Dataset Information

Application of a core genome sequence typing (cgMLST) pipeline for surveillance of Clostridioides difficile in China.

ABSTRACT:

Introduction

Clostridioides difficile (C. difficile) is a nosocomial bacterial pathogen that causes antibiotic-associated diarrhea mediated by cellular exotoxins secreted into the intestine during bacterial growth. Multilocus sequence typing (MLST) and PCR ribotyping are the main molecular typing for C. difficile. Whole genome sequencing (WGS) core genome multilocus sequence typing (cgMLST) was developed for genetic evolution and outbreak investigation of C. difficile with higher precision and accuracy.

Methods

A total of 699 whole (complete and draft) genome sequences of distinct C. difficile strains were used in this study to identify core gene set (2469 core genes) and the cgMLST scheme for the phylogeny analysis of C. difficile. This cgMLST pipeline was then carried the Chinese Pathogen Identification Net (China PIN) for surveillance of C. difficile in China. Within the China PIN, 195 WGS of C. difficile and an outbreak of CDI with 12 WGS of C. difficile were used to evaluate the cgMLST pipeline.

Results

The result displayed that mostly tested C. difficile isolates could be successfully divided into 5 classic clades and the outbreak event was also successfully identified.

Discussion

The results are meaningful and offer a practicable pipeline for a national-wide surveillance of C. difficile in China.

SUBMITTER: Wang YY

PROVIDER: S-EPMC10040748 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Publications

Application of a core genome sequence typing (cgMLST) pipeline for surveillance of <i>Clostridioides difficile</i> in China.

Wang Yuan Yuan YY Xie Lu L Zhang Wen Zhu WZ Du Xiao Li XL Li Wen Ge WG Bia Lu Lu LL Cui Zhi Gang ZG Wu Yuan Y Lu Jin Xing JX

Frontiers in cellular and infection microbiology 20230313

<h4>Introduction</h4><i>Clostridioides difficile (C. difficile)</i> is a nosocomial bacterial pathogen that causes antibiotic-associated diarrhea mediated by cellular exotoxins secreted into the intestine during bacterial growth. Multilocus sequence typing (MLST) and PCR ribotyping are the main molecular typing for <i>C. difficile</i>. Whole genome sequencing (WGS) core genome multilocus sequence typing (cgMLST) was developed for genetic evolution and outbreak investigation of <i>C. difficile</i ...[more]

PMID: 36992688

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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)