Open Access Highly Accessed Research article

Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island

Willem van Schaik1*, Janetta Top1, David R Riley2, Jos Boekhorst3, Joyce EP Vrijenhoek1, Claudia ME Schapendonk1, Antoni PA Hendrickx15, Isaäc J Nijman4, Marc JM Bonten1, Hervé Tettelin2 and Rob JL Willems1

Author Affiliations

1 Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands

2 Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, BioPark II Room 629, 801 West Baltimore Street, Baltimore, MD 21201, USA

3 Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands

4 Hubrecht Institute for Developmental Biology and Stem Cell Research, Cancer Genomics Center, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

5 Department of Microbiology, University of Chicago, Chicago, USA

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BMC Genomics 2010, 11:239  doi:10.1186/1471-2164-11-239

Published: 14 April 2010



The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients.


We present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A functional comparison between E. faecium and the related opportunistic pathogen E. faecalis based on differences in the presence of protein families, revealed divergence in plant carbohydrate metabolic pathways and oxidative stress defense mechanisms. The E. faecium pan-genome was estimated to be essentially unlimited in size, indicating that E. faecium can efficiently acquire and incorporate exogenous DNA in its gene pool. One of the most prominent sources of genomic diversity consists of bacteriophages that have integrated in the genome. The CRISPR-Cas system, which contributes to immunity against bacteriophage infection in prokaryotes, is not present in the sequenced strains. Three sequenced isolates carry the esp gene, which is involved in urinary tract infections and biofilm formation. The esp gene is located on a large pathogenicity island (PAI), which is between 64 and 104 kb in size. Conjugation experiments showed that the entire esp PAI can be transferred horizontally and inserts in a site-specific manner.


Genes involved in environmental persistence, colonization and virulence can easily be aquired by E. faecium. This will make the development of successful treatment strategies targeted against this organism a challenge for years to come.