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Pipeline publication

[…] is and to further understand the evolution and molecular epidemiology of E. faecium infective strains., The E. faecium TX16 genome consists of one chromosome and three plasmids. The chromosome (Figure ) 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 ). The chromosome has a GC content of 38.15%, and it shows a clear GC skew at the origin of replication (Figure ). 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 )., 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 []. 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 [,]) and all ORF synteny blocks were relatively short (Additional file : 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 : Figure S2). The two isolates had very similar synteny, although two regions found in TX16 were inverted in Aus0004. Two site-specific tyrosine family recombinases (EFAU004_01466 and EFAU004_02416) were found flanking these two inversions (Additional file : Figure S2)., The genome size of the E. faecium strains vary substantially from 2.50 Mb (E1039) to 3.14 Mb (1,230,933), while the number of ORFs varies from 2,587 (E1039) to 3,118 (TX0133A). Ortholog analysis of TX16 compared to TX1330 and all the availa […]

Pipeline specifications

Software tools BLASTP, DAGchainer, Mauve
Organisms Enterococcus faecium, Enterococcus faecalis
Diseases Infection, Sprains and Strains