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Genome-based characterization of hospital-adapted Enterococcus faecalis lineages.

Accepted version
Peer-reviewed

Repository DOI


Type

Article

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Authors

Raven, Kathy E 
Reuter, Sandra 
Gouliouris, Theodore 
Reynolds, Rosy 
Russell, Julie E 

Abstract

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.

Description

Keywords

3107 Microbiology, 31 Biological Sciences, Emerging Infectious Diseases, Biodefense, Antimicrobial Resistance, Infectious Diseases, Genetics, Infection, Bacteremia, Cross Infection, Enterococcus faecalis, Genome, Bacterial, Genotype, Gram-Positive Bacterial Infections, Hospitals, Ireland, Molecular Epidemiology, Phylogeography, Sequence Analysis, DNA, United Kingdom, Vancomycin-Resistant Enterococci, Virulence Factors

Journal Title

Nat Microbiol

Conference Name

Journal ISSN

2058-5276
2058-5276

Volume Title

1

Publisher

Springer Science and Business Media LLC
Sponsorship
Academy of Medical Sciences (unknown)
Medical Research Council (MR/N029399/1)
Wellcome Trust (098600/Z/12/Z)
National Institute for Health and Care Research (HICF-T5-342)
We 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 Hayley Brodrick, Amy Cain, Derek Pickard, Kim Judge and Elizabeth Blane for their technical support. We thank the BSAC for allowing 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 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). MET is a Clinical Scientist Fellow supported by the Academy of Medical Sciences, the Health Foundation and the NIHR Cambridge Biomedical Research Centre.