Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Genome-based characterization of hospital-adapted Enterococcus faecalis lineages

Nature Microbiology volume 1, Article number: 15033 (2016) Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Phylogeny of E. faecalis isolates drawn from across the UK and Ireland.
Figure 2: Global population structure of E. faecalis.
Figure 3: Prevalence of virulence and antibiotic resistance genes in the dominant lineages (L1–L3, n = 89) and remainder (n = 79).
Figure 4: Mapping variation in the vancomycin resistance transposon.

Similar content being viewed by others

References

  1. Sievert, D. M. et al. Antimicrobial-resistant pathogens associated with healthcare-associated infections: summary of data reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2009–2010. Infect. Control Hosp. Epidemiol. 34, 1–14 (2013).

    Article  Google Scholar 

  2. Suetens, C., Hopkins, S., Kolman, J. & Diaz Högberg, L. Point prevalence survey of healthcare-associated infections and antimicrobial use in the European acute care hospitals (ECDC, 2013).

  3. Uttley, A. H. C., Collins, C. H., Naidoo, J. & George, R. C. Vancomycin-resistant Enterococci. Lancet 2, 57–58 (1988).

    Article  Google Scholar 

  4. Ruiz-Garbajosa, P. et al. Multilocus sequence typing scheme for Enterococcus faecalis reveals hospital-adapted genetic complexes in a background of high rates of recombination. J. Clin. Microbiol. 44, 2220–2228 (2006).

    Article  Google Scholar 

  5. Freitas, A. R., Novais, C., Ruiz-Garbajosa, P., Coque, T. M. & Peixe, L. Clonal expansion within clonal complex 2 and spread of vancomycin-resistant plasmids among different genetic lineages of Enterococcus faecalis from Portugal. J. Antimicrob. Chemother. 63, 1104–1111 (2009).

    Article  Google Scholar 

  6. Kuch, A. et al. Insight into antimicrobial susceptibility and population structure of contemporary human Enterococcus faecalis isolates from Europe. J. Antimicrob. Chemother. 67, 551–558 (2012).

    Article  Google Scholar 

  7. Kawalec, M. et al. Clonal structure of Enterococcus faecalis isolated from Polish hospitals: characterization of epidemic clones. J. Clin. Microbiol. 45, 147–153 (2007).

    Article  Google Scholar 

  8. Paulsen, I. T. et al. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299, 2071–2074 (2003).

    Article  Google Scholar 

  9. Palmer, K. L. et al. Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. MBio 3, 1–11 (2012).

    Article  Google Scholar 

  10. Kim, E. B. & Marco, M. L. Nonclinical and clinical Enterococcus faecium strains, but not Enterococcus faecalis strains, have distinct structural and functional genomic features. Appl. Environ. Microbiol. 80, 154–165 (2014).

    Article  Google Scholar 

  11. Hsu, L.-Y. et al. Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system. Genome Biol. 16, 81 (2015).

    Article  Google Scholar 

  12. Donker, T., Wallinga, J., Slack, R. & Grundmann, H. Hospital networks and the dispersal of hospital-acquired pathogens by patient transfer. PLoS ONE 7, e35002 (2012).

    Article  Google Scholar 

  13. Coque, T. M., Tomayko, J. F., Ricke, S. C., Okhyusen, P. C. & Murray, B. E. Vancomycin-resistant enterococci from nosocomial, community, and animal sources in the United States. Antimicrob. Agents Chemother. 40, 2605–2609 (1996).

    Article  Google Scholar 

  14. Jordens, J. Z., Bates, J. & Griffiths, D. T. Faecal carriage and nosocomial spread of vancomycin-resistant Enterococcus faecium. J. Antimicrob. Chemother. 34, 515–528 (1994).

    Article  Google Scholar 

  15. Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).

    Article  Google Scholar 

  16. Palmer, K. L. et al. Enterococcal genomics, in Enterococci: From Commensals to Leading Causes of Drug Resistant Infection (eds Gilmore, M. S. et al.) (Massachusetts Eye and Ear Infirmary, 2014); http://www.ncbi.nlm.nih.gov/books/NBK190425/

    Google Scholar 

  17. Köser, C. U. et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N. Engl. J. Med. 366, 2267–2275 (2013).

    Article  Google Scholar 

  18. Harris, S. R. et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327, 469–474 (2010).

    Article  Google Scholar 

  19. Walker, T. M. et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect. Dis. 13, 137–146 (2013).

    Article  Google Scholar 

  20. Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691–3693 (2015).

    Article  CAS  Google Scholar 

  21. The Human Microbiome Jumpstart Reference Strains Consortium. A catalog of reference genomes from the human microbiome. Science 328, 994–999 (2010).

