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Updated: Jan 4, 2026
Fecal Microbiota Transplantation via Colonoscopy for Recurrent C. difficile Infection
Published on: December 8, 2014
Fecal Transplant in Children With Clostridioides difficile Gives Sustained Reduction in Antimicrobial Resistance and
Suchitra K Hourigan1,2,3,4, Michelle Ahn5, Keylie M Gibson5
1Inova Translational Medicine Institute, Falls Church, Virginia.
Insights
Fecal microbiota transplantation (FMT) for Clostridioides difficile infection (CDI) in children reduces antimicrobial resistance genes and pathogens. Donor screening via metagenomics is recommended due to potential AMR gene acquisition.
Area of Science:
- Microbiology
- Genetics
- Pediatric Gastroenterology
Background:
- Clostridioides difficile infection (CDI) is treated with fecal microbiota transplantation (FMT).
- Limited data exists on antimicrobial resistance (AMR) genes and pathogen burden changes in pediatric FMT recipients.
- This study investigated these changes in children undergoing FMT.
Purpose of the Study:
- To assess alterations in AMR genes, potential pathogens, microbial species, and functional pathways following FMT in pediatric CDI patients.
- To evaluate the safety and efficacy of FMT in reducing AMR and pathogen load in children.
Main Methods:
- Nine children with recurrent CDI received FMT.
- Stool samples were collected from donors and recipients pre- and post-FMT (up to 24 weeks).
- Shotgun metagenomic sequencing and PathoScope 2.0 analysis were employed.
Main Results:
- FMT resolved CDI in all children, with a significant decrease in overall AMR genes (P < .001).
- Tetracycline resistance genes increased (P < .001), while multidrug resistance genes decreased (P < .001).
- Potential pathogens decreased (P < .001), and microbial diversity and beneficial species like *Faecalibacterium prausnitzii* and *Bacteroides ovatus* increased post-FMT.
Conclusions:
- FMT in children with CDI effectively reduces AMR genes and potential pathogens, altering microbiota composition and function.
- The observed increase in certain AMR genes post-FMT necessitates further investigation into donor screening methods, including metagenomic sequencing.
- Metagenomic screening of donors is crucial to mitigate the risk of AMR gene transfer during FMT.
Background:
Fecal microbiota transplantation (FMT) treats Clostridioides difficile infection (CDI). Little is known regarding the changes in antimicrobial resistance (AMR) genes and potential pathogen burden that occur in pediatric recipients of FMT. The aim of this study was to investigate changes in AMR genes, potential pathogens, species, and functional pathways with FMT in children.
Methods:
Nine children with recurrent CDI underwent FMT. Stool was collected from donor and recipient pre-FMT and longitudinally post-FMT for up to 24 weeks. Shotgun metagenomic sequencing was performed. Reads were analyzed using PathoScope 2.0.
Results:
All children had resolution of CDI. AMR genes decreased post-FMT (P < .001), with a sustained decrease in multidrug resistance genes (P < .001). Tetracycline resistance genes increased post-FMT (P < .001). Very low levels of potential pathogens were identified in donors and recipients, with an overall decrease post-FMT (P < .001). Prevotella sp. 109 expanded in all recipients post-FMT, and no recipients had any clinical infection. Alpha diversity was lower in recipients vs donors pre-FMT (P < .001), with an increase post-FMT (P ≤ .002) that was sustained. Beta diversity differed significantly in pre- vs post-FMT recipient samples (P < .001). Bacterial species Faecalibacterium prausnitzii and Bacteroides ovatus showed higher abundance in donors than recipients (P = .008 and P = .040, respectively), with expansion post-FMT. Biosynthetic pathways predominated in the donor and increased in the recipient post-FMT.
Conclusions:
FMT for CDI in children decreases AMR genes and potential pathogens and changes microbiota composition and function. However, acquisition of certain AMR genes post-FMT combined with low levels of potential pathogens found in donors suggests that further study is warranted regarding screening donors using metagenomics sequencing before FMT.
