Association Between Clostridium innocuum and Antibiotic-Associated Diarrhea in Adults and Children: A Cross-sectional Study and Comparative Genomics Analysis

Background A recent study from Taiwan suggested that Clostridium innocuum may be an unrecognized cause of antibiotic-associated diarrhea (AAD) and clinically indistinguishable from Clostridioides difficile infection. Our objective was to compare C. innocuum prevalence and strain between those with AAD and asymptomatic controls. Methods In this cross-sectional study, we collected stool from 200 individuals with AAD and 100 asymptomatic controls. We evaluated the association between AAD and C. innocuum in stool using anaerobic culture and quantitative polymerase chain reaction (qPCR). To identify strain-specific associations with AAD, we performed whole-genome sequencing of C. innocuum isolates using Illumina MiSeq and constructed comparative genomics analyses. Results C. innocuum was isolated from stool of 126/300 (42%) subjects and more frequently from asymptomatic controls than AAD subjects (50/100 [50%] vs 76/200 [38%], respectively; P = .047). C. innocuum isolation frequency was not associated with AAD in either the adult or pediatric subgroups. C. innocuum and C. difficile were frequently co-prevalent in individuals with and without diarrhea. There were no phylogenetic differences or accessory genome associations between C. innocuum isolates from AAD subjects and asymptomatic controls. Conclusions C. innocuum was frequently isolated and at a greater frequency in asymptomatic controls than those with AAD. We did not identify strain lineages or accessory genomic elements associated with AAD. These data highlight that differentiating C. innocuum-associated diarrhea from asymptomatic colonization, and differentiating diarrhea caused by C. difficile from C. innocuum, are clinical microbiology challenges that require additional investigation to identify host-specific factors and/or biomarkers that distinguish these conditions. In a cross-sectional study, we evaluated Clostridium innocuum as an emerging etiology of antibiotic-associated diarrhea. Using anaerobic culturing techniques and qPCR, we determined C. innocuum was frequently isolated at similar frequencies and with similar strain types irrespective of diarrheal symptoms.

Automated summary

This study compared the prevalence and strains of Clostridium innocuum between individuals with antibiotic-associated diarrhea (AAD) and asymptomatic controls. The findings showed that C. innocuum was more frequently isolated from asymptomatic controls than AAD subjects, with similar strain types regardless of diarrheal symptoms. The study highlights the clinical microbiology challenges of differentiating C. innocuum-associated diarrhea from asymptomatic colonization and distinguishing diarrhea caused by C. difficile from C. innocuum.