Fecal microbiota transplantation in children with severe gastrointestinal disorders: the first Hungarian paediatric experience with 1-year follow-up

Fecal microbiota transplantation (FMT) is increasingly used for severe gastrointestinal disorders, but paediatric data outside recurrent Clostridioides difficile infection (CDI) remain limited. We prospectively described four children treated at two tertiary paediatric centres between 2025 and 2026 in Budapest, Hungary. Case-specific indications for FMT were fulminant treatment-refractory Clostridioides difficile infection (CDI), severe treatment-refractory CDI in a child with Crohn’s disease, pan-refractory acute gastrointestinal graft-versus-host disease (GvHD), and intestinal carriage of multidrug-resistant organisms (MDROs) in a child with IPEX syndrome, with decolonisation as the therapeutic aim. FMT was delivered by nasojejunal or nasogastric tube, colonoscopy, or lyophilised oral capsules, respectively. Clinical courses were recorded through 1 year. The child with fulminant CDI achieved remission by day + 14, and remained recurrence-free at 1 year. The child with Crohn’s disease and severe CDI returned to her pre-CDI stool pattern by day + 14, and remained CDI recurrence-free at 1 year. The child with gastrointestinal GvHD achieved complete clinical control by day + 14, but died on day + 50 from haemorrhagic complications of cerebral fungal infection. In the child with IPEX syndrome and intestinal MDRO carriage, carriage persisted at day + 14. Repeat FMT was performed on day + 60, and cultures were negative at days + 90 and + 365. No adverse event was judged directly attributable to FMT, however, donor-derived transmission of the fatal fungal infection in Patient 3 could not be definitively excluded, and the inclusion of distinct conditions, FMT routes, and the absence of a comparator precludes causal conclusions regarding efficacy or safety. Our cases highlight the delivery and clinical course of FMT in selected seriously ill children. Larger controlled studies are required to assess optimal patient selection and long-term outcomes.