A single session of FMT did not significantly enhance MDRO decolonization or decrease AMR genes in patients with GI diseases, though it modulated gut microbiome diversity and composition.
FMT did not significantly improve MDRO decolonization rates compared to sham intervention at 4 weeks.
FMT did not significantly reduce antimicrobial resistance (AMR) gene burden compared to sham at 4 weeks.
The study population was predominantly colonized with carbapenem-resistant Enterobacteriaceae (CRE) or extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) at baseline.
FMT resulted in enrichment of short-chain fatty acid (SCFA)-producing bacteria in the gut microbiome, an effect not observed in the sham group.
FMT induced only modest, transient alterations in the gut mycobiome.
Viral diversity in the gut remained unchanged after FMT.
Adverse events were comparable between the FMT and sham intervention groups.
This research suggests that a single session of fecal microbiota transplant (FMT) — a procedure where stool from a healthy donor is transferred into a patient's gut — did not help patients with gastrointestinal diseases get rid of dangerous drug-resistant bacteria (called multidrug-resistant organisms, or MDROs) any better than a fake procedure using saline. The trial enrolled 114 patients in India, most of whom had pancreatitis or cirrhosis, and about a third of patients in both the FMT and sham groups cleared their drug-resistant bacteria after four weeks, with no meaningful difference between them. The genetic markers of antibiotic resistance in the gut were also similarly unchanged in both groups. Despite failing to clear the drug-resistant bacteria, FMT did produce some changes in the gut's microbial ecosystem. Patients who received FMT showed increases in bacteria that produce short-chain fatty acids, which are generally considered beneficial for gut health. However, the fungal community (mycobiome) showed only small and temporary changes after FMT, and the viral community (virome) was essentially unaffected. Safety was comparable between the two groups. This research suggests that while FMT can shift the overall bacterial landscape of the gut, a single colonoscopy-based FMT session is not sufficient to reliably eliminate drug-resistant bacteria in hospitalized patients with serious gastrointestinal diseases. This is an important finding given the growing global problem of antibiotic resistance and the lack of approved treatments for gut colonization by these dangerous organisms. Future research may need to explore repeated FMT sessions, different delivery methods, or different patient populations to determine whether FMT could play a role in combating antibiotic-resistant gut colonization.
Narang H, Talukdar D, Kumar B, Mathur P, Ningombam A, Singh M, et al.. (2026). Fecal Microbiota Transplant and Multidrug-Resistant Organism Decolonization in Gastrointestinal Disease: A Randomized Clinical Trial.. JAMA internal medicine. https://doi.org/10.1001/jamainternmed.2026.0655