Antimicrobial Susceptibility and Molecular Characterization Using Whole-Genome Sequencing of Clostridioides difficile Collected in 82 Hospitals in Japan between 2014 and 2016

We studied the antimicrobial susceptibility and the molecular characteristics using draft whole-genome sequencing of Clostridioides ( Clostridium ) difficile strains before and after treatment in adults with C. difficile infection (CDI) enrolled in a Phase III, randomised, nationwide study of fidaxomicin versus vancomycin in Japan (NCT02179658). C. difficile strains were cultured from stool samples collected before and after standard treatment with either fidaxomicin or vancomycin. Overall, 285 C. difficile strains were recovered, with 188 derived from CDI cases at baseline (87 patients received fidaxomicin and 101 received vancomycin). No strains isolated from episodes of CDI at baseline were shown to have reduced susceptibilities to fidaxomicin (MIC ≥1 mg/L), or resistance to vancomycin and metronidazole. Thirty-three sequence types (STs) were identified, the most common being ST17 (n=61; 32.4%), ST8 (n=26; 13.8%) and ST2 (n=21; 11.2%). Core-genome single nucleotide polymorphism analysis showed that outbreaks of C. difficile were unlikely to have occurred at each hospital. The predominant toxin gene profile was tcdA + tcdB + cdtA/cdtB - (n=149; 79.3%). Six of 87 patients who received fidaxomicin harboured C. difficile isolates with reduced fidaxomicin susceptibilities conferred by previously described mutations, Val1143Leu/Gly/Asp in RpoB or Arg89Gly in RpoC or putative mutations, Gln1149Pro in RpoB or Arg326Cys in RpoC. Allelic exchange studies of these putative mutations were not performed. Prior to fidaxomicin use, we found no C. difficile strains with reduced fidaxomicin susceptibilities causing CDI in Japan; however, mutant strains with reduced fidaxomicin susceptibilities were detected after fidaxomicin treatment.