterococcus faecalis lineages. Nat Microbiol 1, 15033 (2016). https://doi.org/10.1038/nmicrobiol.2015.33
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