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

TitleComplete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes.
Publication TypeJournal Article
Year of Publication2012
AuthorsQin, X, Galloway-Peña, JR, Sillanpaa, J, Roh, JHyeob, Nallapareddy, SR, Chowdhury, S, Bourgogne, A, Choudhury, T, Muzny, 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
JournalBMC Microbiol
Date Published2012 Jul 07
KeywordsDNA, Bacterial, Enterococcus faecium, Genome, Bacterial, Humans, Molecular Sequence Data, Sequence Analysis, DNA

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.

Alternate JournalBMC Microbiol
PubMed ID22769602
PubMed Central IDPMC3433357
Grant ListR01 AI067861 / AI / NIAID NIH HHS / United States
F31 AI092891 / AI / NIAID NIH HHS / United States
T32 AI55449 / AI / NIAID NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
R01 AI42399 / AI / NIAID NIH HHS / United States
1U54HG004973-0 / HG / NHGRI NIH HHS / United States
T32 AI055449 / AI / NIAID NIH HHS / United States

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