AUTHOR=Wang Yuan Yuan , Xie Lu , Zhang Wen Zhu , Du Xiao li , Li Wen Ge , Bia Lu Lu , Cui Zhi Gang , Wu Yuan , Lu Jin Xing 

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

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1109153

DOI=10.3389/fcimb.2023.1109153

ISSN=2235-2988

ABSTRACT=<sec><title>Introduction</title><p><italic>Clostridioides difficile (C. difficile)</italic> 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 <italic>C. difficile</italic>. Whole genome sequencing (WGS) core genome multilocus sequence typing (cgMLST) was developed for genetic evolution and outbreak investigation of <italic>C. difficile</italic> with higher precision and accuracy.</p></sec><sec><title>Methods</title><p>A total of 699 whole (complete and draft) genome sequences of distinct <italic>C. difficile</italic> strains were used in this study to identify core gene set (2469 core genes) and the cgMLST scheme for the phylogeny analysis of <italic>C. difficile</italic>. This cgMLST pipeline was then carried the Chinese Pathogen Identification Net (China PIN) for surveillance of <italic>C. difficile</italic> in China. Within the China PIN, 195 WGS of <italic>C. difficile</italic> and an outbreak of CDI with 12 WGS of <italic>C. difficile</italic> were used to evaluate the cgMLST pipeline.</p></sec><sec><title>Results</title><p>The result displayed that mostly tested <italic>C. difficile</italic> isolates could be successfully divided into 5 classic clades and the outbreak event was also successfully identified.</p></sec><sec><title>Discussion</title><p>The results are meaningful and offer a practicable pipeline for a national-wide surveillance of <italic>C. difficile</italic> in China.</p></sec>