    Article  Google Scholar 

  22. Brinster, S., Furlan, S. & Serror, P. C-terminal WxL domain mediates cell wall binding in Enterococcus faecalis and other gram-positive bacteria. J. Bacteriol. 189, 1244–1253 (2007).

    Article  Google Scholar 

  23. Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 43, e15 (2014).

    Article  Google Scholar 

  24. Marttinen, P. et al. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res. 40, e6 (2012).

    Article  Google Scholar 

  25. Foucault, M., Depardieu, F., Courvalin, P. & Grillot-Courvalin, C. Inducible expression eliminates the fitness cost of vancomycin resistance in enterococci. Proc. Natl Acad. Sci. USA 107, 16964–16969 (2010).

    Article  Google Scholar 

  26. Andrews, J. M. Determination of minimum inhibitory concentrations. J. Antimicrob. Chemother. 48, 5–16 (2001).

    Article  Google Scholar 

  27. Zhou, Y., Liang, Y., Lynch, K. H., Dennis, J. J. & Wishart, D. S. PHAST: a fast phage search tool. Nucleic Acids Res. 39, W347–W352 (2011).

    Article  Google Scholar 

  28. Abbott, J. C., Aanensen, D. M., Rutherford, K., Butcher, S. & Spratt, B. G. WebACT—an online companion for the Artemis Comparison Tool. Bioinformatics 21, 3665–3666 (2005).

    Article  Google Scholar 

  29. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article  Google Scholar 

  30. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006).

    Article  Google Scholar 

  31. Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127–128 (2007).

    Article  Google Scholar 

  32. Jolley, K. A. & Maiden, M. C. J. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11, 595 (2010).

    Article  Google Scholar 

  33. Baele, G. et al. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol. 29, 2157–2167 (2012).

    Article  Google Scholar 

  34. Baele, G., Li, W. L. S., Drummond, A. J., Suchard, M. A. & Lemey, P. Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol. 30, 239–243 (2013).

    Article  Google Scholar 

  35. Depardieu, F., Perichon, B. & Courvalin, P. Detection of the van alphabet and identification of enterococci and staphylococci at the species level by multiplex PCR. J. Clin. Microbiol. 42, 5857–5860 (2004).

    Article  Google Scholar 

  36. Nallapareddy, S. R., Singh, K. V., Duh, R.-W., Weinstock, G. M. & Murray, B. E. Diversity of ace, a gene encoding a microbial surface component recognizing adhesive matrix molecules, from different strains of Enterococcus faecalis and evidence for production of ace during human infections. Infect. Immun. 68, 5210–5217 (2000).

    Article  Google Scholar 

  37. Shankar, V., Baghdayan, A. S., Huycke, M. M., Lindahl, G. & Gilmore, M. S. Infection-derived Enterococcus faecalis strains are enriched in esp, a gene encoding a novel surface protein. Infect. Immun. 67, 193–200 (1999).

    Google Scholar 

  38. Eaton, T. J. & Gasson, M. J. Molecular screening of Enterococcus virulence determinants and potential for genetic exchange between food and medical isolates. Appl. Environ. Microbiol. 67, 1628–1635 (2001).

    Article  Google Scholar 

  39. Vankerckhoven, V. et al. Development of a multiplex PCR for the detection of asa1, gelE, cylA, esp, and hyl genes in enterococci and survey for virulence determinants among European hospital isolates of Enterococcus faecium. J. Clin. Microbiol. 42, 4473–4479 (2004).

    Article  Google Scholar 

  40. Jurkovic, D. et al. Identification and characterization of enterococci from bryndza cheese. Lett. Appl. Microbiol. 42, 553–559 (2006).

    Google Scholar 

  41. Brinster, S. et al. Enterococcal leucine-rich repeat-containing protein involved in virulence and host inflammatory response. Infect. Immun. 75, 4463–4471 (2007).

    Article  Google Scholar 

  42. Nallapareddy, S. R., Wenxiang, H., Weinstock, G. M. & Murray, B. E. Molecular characterization of a widespread, pathogenic, and antibiotic resistance-receptive Enterococcus faecalis lineage and dissemination of its putative pathogenicity island. J. Bacteriol. 187, 5709–5718 (2005).

    Article  Google Scholar 

  43. La Carbona, S. et al. Comparative study of the physiological roles of three peroxidases (NADH peroxidase, alkyl hydroperoxide reductase and thiol peroxidase) in oxidative stress response, survival inside macrophages and virulence of Enterococcus faecalis. Mol. Microbiol. 66, 1148–1163 (2007).

