Genomic characterization of Clostridioides (Clostridium) difficile in Cambodia

Background. Genomic studies can provide insights into genetic determinants of virulence, antimicrobial resistance (AMR) and transmission pathways of Clostridioides difficile . Here, we characterized the core genome of C. difficile strains belonging to the five most common ribotypes (RTs) found in Cambodia. Methods. Whole-genome sequencing was conducted on 48 toxigenic C. difficile strains belonging to RTs 017, 012, 046, 014/020 and 056, recovered in 3 previous epidemiological studies in Cambodia between 2022 and 2023. Toxin and AMR genes were detected, and MLST was determined. Comparative genomic analysis was conducted within strains isolated in Cambodia and between strains from Cambodia and Thailand. Results. C. difficile ST2/RT 014/020 was the most genetically diverse [14–2,563 core-genome SNPs (cgSNPs)], whilst ST37/RT 017 was the most clonal (0–32 cgSNPs). Clonal strains (defined as sharing ≤2 cgSNPs) were observed within ST34/RT 056, ST37/RT 017 and ST54/RT 012 groups. One strain of ST37/RT 017 from Cambodia differed by eight cgSNPs from a strain from Thailand isolated in 2018. Resistance genes vanZ1 was the most prevalent, followed by tet(M) , vanR-Cd , vanS-Cd , vanG-Cd , vanT-Cd , blaCDD-2 , erm(B) , blaCDD-1 and aph(2’)-Ih . Genotypic multidrug resistance, genotype associated with the phenotype, was found in 100% of ST37/RT 017 strains and 67% of other strains. Conclusions. The transmission of C. difficile in Cambodia occurred not only among genetically distinct strains but also clonal strains. Besides sources within the country, C. difficile could have also originated from neighbouring countries such as Thailand. A high number of AMR determinants in most strains indicates the necessity for strict AMR surveillance in the country.