The fifteen genes, for which no transcripts were detected,
were mainly located within efaB5 and phage04. A constraint of the comparative genomic analyses presented here, is that the comparison of gene content is based on a single reference strain only (V583). To compensate, we conducted a CC2 pangenome analysis with the draft genomes of CC2-strains HH22 and TX0104 to identify putative CC2-enriched non-V583 genes. selleck kinase inhibitor The pangenome analysis identified a total of 298 non-V583 ORFs in the HH22 and TX0104 (learn more Additional file 4). Among these ORFs, one gene cluster was identified as particularly interesting (Fisher’s exact; Additional file 4 and Figure 2). Notably, HMPREF0348_0426 in TX0104 represented the best BLAST hit for all the three ORFs HMPREF0364_1864 to -66 in HH22, suggesting discrepancy in annotation between the two strains. Sequencing across the gap between contig 00034 and contig 00035 in TX0104 confirmed that HMPREF0348_0427
and HMPREF0348_0428 represent the two respective ends of a gene homologous to HMPREF0346_1863 in HH22. (Additional file 5). The presence of the putative non-V583 CC2-enriched gene cluster among E. faecalis was further elucidated by PCR in our collection of strains (Additional file 3). Strains were screened for the presence of three individual genes (HMPREF0346_1861, HMPREF0346_1864 and HMPREF0346_1868) and the entire element, with primers hmpref0346_1868-F and hmpref0346_1861-R. Fisher’s exact testing (q < 0.01) GW572016 on the basis of the PCR data confirmed that the gene cluster was significantly enriched among CC2. Comparative sequence analysis of the flanking regions suggests check details that the gene cluster is located in the
HH22 and TX0104 versions of the E. faecalis pathogenicity island . Recently, a microarray-based assessment of PAI-content in a set of clinical E. faecalis isolates revealed high degree of variation within the island, and an evidently modular evolution of the PAI , which would be consistent with acquisition by an indel event of this locus in the PAI of TX0104, HH22 and other positive CC2-strains. Figure 2 Schematic representation of a putative non-V583 CC2-enriched gene cluster, as annotated in the Enterococcus faecalis HH22 and TX0104 draft genomes (GenBank accession numbers ACIX00000000 and ACGL00000000 , respectively). The EF-numbers of flanking genes indicate the insert site location compared to the E. faecalis V583 pathogenicity island. CC2-enriched surface-related structures Lepage et al.  have previously identified eight genes as potential markers for the V583/MMH594-lineage, of which all except one gene (EF2513) are found among the CC2-enriched genes in this study. Interestingly, several of these genes were later assigned to a recently classified family of surface proteins, with a C-terminal WxL domain, proposed to form multi-component complexes on the cell surface [39, 40]. Siezen et al.