Long-Term Outcomes After CDI: FMT Versus Antibiotic-Only Treatment

Long-Term Outcomes After Clostridioides Difficile Infection (CDI): Comparative Follow-Up of FMT Versus Antibiotic-Only Treatments (LTO-CDI Cohort)

The goal of this observational study is to learn about the long-term effects of fecal microbiota transplantation (FMT) compared with antibiotic-only treatment in adults who were treated for Clostridioides difficile infection (CDI) at Umeå University Hospital between 2016 and 2024. The main questions it aims to answer are:

• Do patients treated with FMT maintain higher gut bacterial diversity up to 10 years after CDI compared with patients treated with antibiotics only?
• Do donor gut bacteria introduced by FMT persist long-term in the recipient's gut?
• Are there differences in gut metabolism, gut barrier function, and systemic inflammation between FMT-treated and antibiotic-only treated patients at long-term follow-up?
• What are the long-term safety outcomes - including new diseases, hospitalizations, and mortality - in FMT-treated versus antibiotic-only treated patients?

Researchers will compare patients who received FMT to patients who received antibiotics only to see if FMT leads to lasting differences in gut microbiota, metabolism, immune markers, and clinical outcomes.

Participants will:

• Attend a single study visit at Umeå University Hospital
• Provide samples of blood, stool, urine, and a nasal swab
• Complete two quality-of-life questionnaires

Clinical data will be collected from medical records for all participants.

Study design and setting This is a single-center, long-term observational cohort study conducted at the Department of Infectious Diseases, Umeå University Hospital, Sweden. The study enrolls adult patients treated for CDI between February 1, 2016 and December 31, 2024, providing up to 10 years of follow-up from the index CDI episode. Participants are stratified into two groups: FMT-treated and antibiotic-only treated.

CDI case definition Compatible clinical presentation (≥3 loose stools in 24 hours) plus a positive nucleic acid amplification test (LAMP) for C. difficile, consistent with ESCMID diagnostic criteria.

Recruitment Potentially eligible living subjects are identified from departmental diagnosis records and contacted by mail with written study information and an opt-out form. Those who do not return the opt-out form are contacted by telephone and invited to a single study visit for informed consent and enrollment. Deceased individuals are included in safety analyses only, without contact with next of kin.

Biological sampling Blood: EDTA plasma, serum, PBMC isolation Fecal sample Urine sample Nasopharyngeal swab

Archived donor fecal samples and pre- and post-FMT patient samples from the Umeå FMT biobank will be retrieved for longitudinal comparisons.

Observational measures Gut and nasopharyngeal microbiota will be characterized by shotgun metagenomics (strain-level resolution) and 16S rRNA sequencing. Resistome profiling and detection of multidrug-resistant organisms by culture will be performed on fecal samples. Global and targeted metabolomics (short-chain fatty acids, bile acids, redox metabolites) will be performed on feces, urine, and blood. Gut barrier markers in blood will include LPS, LPS-binding protein (LBP), and EndoCAb. Systemic immune profiling will include cytokine panels, soluble immune mediators, antibodies, and transcriptomic profiling of peripheral blood mononuclear cells. The host genome will not be sequenced. Clinical observational measures will include additional CDI after index CDI. Pharmacological treatments and comorbidity at index CDI and follow-up, as well as any antibiotic exposure during follow-up will be collected from the medical records.

Inclusion Criteria:

• Adults aged 18 years or older
• Symptomatic, microbiologically verified index CDI from February 1 2016 to December 31 2024
• Having received CDI treatment at Umeå University Hospital (antibiotic-only or FMT)

Exclusion Criteria:

• Age below 18 years at follow-up
• Index CDI diagnosis not meeting ESCMID case definition
• Testing positive for another gastrointestinal pathogen (virus/bacteria) that is more plausible to explain the clinical picture at index CDI episode
• Declines participation