Background: Fecal microbiota therapy is being actively pursued as treatment for recurrent C. difficile infection (rCDI), as well as for other GI disease indications associated with dysbiosis, e.g. irritable bowel syndrome (IBS). RBX2660 is a microbiota-based drug designed to restore a healthier microbiome and has demonstrated clinical efficacy for preventing rCDI. Despite this and other treatment successes, our understanding of functional microbiota reconstitution at the population scale is still evolving, as is the ability to distinguish IBS from CDI recurrence. Herein we describe development of a Random Forest classifier for CDI diagnosis, and we evaluate microbiome restoration in participants of the Phase 2 trial of RBX2660.
Methods: Fecal 16S rDNA sequences from 2,129 subjects enrolled in diverse multi-center cohorts were analyzed (1,235 adults and 447 children with CDI, AAD, IBS or controls). Technical variations due to different DNA extraction, primer region coverage and sequencing platforms were addressed using closed-reference OTU picking with UCLUST. The RDP classifier and SILVA database assigned taxonomy for each OTU sequence. Stratified random sampling with 50 repeated tests of microbiota training sets was performed for supervised learning. Microbiota signatures of patients in the RBX2660 PUNCH CD2 trial were then assessed using classifiers built to predict CDI treatment outcomes and IBS misdiagnosis.
Results: Random Forest built the best classifiers accurately predicting 97.7% of CDI cases, and confidently distinguished CDI from IBS patients based on their microbiome signatures (Figure). RBX2660 treatment significantly restored microbiota community composition in rCDI cases compared with placebo controls.
Conclusion: Random Forest classifiers built on a population-scale study of microbiota composition in patients with GI disease provide a highly accurate predictor of CDI cases vs potential IBS misdiagnosis in adults and children. RBX2660 significantly reduced disease classification scores in rCDI patients with a healthy-like microbiota reconstitution markedly accelerating after 30 days of treatment.
Funded by 1UO1 AI24290-01 and Rebiotix, Inc.
C. Jones, Rebiotix, Inc.: Employee , Salary .
K. Blount, Rebiotix, Inc.: Employee , Salary .
T. Savidge, Rebiotix: Grant Investigator , Research grant .