Clostridioides Difficile: Understanding Responses and Treatment Effects

Clostridioides difficile infection (CDI) is a frequent cause of antibiotic-associated colitis and is characterized by high rates of recurrence and, in some patients, refractory disease. Although fecal microbiota transplantation (FMT) is an effective treatment for recurrent and refractory CDI, the biological mechanisms underlying treatment response, early clinical improvement, long-term effects, and vulnerability to subsequent antibiotic exposure remain incompletely understood.

This is an observational study designed to characterize biological and clinical changes associated with standard antibiotic treatment and FMT in patients with CDI. The study will investigate intestinal microbiota composition, microbial metabolites, mucosal and systemic immune responses, intestinal barrier function, and patient-reported outcomes, and relate these findings to clinical disease course and treatment outcome.

Adult patients with symptomatic, microbiologically verified CDI receiving routine clinical care will be included. Treatment decisions, including the use of antibiotics or FMT, are made by the treating physician according to clinical guidelines and are not influenced by study participation. Participants will be followed longitudinally for up to five years.

Biological samples will be collected during the acute CDI episode and at predefined follow-up time points. Stool samples will be obtained to characterize intestinal microbiota composition and metabolic profiles over time. In participants treated with FMT, stool sampling will be more frequent during the first week after treatment to capture early post-treatment changes. Blood samples will be collected for assessment of systemic immune and inflammatory markers. Urine samples will be collected for analysis of metabolites related to intestinal barrier integrity. Nasopharyngeal swabs will be obtained to explore whether modulation of the intestinal microbiota is associated with changes in microbiota composition and immune responses at distant mucosal sites.

In a subgroup of participants deemed suitable by the responsible clinician, repeated lower colonic biopsies will be obtained using sigmoidoscopy. These samples will be used to assess colonic mucosal healing, mucus barrier function, mucosa-associated microbiota, and local immune responses.

Microbiota analyses will include metagenomic sequencing approaches, and metabolomic analyses will be performed on stool and other biological samples. Immune responses will be assessed using biochemical and cellular assays in blood, mucosal tissue, and relevant sample types. Donor fecal material used for FMT will be analyzed and related to recipient outcomes.

Clinical outcomes will be assessed at 2 and 8 weeks after initiation of the current CDI treatment and during long-term follow-up. Disease severity and treatment outcomes, including treatment response, recurrence, refractory disease, and sustained cure, will be classified according to established clinical guidelines. Participants experiencing treatment failure may re-enter sampling schedules corresponding to subsequent treatment courses.

Patient-reported health-related quality of life will be assessed during acute infection and follow-up using validated generic and disease-specific instruments.

This study aims to provide a detailed characterization of biological and clinical processes associated with FMT and antibiotic treatment in CDI, including early and long-term effects, and to support future optimization of microbiota-based therapeutic strategies.