title: Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes.
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.
authors: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
authors: Xiang
authors: X
authors: Qin
authors: Jessica R
authors: JR
authors: Galloway-Peña
authors: Jouko
authors: J
authors: Sillanpaa
authors: Jung Hyeob
authors: JH
authors: Roh
authors: Sreedhar R
authors: SR
authors: Nallapareddy
authors: Shahreen
authors: S
authors: Chowdhury
authors: Agathe
authors: A
authors: Bourgogne
authors: Tina
authors: T
authors: Choudhury
authors: Donna M
authors: DM
authors: Muzny
authors: Christian J
authors: CJ
authors: Buhay
authors: Yan
authors: Y
authors: Ding
authors: Shannon
authors: S
authors: Dugan-Rocha
authors: Wen
authors: W
authors: Liu
authors: Christie
authors: C
authors: Kovar
authors: Erica
authors: E
authors: Sodergren
authors: Sarah
authors: S
authors: Highlander
authors: Joseph F
authors: JF
authors: Petrosino
authors: Kim C
authors: KC
authors: Worley
authors: Richard A
authors: RA
authors: Gibbs
authors: George M
authors: GM
authors: Weinstock
authors: Barbara E
authors: BE
authors: Murray
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D016984:Enterococcus faecium / Q000235:genetics* / Q000302:isolation & purification; D016680:Genome, Bacterial; D006801:Humans; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial