Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile

Journal of Pediatric Gastroenterology and Nutrition
16 Apr, 2019 ,

Chen et.al. conducted a study to evaluate the fecal microbiome of children based on C difficilecolonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease. They concluded that  antibiotic use and IBD status were seen to be present in association with  decreased gut bacterial diversity and altered microbiome composition. 

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Objectives: The gut microbiome is believed to play a role in the susceptibility to and treatment of Clostridium difficile infections (CDIs). It is, however, unknown whether the gut microbiome is also affected by asymptomatic C difficile colonization. Our study aimed to evaluate the fecal microbiome of children based on C difficilecolonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease (IBD).

Methods: Subjects with IBD and non-IBD controls were prospectively enrolled from pediatric clinics for a biobanking project (n = 113). A fecal sample was collected from each subject for research purposes only and was evaluated for asymptomatic toxigenic C difficile colonization. Fecal microbiome composition was determined by 16S rRNA sequencing.

Results: We found reduced bacterial diversity and altered microbiome composition in subjects with C difficilecolonization, concurrent antibiotic use, and/or concomitant IBD (all P < 0.05). Accounting for antibiotic use and IBD status, children colonized with C difficile had significant enrichment in taxa from the genera RuminococcusEggerthella, and Clostridium. Children without C difficile had increased relative abundances of Faecalibacteriumand Rikenellaceae. Imputed metagenomic functions of those colonized were enriched for genes in oxidative phosphorylation and beta-lactam resistance, whereas in the subjects without C difficile, several functions in translation and metabolism were over-represented.

Conclusions: In children, C difficile colonization, or factors that predispose to colonization such as antibiotic use and IBD status were associated with decreased gut bacterial diversity and altered microbiome composition. Averting such microbiome alterations may be a method to prevent or treat CDI.