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Background   Clostridioides difficile  infection (CDI) is an infectious nosocomial disease caused by  Clostridioides difficile , an opportunistic pathogen that occurs in the intestine after extensive antibiotic regimens.    Results  Nine  C. difficile  strains (CBA7201–CBA7209) were isolated from nine patients diagnosed with CDI at the national university hospital in Korea, and the whole genomes of these strains were sequenced to identify their genomic characteristics. Comparative genomic analysis was performed using 51 reference strains and the nine isolated herein. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that all 60  C. difficile  strains belong to the genus  Clostridioides , while core-genome tree indicated that they were divided into five groups, which was consistent with the results of MLST clade analysis. All strains were confirmed to have a clindamycin antibiotic resistance gene, but the other antibiotic resistance genes differ depending on the MLST clade. Interestingly, the six strains belonging to the sequence type 17 among the nine  C. difficile  strains isolated here exhibited unique genomic characteristics for PaLoc and CdtLoc, the two toxin gene loci identified in this study, and harbored similar antibiotic resistance genes.    Conclusion  In this study, we identified the specific genomic characteristics of Korean  C. difficile  strains, which could serve as basic information for CDI prevention and treatment in Korea.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13099-021-00451-3.

Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection