Whole genome sequences of three Clade 3 Clostridium difficile strains carrying binary toxin genes in China

Sci Rep. 2017 Mar 6:7:43555. doi: 10.1038/srep43555.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Bacterial Proteins / genetics
  • Bacterial Toxins / genetics*
  • China / epidemiology
  • Clostridioides difficile / classification*
  • Clostridioides difficile / drug effects
  • Clostridioides difficile / genetics*
  • Clostridioides difficile / isolation & purification
  • Clostridium Infections / epidemiology*
  • Clostridium Infections / microbiology*
  • Drug Resistance, Bacterial
  • Gene Order
  • Genome, Bacterial*
  • Humans
  • Microbial Sensitivity Tests
  • Multilocus Sequence Typing
  • Phylogeny
  • Polymorphism, Single Nucleotide


  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Bacterial Toxins