Comparing three ways to clear antibiotic-resistant bacteria from the gut

Inclusion Criteria:

* Age ≥ 18 years;
* Documented intestinal colonization with antibiotic-resistant bacteria confirmed by at least two positive cultures (rectal swabs or, alternatively, stool cultures), with the last positive result obtained at least 28 days prior to the planned procedure;
* Documented colonization by one or more of the following bacterial strains:

  1. Carbapenem-resistant strains with confirmed resistance mechanisms, including MBL+ (NDM+, VIM+, or others), KPC+, OXA-48+, or phenotypic carbapenem resistance without identified genetic mechanism;
  2. Multidrug-resistant Enterobacteriaceae resistant to beta-lactams and other antibiotics, especially ESBL-producing strains, including Escherichia, Enterobacter, Klebsiella spp., and/or P. aeruginosa, A. baumannii (commonly associated with the ESKAPE group);
  3. Gram-positive bacteria such as Enterococcus faecalis, Enterococcus faecium, or other vancomycin-resistant enterococci (VRE), as well as Staphylococcus aureus strains resistant to methicillin (MRSA) and/or vancomycin;
* Absolute neutrophil count (ANC) in peripheral blood \>500/μL within 3 days prior to FMT; In case of tandem or repeated FMTs and expected neutrophil decline, the ANC test should be repeated before each FMT if the interval exceeds 3 days.

For patients without expected neutropenia (\<500/μL), the blood count remains valid for 28 days;

* Estimated life expectancy of at least 12 months;
* Ability to swallow large capsules (confirmed using a test capsule) or absence of contraindications to colonoscopy;
* No history of anaphylactic shock due to food allergies and ability to tolerate probiotic supplementation;
* Provision of written informed consent to participate in the study.

Exclusion Criteria:

* Lack of consent to participate in the study or inability to establish logical contact and obtain consent from an authorized representative;
* Absolute neutrophil count (ANC) \< 500 cells/μL on the day of FMT (within 3 days prior) or predicted decline to this level within the next 2 days;
* Diagnosed HIV infection with CD4 lymphocyte count \< 250 cells/μL;
* Active infection requiring antibiotic therapy on the day of FMT or planned antibiotic use during the first 7 days following FMT;
* Symptoms or radiological/endoscopic evidence of gastrointestinal mucosal damage within 7 days prior to FMT (e.g., ulceration, perforation, gastrointestinal bleeding) posing a risk of serious adverse events;
* Contraindications for FMT administration via upper or lower gastrointestinal tract routes (e.g., gastrointestinal perforation, anal atresia, lack of intestinal continuity, or other);
* Inability to undergo preparatory therapy (oral antibiotics: colistin, vancomycin, gentamicin and/or bowel cleansing agents) prior to FMT;
* Inability to swallow large capsules (confirmed with test capsules) or contraindications for colonoscopy;
* Severe food allergy with history of anaphylactic shock or inability to tolerate probiotics;
* Pregnancy or breastfeeding;
* Severe medical conditions contraindicating study protocol adherence as determined by the treating physician (e.g., severe heart failure precluding bowel cleansing due to risk of fluid overload or dehydration);
* Participation in another clinical trial and administration of an investigational drug or device within 3 months prior to randomization;
* Reluctance or inability to comply with protocol requirements, including any physical, mental, or social condition that may impair the participant's ability to adhere to the protocol.