Open Access Highly Accessed Research article

Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes

Xiang Qin1, Jessica R Galloway-Peña345, Jouko Sillanpaa34, Jung Hyeob Roh34, Sreedhar R Nallapareddy34, Shahreen Chowdhury34, Agathe Bourgogne34, Tina Choudhury34, Donna M Muzny1, Christian J Buhay1, Yan Ding1, Shannon Dugan-Rocha1, Wen Liu1, Christie Kovar1, Erica Sodergren6, Sarah Highlander2, Joseph F Petrosino2, Kim C Worley1, Richard A Gibbs1, George M Weinstock6 and Barbara E Murray345*

Author Affiliations

1 Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza MSC-226, Houston, TX, USA

2 Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza MSC-226, Houston, TX, USA

3 Department of Medicine, Division of Infectious Disease, Houston, TX, USA

4 Center for the Study of Emerging and Reemerging Pathogens, Houston, TX, USA

5 Department of Microbiology and Molecular Genetics, University of Texas Medical School, 6431 Fannin Street, Houston, TX, 77030, USA

6 The Genome Institute, Washington University, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO, 63108, USA

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BMC Microbiology 2012, 12:135  doi:10.1186/1471-2180-12-135

Published: 7 July 2012

Abstract

Background

Enterococci are among the leading causes of hospital-acquired infections in the United States and Europe, with Enterococcus faecalis and Enterococcus faecium being the two most common species isolated from enterococcal infections. In the last decade, the proportion of enterococcal infections caused by E. faecium has steadily increased compared to other Enterococcus species. Although the underlying mechanism for the gradual replacement of E. faecalis by E. faecium in the hospital environment is not yet understood, many studies using genotyping and phylogenetic analysis have shown the emergence of a globally dispersed polyclonal subcluster of E. faecium strains in clinical environments. Systematic study of the molecular epidemiology and pathogenesis of E. faecium has been hindered by the lack of closed, complete E. faecium genomes that can be used as references.

Results

In this study, we report the complete genome sequence of the E. faecium strain TX16, also known as DO, which belongs to multilocus sequence type (ST) 18, and was the first E. faecium strain ever sequenced. Whole genome comparison of the TX16 genome with 21 E. faecium draft genomes confirmed that most clinical, outbreak, and hospital-associated (HA) strains (including STs 16, 17, 18, and 78), in addition to strains of non-hospital origin, group in the same clade (referred to as the HA clade) and are evolutionally considerably more closely related to each other by phylogenetic and gene content similarity analyses than to isolates in the community-associated (CA) clade with approximately a 3–4% average nucleotide sequence difference between the two clades at the core genome level. Our study also revealed that many genomic loci in the TX16 genome are unique to the HA clade. 380 ORFs in TX16 are HA-clade specific and antibiotic resistance genes are enriched in HA-clade strains. Mobile elements such as IS16 and transposons were also found almost exclusively in HA strains, as previously reported.

Conclusions

Our findings along with other studies show that HA clonal lineages harbor specific genetic elements as well as sequence differences in the core genome which may confer selection advantages over the more heterogeneous CA E. faecium isolates. Which of these differences are important for the success of specific E. faecium lineages in the hospital environment remain(s) to be determined.