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Work Package 1

A genomic perspective on evolution and niche-adaptation of Enterococcus faecium

In the last two decades Enterococcus faecium has emerged as an important nosocomial pathogen that is difficult to treat due to resistance to multiple antibiotics, including ampicillin, aminoglycosides, and vancomycin1. Genome sequence-based studies of E. faecium have almost exclusively focused on strains that have caused hospital-acquired infection2 3 4. Recently, we showed the existence of two distinct populations of E. faecium, distinguishing hospital-adapted isolates from commensal strains, as well as the existence of hybrids between them, and made this data publicly available5. Others built on this data with sequence from additional strains to make similar observations6. This work, which mainly sampled hospital-adapted and a few human commensal strains, showed that there was tremendous diversity within the E. faecium species even within this limited set. It was therefore of interest to conduct a more systematic examination of the genomes that represent the diversity of the E. faecium species, where most strains harmlessly colonize the gastrointestinal tract of animals1. In this project, 51 E. faecium strains isolated from a variety of niches, hosts and countries between the 1950s and 2010, and shown to represent the broad diversity of Multi Locus Sequence Types (MLST), are being examined at the level of genome sequence. The central aim of this research is to determine the relatedness and infer evolutionary patterns related to host adaptation and the emergence of antibiotic resistance. These analyses will be correlated with meta-information collected with those strains, leading to the identification of genes and genetic elements that have played a role in the adaptation of E. faecium to different environments.

Among the 51 E. faecium strains, 44 isolates from different ecological niches (environment, animal and human, both hospitalized and non-hospitalized) have been collected from different continents, representing 35 STs covering the breadth of the MLST landscape. In addition, seven strains representative of the E. faecium ST78, which is currently circulating in Europe and Asia, where it recently emerged as a leading cause of hospital-acquired E. faecium infections7, are being examined.

Work plan

Divergence among the isolates will be examined using a SNP-based phylogenomic tree based on the E. faecium core genome. Diversity will also be quantified by pan-genome analysis to estimate the capability of E. faecium to incorporate genetic material in its genome3. In addition, gene content will be investigated to determine orthologous genes that are enriched in E. faecium strains isolated from different ecological niches. Besides gene content, the variable presence of metabolic pathways in E. faecium will be characterized and correlated with adaptations of enterococci to various niches. The diversity of mobile genetic elements, especially the pathogenicity island that carries the esp gene8, but also plasmids, bacteriophages and others genomic islands, will be examined in each of the 51 E. faecium genomes. In addition, as recently described in E. faecalis9, the role of CRISPR elements in E. faecium as well as their distribution on the phylogenetic tree will be of interest. Finally, to identify genes that are under selection during niche adaptation of E. faecium, the areas of rapid genetic drift will be examined by determining the ratio of the rate of non-synonymous substitutions to the rate of synonymous substitutions.


  1. Willems, R. J., and W. van Schaik. 2009. Transition of Enterococcus faecium from commensal organism to nosocomial pathogen. Future Microbiol 4:1125-1135. 

  2. van Schaik, W., and R. J. L. Willems. 2010. Genome-based insights into the evolution of enterococci. Clin. Microbiol. Infect 16:527-532. 

  3. van Schaik, W., J. Top, D. Riley, J. Boekhorst, J. Vrijenhoek, C. Schapendonk, A. Hendrickx, I. Nijman, M. Bonten, H. Tettelin, and R. Willems. 2010. Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island. BMC Genomics 11:239. 

  4. Qin X, Galloway-Pena JR, Sillanpaa J, Hyeob Roh J, Nallapareddy SR, Chowdhury S, Bourgogne A, Choudhury T, Munzy DM, Buhay CJ, Ding Y, Dugan-Rocha S, Liu W, Kovar C, Sodergren E, Highlander S, Petrosino JF, Worley KC, Gibbs RA, Weinstock GM, Murray BE. Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. BMC Microbiol. 2012 Jul 7;12(1):135. 

  5. Palmer KL, Godfrey P, Griggs A, Kos VN, Zucker J, Desjardins C, Cerqueira G, Gevers D, Walker S, Wortman J, Feldgarden M, Haas B, Birren B, Gilmore MS. Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. MBio. 2012 Mar 1;3(1):e00318-11. 

  6. Galloway-Peña J, Roh JH, Latorre M, Qin X, Murray BE. Genomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium. PLoS One. 2012;7(1):e30187. 

  7. Willems, R. J. L., J. Top, M. van Santen, D. A. Robinson, T. M. Coque, F. Baquero, H. Grundmann, and M. J. M. Bonten. 2005. Global spread of vancomycin-resistant Enterococcus faecium from distinct nosocomial genetic complex. Emerging Infect. Dis 11:821-828. 

  8. Leavis, H., J. Top, N. Shankar, K. Borgen, M. Bonten, J. van Embden, and R. J. L. Willems. 2004. A novel putative enterococcal pathogenicity island linked to the esp virulence gene of Enterococcus faecium and associated with epidemicity. J. Bacteriol 186:672-682. 

  9. Palmer KL, Gilmore MS. Multidrug-resistant enterococci lack CRISPR-cas. MBio. 2010 Oct 12;1(4). pii: e00227-10. 

Bermuda principles and public data release

Our goal is to make the genome sequence of organisms rapidly and broadly available to the scientific community. The genome sequencing community recently adopted a statement of principles for the distribution and acceptable uses of large-scale sequencing data. It is our intention to publish the work of this project in a timely fashion, and we welcome collaborative interaction on the project and analyses.


Please cite all data relating to this initiative (including individual genes and genomes) as:
"Enterococcus II initiative, Broad Institute ("