Table 3.

Proposed Practical Research Agenda for Future Study of Fecal Microbiota Transplantation for Antibiotic-Resistant Organism Decolonization

Existing Challenge	Recommendations
Wide variability in FMT approaches in published literature	Multicenter clinical trial consortia should be funded to reduce variability in research approaches, improve rigor and reproducibility, and streamline protocol development to study the following prospectively: Ideal feces donor characteristics for ARO decolonization FMT dosing frequency and thresholds for repeating treatment Risks/benefits of bowel-preparation, antibiotic pretreatment Differential effects on specific AROs FMT recipient host factors that modulate FMT efficacy Improve recruiting capacity for rare cases (extreme multidrug resistance) ARO detection in feces in control groups in setting of ongoing antibiotic pressure and varied place of residence Benefits to patients of tailored microbiome therapies of microbial consortia or rationally matched donors
Regulatory future of FMT remains unclear	FDA, industry, and academics should work collaboratively to maintain patient-centered regulatory approaches that balance needs for further study with access to therapies with an immediate need
Unrefined end points of clinical studies	Benchmarking studies are needed to compare the performance characteristics of culture-based, culture-independent, and mixed methods that incorporate both approaches; measures of ARO decolonization should be studied to better estimate precision by number of consecutive swab samples, combining swab samples with PCR- or NGS-based techniques
Limited long-term safety outcomes data	Long-term cohorts and registries are needed to study the long-term safety of microbiome therapeutics

Abbreviations: ARO, antibiotic-resistant organism; FDA, Food and Drug Administration; FMT, fecal microbiota transplantation; NGS, next-generation sequencing; PCR, polymerase chain reaction.