title: Whole genome sequences of three Clade 3 Clostridium difficile strains carrying binary toxin genes in China.
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.
authors.affiliation: Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.|Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.affiliation: Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.|Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Feng
authors.affiliation: Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.|Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Wang
authors.affiliation: Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.|Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
authors.forename: Jingyu
authors.initials: J
authors.lastname: Yang
authors.affiliation: Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.|Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
authors.forename: Xiaoxia
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.|Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
authors.forename: Xiaoju
authors.initials: X
authors.lastname: Lü
authors.affiliation: Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.|Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.|Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Zong
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics; D001427:Bacterial Toxins / Q000235:genetics*; D002681:China / Q000453:epidemiology; D016360:Clostridioides difficile / Q000145:classification* / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D003015:Clostridium Infections / Q000453:epidemiology* / Q000382:microbiology*; D024881:Drug Resistance, Bacterial; D023061:Gene Order; D016680:Genome, Bacterial; D006801:Humans; D008826:Microbial Sensitivity Tests; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D001427:Bacterial Toxins