Altering the Microbiome: Patients with a Successful Outcome Following Microbiota-Based RBX2660 Treatment Trend Toward Human Microbiome Project Healthy Subjects’ Profile

Sahil Khanna MBBS, Dale Gerding MD, Ken Blount PhD, Courtney Jones BS, Bill Shannon PhD MBA, Sharina Carter PhD

Background

• Recurrent Clostridium difficile infections (rCDI) are strongly associated with intestinal dysbiosis.
• RBX2660 is a standardized microbiota-based drug designed to prevent rCDI by potentially restoring a healthier intestinal microbiome.
• The effect of RBX2660 on rCDI patient microbiomes was evaluated by comparing pre- and post-treatment samples collected from a Phase 2 controlled open-label study of RBX2660 to a healthy intestinal microbiome, as defined by the Human Microbiome Project (HMP).

Methods

• Prospective, multicenter, controlled open-label Phase 2 study (NCT02589847) consisting of an RBX2660 treatment arm and a historical control group.
• Antibiotics were discontinued 24-48 hours prior to administration of the first enema.
• Participants received up to 2 doses of RBX2660 delivered via enema with doses 7 + 2 days apart.
• Success was defined as the absence of CDI at 8 weeks following completion of the last treatment.
• Patients were classified as a treatment failure if all four (4) of the following criteria were met: recurrence of diarrhea less than 8 weeks after administration of the last assigned study enema, a positive laboratory diagnosis of C. diff icile as conducted and reported by the study investigator, a need for retreatment for CDI, and no other cause for diarrhea.
• Clinical efficcy results have been previously presented (Figure 1).

Microbiome Analysis

• Patients in the RBX2660 treatment arm were asked to voluntarily submit stool samples at baseline (pre-treatment) and at multiple time points up to 12 months after treatment.
• Longitudinal sample sets (baseline, 7, and 30 days after treatment) were collected from 17 successful patients (n=45 samples) and 17 failed patients (n=34 samples).
• Stool samples were sequenced using BoosterShot (CoreBiome, Minneapolis, MN), an ultra-shallow shotgun sequencing that generates taxonomic profiles with species-level resolution.
• Relative abundance data from successful patient samples were grouped longitudinally and compared using a Bray-Curtis dissimilarity calculation with non-metric multi-dimensional scaling. Additional analyses were performed based on the Dirichlet-Multinomial distribution to compare group mean relative taxonomic abundances(pi) and within group over dispersion (theta).
• Differentiation between sample communities was visualized using a Kullback-Leibler(KL) divergence analysis model (BioRankings, St. Louis, MO), a measure of the difference between microbial diversity at different time points or between different samples.

Microbiome Analysis

• See poster (PDF 426 KB)

Conclusions

• RBX2660 restores a healthier microbiome profile among patients who responded to open-label RBX2660 treatment.
• Patient microbiota trended toward increased diversity relative to baseline following RBX2660 treatment.