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Updated: Apr 6, 2026
Fecal Microbiota Transplantation via Colonoscopy for Recurrent C. difficile Infection
Published on: December 8, 2014
Microbiome changes associated with sustained eradication of Clostridium difficile after single faecal microbiota
S K Hourigan1,2, L A Chen1,3, Z Grigoryan3
1Johns Hopkins School of Medicine, Baltimore, MD, USA.
Insights
Faecal microbiota transplantation (FMT) effectively eradicates Clostridium difficile infection (CDI) in children, restoring gut microbiome diversity. However, in children with inflammatory bowel disease (IBD), diversity returns to baseline, indicating host-specific factors influence microbiome recovery.
Area of Science:
- Gastroenterology
- Microbiome Research
- Pediatric Infectious Diseases
Background:
- Limited data exist on fecal microbiota transplantation (FMT) effectiveness for Clostridium difficile infection (CDI) in children, particularly those with underlying inflammatory bowel disease (IBD) and dysbiosis.
- Investigating microbiome alterations alongside CDI treatment is crucial for understanding therapeutic outcomes.
Purpose of the Study:
- To evaluate the efficacy of FMT in eradicating CDI in pediatric patients.
- To analyze changes in the gut microbiome composition following FMT in children with and without IBD.
Main Methods:
- Pediatric patients with recurrent CDI (≥3 episodes) received FMT via colonoscopy.
- Stool samples were collected pre- and post-FMT (2-10 weeks, 10-20 weeks, 6 months) for 16S rRNA gene sequencing.
- C. difficile toxin B gene PCR was used to confirm eradication.
Main Results:
- FMT led to sustained CDI symptom resolution and C. difficile eradication in all pediatric patients studied (n=8), including those with IBD (n=5).
- Pre-FMT, patients exhibited significantly reduced bacterial richness compared to donors. Post-FMT, bacterial diversity increased.
- While diversity normalized to donor levels in IBD-negative patients by 6 months, it reverted to pre-FMT levels in IBD patients, suggesting host-specific modulation.
Conclusions:
- FMT is an effective treatment for sustained C. difficile eradication in children, irrespective of IBD status.
- FMT-induced microbiome restoration is durable in children without IBD.
- In pediatric IBD patients, the gut microbiome's return to baseline post-FMT highlights the influence of host-related mechanisms on microbial diversity.
Background:
Little data are available regarding the effectiveness and associated microbiome changes of faecal microbiota transplantation (FMT) for Clostridium difficile infection (CDI) in children, especially in those with inflammatory bowel disease (IBD) with presumed underlying dysbiosis.
Aim:
To investigate C. difficile eradication and microbiome changes with FMT in children with and without IBD.
Methods:
Children with a history of recurrent CDI (≥3 recurrences) underwent FMT via colonoscopy. Stool samples were collected pre-FMT and post-FMT at 2-10 weeks, 10-20 weeks and 6 months. The v4 hypervariable region of the 16S rRNA gene was sequenced. C. difficile toxin B gene polymerase chain reaction was performed.
Results:
Eight children underwent FMT for CDI; five had IBD. All had resolution of CDI symptoms. All tested had eradication of C. difficile at 10-20 weeks and 6 months post-FMT. Pre-FMT patient samples had significantly decreased bacterial richness compared with donors (P = 0.01), in those with IBD (P = 0.02) and without IBD (P = 0.01). Post-FMT, bacterial diversity in patients increased. Six months post-FMT, there was no significant difference between bacterial diversity of donors and patients without IBD; however, bacterial diversity in those with IBD returned to pre-FMT baseline. Microbiome composition at 6 months in IBD-negative patients more closely approximated donor composition compared to IBD-positive patients.
Conclusions:
FMT gives sustained C. difficile eradication in children with and without IBD. FMT-restored diversity is sustained in children without IBD. In those with IBD, bacterial diversity returns to pre-FMT baseline by 6 months, suggesting IBD host-related mechanisms modify faecal microbiome diversity.
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