Recently, while this manuscript JQ1 cell line was in review, a closed E. faecium GSK2245840 in vivo genome was published by Lam et al. using the ST17 isolate Aus0004, which was isolated from the bloodstream of a patient in Melbourne, Australia [37]. In this study, we report the closed genome of the US E. faecium endocarditis isolate TX16 (DO), and a comparative analysis of this strain’s genome with 21 other available E. faecium draft genomes [32, 38], as well as the recently published

Aus0004 [37]. Due to the fact the TX16 genome has been used in multiple pathogenesis studies and is a part of the clonal group representing the majority of clinical strains globally [2, 5, 30, 36], the complete genome sequence of E. faecium TX16 will facilitate future research by providing a critical starting point for genome-wide functional studies to determine the molecular basis of pathogenesis and to find more further understand the evolution and molecular epidemiology of E. faecium infective strains. Results E. faecium TX16 general genome features The E. faecium TX16 genome consists of one chromosome and three plasmids. The chromosome (Figure 1) contains 2,698,137 bp with 2,703 protein-coding ORFs,

62 tRNAs, 6 copies of ribosomal rRNA and 32 other non-coding RNAs (Table 1). The chromosome has a GC content of 38.15%, and it shows a clear GC skew at the origin of replication (Figure 1). The sizes of the three plasmids (pDO1, pDO2, and pDO3) are 36,262, 66,247 and 251,926 bp, encoding 43, 85, and 283 ORFs, respectively (Table 1). Figure 1 Circular map of the E. faecium TX16 genome. Tracks from inside to outside

are as follows: GC skew (G-C)/(G + C), GC Dichloromethane dehalogenase content, forward and reverse RNA, reverse genes, and forward genes. Table 1 General features of E. faecium TX16 genome Features Chromosome Plasmid pDO1 Plasmid pDO2 Plasmid pDO3 Size (bp) 2698137 36262 66247 251926 G + C % 38.15 36.51 34.38 35.97 ORFs 2703 43 85 283 rRNA operons 6 0 0 0 tRNAs 62 0 2 0 ncRNAs 32 1 0 0 To investigate the conservation of the gene order of E. faecium compared to its close relative E. faecalis, a BLASTP alignment of all the predicted proteins from the TX16 and V583 genomes was performed followed by ORF synteny analysis using DAGchainer [39]. The result showed that E. faecium TX16 gene order is very different from that of E. faecalis strain V583 (and therefore OG1RF, which has a very similar synteny to V583 [40, 41]) and all ORF synteny blocks were relatively short (Additional file 1: Figure S1). Interestingly, when comparing TX16 to the closed genome Aus0004, which was published while this paper was in review, Mauve genome alignment analysis resulted in 5 locally collinear blocks for both TX16 and Aus0004 ranging from 33,563–836,291 bp for TX16 and 32,326–905,025 bp for Aus0004 (Additional file 2: Figure S2). The two isolates had very similar synteny, although two regions found in TX16 were inverted in Aus0004.