Table 1.

Human Studies of Microbiome Modulation to Treat or Prevent MDRO Infection and Colonization

Reference	Number of Patients	Study Type	Intervention	Outcomes/notes
Bier et al [58]	1	Case report	FMT (lyophilized capsules) administered orally	Decolonization of ESBL-producing K. pneumoniae in patient with an ileal conduit and urostomy
Davido et al [59]	8	Case series	FMT with frozen, stored feces from healthy volunteers administrered via nasoduodenal tube	Decolonization of 7/9 patients with vancomycin-resistant enterococci (VRE) during outbreak setting
Silva et al [60]	13	Case series	FMT with fresh stool administered via esophagogastroduodenoscopy (EGD)	Decoloniztion of 10/13 patients with carbapenamase-producing Enterobacteriaceae (CPE). Eight of the patients also had refractory or recurrent CDI in addition to CPE colonization.
Bar-Yoseph et al [61]	15	Prospective cohort	FMT with oral capsules	Decolonization of 9/15 patients colonized with CPE.
Lee et al [62]	10	Prospective cohort	FMT via several modalities including colonoscopy (with EGD as backup for failed colonoscopy) and in 1 patient, encapsulated feces. Patients received between 1 and 3 FMT	Non-standardized administration of FMT in patients with CPE. Overall, 4/10 decolonized at 1 m, 5/10 at 3 m and 5 of 10 at 5 m.
Seong et al [63]	35	Prospective cohort	FMT with multiple modalities including colonoscopy, duodenoscopy, percutaneous jejunostomy tube and capsules	35 patients: 4 with CPE, 19 with VRE and 12 with both CPE/VRE colonization. Overall, 24 of 35 were decolonized.
Liu et al [64]	3	Case series	Frozen stool administrered via EGD × 2	All the patients were decolonized for CRE. Not a trial, main focus was on characterizing the longitudinal changes in the bacterial and viral microbiota after FMT using shotgun metagenomic sequencing.
Huttner et al [65]	22 treated, 17 controls	Randomized controlled trial (multicenter)	antibiotic therapy (colistin/neomycin × 5 d) followed by FMT given either by nasogastric tube of capsules.	All subjects colonized with extended spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) or CRE. 9/22 (41%) treated patients and 7/17 (29%). Difference did not reach statistical significance. Did not reach the calculated sample size of 64 participants. A followup paper did report the changes FMT had on the microbiota [66].
Saidani et al [67]	10 treated, 20 controls	Retrospective case-control	FMT via NG tube or gastric tube if present. Extensive pretreatment with chlorhexidine, bowel lavage, and non-absorbable antibiotics	8/10 treated patients and 2/20 controls were decolonized CRE or CR-Acinetobacter. The authors state that the pretreatment regimen was potentially responsible for the high success rate, but it is not clear if the controls had the same regimen but no FMT as the study design was retrospective.

Abbreviations: CDI, Clostridioides difficile infection; CPE, carbapenemase-producing Enterobacteriadeae; CR-Acinetobacter, xxx; CRE, carbapenem-resistant Enterobacteriaceae; EGD, esophagogastroduodenoscopy; FMT, fecal microbial transplantation; K. pneumoniae, xxx.