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Draft Genome Sequence of a Clostridioides difficile Sequence Type 97 Strain Belonging to Hypervirulent Clade 2.

ABSTRACT: Clostridioides difficile hypervirulent clade 2 lineages are the major lineages responsible for the outbreaks in North America and Europe. However, the genome sequences of Japanese isolates are scarcely available. Herein, we report the draft genome sequence of C. difficile strain TMD0138 sequence type 97 (ST97), belonging to hypervirulent clade 2, isolated in Japan.

SUBMITTER: Usui Y

PROVIDER: S-EPMC7118186 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Draft Genome Sequence of a Clostridioides difficile Sequence Type 97 Strain Belonging to Hypervirulent Clade 2.

Usui Yukino Y Nukui Yoko Y Koike Ryuji R Tohda Shuji S Saito Ryoichi R

Microbiology resource announcements 20200402 14

<i>Clostridioides difficile</i> hypervirulent clade 2 lineages are the major lineages responsible for the outbreaks in North America and Europe. However, the genome sequences of Japanese isolates are scarcely available. Herein, we report the draft genome sequence of <i>C. difficile</i> strain TMD0138 sequence type 97 (ST97), belonging to hypervirulent clade 2, isolated in Japan. ...[more]

PMID: 32241860

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Project description:Abstract Background Clostridioides difficile is a leading cause of healthcare-associated infection (HAI), most often following antibiotic therapy. The source of these infections may be endogenous or nosocomial; effective intervention requires distinquishing between these, which in turn requires strain typing. Numerous methods have been developed for C. difficile typing, ranging from length-based ribotyping and MLVA to whole genome sequencing. However, none are routinely used in clinical settings due to low resolution, high cost, technical complexity, or requirement for cultured isolates. The application of polymorphic locus sequence typing (PLST) to epidemiological analysis of HAI and foodborne infections has recently been described; here this approach is extended to C. difficile. Methods Tandem repeats were bioinformatically identified in the genome sequence of ribotype 027 strain R20291. These were screened by BLASTN of GenBank databases for the most polymorphic locus, which identified CdMT1 (Mbp 3.149). DNA was purified from colonies or environmental (Banana Broth) cultures; bead-beating and PCR inhibitor removal steps were required for consistent results. Results CdMT1 encompassed MLVA repeat C6cd which, based on length alone, yielded the highest diversity index (DI) of 0.96. In contrast, CdMT1 sequence analysis yielded DI of >0.99. Comparison to ribotype further illustrated high level resolution; e.g., 9 ribotype 027 strains were resolved into 8 CdMT1 alleles. For initial laboratory evalulation, veterinary C. difficile isolates (44 canine, 4 bovine) were CdMT1 typed. Bioinformatic analysis of the 48 sequences resolved 24 CdMT1 alleles, including 8 clusters of 2 to 6 canine strains. Six of these clusters represented isolates from individual puppies in the same litter, or from different litters but the same household, while the bovine isolates formed a phylogenetically distinct group. Using the same DNA purification protocol, CdMT1 typing demonstrated compatibility with C. difficile-spiked stool samples and Banana Broth environmental cultures. Conclusion CdMT1 typing represents a potentially useful tool for outbreak detection and investigation in healthcare facilities, particularly in light of its compatibility with both stool and environmental samples. Disclosures Tom Edlind, PhD, MicrobiType LLC (Employee, Scientific Research Study Investigator)

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Draft Genome Sequence of a Clostridioides difficile Sequence Type 97 Strain Belonging to Hypervirulent Clade 2.

Publications

Draft Genome Sequence of a Clostridioides difficile Sequence Type 97 Strain Belonging to Hypervirulent Clade 2.

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