In contrast, the recently reported C. ulcerans 809 and C. pseudotuberculosis

FRC41 genomes possess a phage-related integrase (intC) and a nitric oxide reductase (nor) gene, respectively, instead of a BIBW2992 clinical trial prophage (Figure 2). Putative attachment sequences were similar between both prophages carrying the tox genes (Additional file 4). Figure 2 Schematic representation and comparative analysis of tox -positive prophages and flanking regions. The tox-positive prophage and flanking regions of C. ulcerans 0102 and C. diphtheriae NCTC13129 are shown. The corresponding region of C. BMS202 mouse pseudotuberculosis FRC41 and C. ulcerans 809 is also shown. Boxes indicate individual coding regions with colors assigned to their functions. GenBank accession numbers are given in parentheses The two tox-positive prophages share the same structural features, with genes aligned in an ‘integrase – packaging – head – tail – lysis – toxin’ orientation (Figure 2). Pair-wise alignment of the prophages indicates a high similarity in the region encoding the putative integrase, the 3′-ends of CULC0102_0211 and CULC0102_0212, tox, and

the attachment sites (Figure 2). The major phage machineries encoded in the internal phage region showed low similarity at the nucleotide and amino acid levels (less than 18%) between C. ulcerans 0102 and C. diphtheriae NCTC13129. Discussion Whole-genome sequencing has revealed that the C. ulcerans 0102 genome is composed of 2,579,188 bp with a G + C content of 53.4%. These values are similar to those recently reported for C. ulcerans strains 809 (2,502,095 bp, 53.3% G + C) and BR-AD22 (2,606,374 bp, 53.4% G + C) Rabusertib mw [24]. C. ulcerans 0102 shares many common features with the two previously reported strains, including 12 virulence factors. Strain 0102 is distinctive with respect to the features of prophages integrated in its genome. It possesses a unique tox-positive prophage, ΦCULC0102-I, in its chromosome (Figure 1 and Additional file 1). In the same position of the recently

reported C. ulcerans 809 genome exists a remnant phage-related integrase (intC) gene [24] (Figure 2). The C. ulcerans 0102 prophage differs from the corresponding prophage in C. diphtheriae. Although the integrase and tox gene sequences of ΦCULC0102-I showed high similarity to those of the corynephage encoding tox in C. diphtheriae NCTC 13129, the major phage machinery Lck genes in ΦCULC0102-I are distinct from those in other corynephages in C. diphtheriae (Figure 2). This suggests that C. ulcerans 0102 did not immediately acquire the C. diphtheriae tox-positive corynephage. There are many possible explanations for the origins of these two prophages that are tox-positive but obviously different. One of the simplest explanations we can postulate is outlined in Figure 3. Generally, bacterial prophages are duplicated by excision from chromosomal DNA and subsequent concatenation at both ends of the att sites (Figure 3A).