Whole-Genome Sequencing Analysis of ST1, ST11, ST17, and ST37 Clostridioidesdifficile Lineages from a Korean Hospital.

Abstract

Clostridioides difficile infection (CDI) is a major cause of antibiotic-associated diarrhea and pseudomembranous colitis and remains one of the most common healthcare-associated infections. Clostridioides difficile sequence types 1 and 11 (ST1 and ST11), which belong to multilocus sequence typing (MLST) clades 2 and 5, respectively, are widely recognized as epidemic-associated lineages. Both lineages harbor virulence-associated genetic features, including truncating variants in tcdC and carriage of the binary toxin locus (CdtLoc). ST37 (clade 4) has been an epidemic lineage in East Asia, whereas ST17 (clade 1) has been reported as a predominant lineage in the Republic of Korea and Japan. We performed short-read whole-genome sequencing (WGS) on 61 clinical isolates collected at a university-affiliated hospital in the Republic of Korea between February 2016 and April 2019. Long-read sequencing was additionally performed for 24 isolates, generating complete genomes by hybrid assembly. ST17 was the most prevalent sequence type (n = 16, 26.2%), followed by ST1 (n = 10, 16.4%). ST1 and ST11 isolates harbored the genetic features reported for these lineages, including truncating variants in tcdC. Genomic profiling further identified virulence-associated genes and antimicrobial resistance (AMR) determinants in diverse lineages. These findings characterize the genomic features of co-circulating C. difficile lineages and reveal the local presence of epidemic-associated strains.