    Article  Google Scholar 

  44. Theilacker, C. et al. Glycolipids are involved in biofilm accumulation and prolonged bacteraemia in Enterococcus faecalis. Mol. Microbiol. 71, 1055–1069 (2009).

    Article  Google Scholar 

  45. Kemp, K. D., Singh, K. V., Nallapareddy, S. R. & Murray, B. E. Relative contributions of Enterococcus faecalis OG1RF sortase-encoding genes, srtA and bps (srtC), to biofilm formation and a murine model of urinary tract infection. Infect. Immun. 75, 5399–5404 (2007).

    Article  Google Scholar 

  46. Le Jeune, A. et al. The extracytoplasmic function sigma factor SigV plays a key role in the original model of lysozyme resistance and virulence of Enterococcus faecalis. PLoS ONE 5, e9658 (2010).

    Article  Google Scholar 

  47. Teng, F., Singh, K. V., Bourgogne, A., Zeng, J. & Murray, B. E. Further characterization of the epa gene cluster and Epa polysaccharides of Enterococcus faecalis. Infect. Immun. 77, 3759–3767 (2009).

    Article  Google Scholar 

  48. Coburn, P. S., Baghdayan, A. S., Dolan, G. T. & Shankar, N. An AraC-type transcriptional regulator encoded on the Enterococcus faecalis pathogenicity island contributes to pathogenesis and intracellular macrophage survival. Infect. Immun. 76, 5668–5676 (2008).

    Article  Google Scholar 

  49. Dutka-Malen, S., Evers, S. & Courvalin, P. Detection of glycopeptide resistance genotypes and identification to the species level of clinically relevant enterococci by PCR. J. Clin. Microbiol. 33, 1434 (1995).

    Google Scholar 

  50. Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640–2644 (2012).

    Article  Google Scholar 

  51. Cattoir, V., Huynh, T. M., Bourdon, N., Auzou, M. & Leclercq, R. Trimethoprim resistance genes in vancomycin-resistant Enterococcus faecium clinical isolates from France. Int. J. Antimicrob. Agents 34, 390–392 (2009).

    Article  Google Scholar 

  52. Braga, T. M., Marujo, P. E., Pomba, C. & Lopes, M. F. S. Involvement, and dissemination, of the enterococcal small multidrug resistance transporter QacZ in resistance to quaternary ammonium compounds. J. Antimicrob. Chemother. 66, 283–286 (2011).

    Article  Google Scholar 

  53. Kado, C. I. & Liu, S.-T. Rapid procedure for detection and isolation of large and small plasmids. J. Bacteriol. 145, 1365–1373 (1981).

    Google Scholar 

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

  1. Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, CB2 0QQ, Cambridge, UK

    Kathy E. Raven, Sandra Reuter, Theodore Gouliouris, M. Estée Török & Sharon J. Peacock

  2. Clinical Microbiology and Public Health Laboratory, Public Health England, Box 236, Addenbrooke's Hospital, Hills Road, CB2 0QQ, Cambridge, UK

    Theodore Gouliouris, Nicholas M. Brown & M. Estée Török

  3. Cambridge University Hospitals NHS Foundation Trust, Hills Road, CB2 0QQ, Cambridge, UK

    Theodore Gouliouris, M. Estée Török & Sharon J. Peacock

  4. British Society for Antimicrobial Chemotherapy, Griffin House, 53 Regent Place, B1 3NJ, Birmingham, UK

    Rosy Reynolds & Nicholas M. Brown

  5. North Bristol NHS Trust, Southmead Hospital, BS10 5NB, Bristol, UK

    Rosy Reynolds

  6. Culture Collections, Public Health England, Porton Down, SP4 0JG, Salisbury, UK

    Julie E. Russell

  7. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, Cambridge, UK

    Julian Parkhill & Sharon J. Peacock

  8. London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK

    Sharon J. Peacock

Authors
  1. Kathy E. Raven
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sandra Reuter
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Theodore Gouliouris
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Rosy Reynolds
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Julie E. Russell
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Nicholas M. Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. M. Estée Török
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Julian Parkhill
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Sharon J. Peacock
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

S.J.P. designed the study. K.E.R. performed bacterial identification, susceptibility testing and DNA extraction, and analysed the data. S.R. assisted with bioinformatic analysis. T.G., R.R., J.E.R., N.M.B. and J.P. contributed materials and data. M.E.T. completed ethical approvals. J.P. and S.J.P. were responsible for supervision and management of the study.

Corresponding author

Correspondence to Kathy E. Raven.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1–5 and Tables 2–4. (PDF 1429 kb)

Supplementary Table 1

Isolate details. (XLSX 5080 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/nmicrobiol.2015.33

This article is cited by

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology