Abstract
Clostridium difficile consists of six clades but studies on Clade 3 are limited. Here, we report genome sequences of three Clade 3 C. difficile strains carrying genes encoding toxin A and B and the binary toxin. Isolates 103 and 133 (both of ST5) and isolate 106 (ST285) were recovered from three ICU patients. Whole genome sequencing using HiSeq 2500 revealed 4.1-Mb genomes with 28–29% GC content. There were ≥1,104 SNP between the isolates, suggesting they were not of a single clone. The toxin A and B gene-carrying pathogenicity locus (PaLoc) of the three isolates were identical and had the insertion of the transposon Tn6218. The genetic components of PaLoc among Clade 3 strains were the same with only a few nucleotide mutations and deletions/insertions, suggesting that the Tn6218 insertion might have occurred before the divergence within Clade 3. The binary toxin-genes carrying CDT locus (CdtLoc) of the three isolates were identical and were highly similar to those of other Clade 3 strains, but were more divergent from those of other clades. In conclusion, Clade 3 has an unusual clade-specific PaLoc characteristic of a Tn6218 insertion which appears to be the main feature to distinguish Clade 3 from other C. difficile.
Highlights
Clostridium difficile, a Gram-positive spore-forming anaerobic bacterium, is the leading cause of antibiotic-associated diarrhea[1] and causes colitis which is not necessarily associated with antibiotic use[2,3]
The infection caused by strains of PCR ribotype 023 is associated with high levels of biomarkers such as white blood cell count and C-reactive protein, the 14-day mortality (7%) in C. difficile infection (CDI) cases caused by PCR ribotype 023 was lower than those (12–25%) caused by PCR ribotypes belonging to clade 1, 2, 4 and 510
Tn6218 is inserted between genes tcdE and tcdA, which results in a larger pathogenicity locus (PaLoc)[5] (28.6 kb; Fig. 1)
Summary
Clostridium difficile, a Gram-positive spore-forming anaerobic bacterium, is the leading cause of antibiotic-associated diarrhea[1] and causes colitis which is not necessarily associated with antibiotic use[2,3]. The main virulent factors of C. difficile are toxin A (enterotoxin, 308 kD) and toxin B (cytotoxin; 270 kD) encoded by genes tcdA and tcdB, respectively. These two genes together with three regulator genes tcdC (a negative regulator), tcdE (encoding a bacteriophage-like putative holin to facilitate the release of toxin A and B) and tcdR (encoding an alternative σfactor) are located on a pathogenicity locus called PaLoc (Fig. 1)[4]. Previous studies demonstrated that binary toxin gene-carrying isolates accounted for no more than 7% of all toxigenic C. difficile[14,19,20,21,22,23,24]. We report their genome sequence and antimicrobial susceptibilities below
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