Response to Microbiota-Based Drug RBX2660 is Associated with Reduction in Antimicrobial Resistance Genes in Patients with Recurrent Clostridioides difficile Infections

Julia Garcia-Diaz MD, Courtney Jones, Hiren Karathia PhD, Brian Fanelli, Nur A Hasan PhD, Ken Blount PhD

Background

• Antibiotic microbial resistance (AMR) is a global health challenge, and is common in recurrent Clostridioides difficile infection (rCDI) population due to high historical exposure to antibiotics.
• The gut microbiota implicated as a reservoir of AMR bacteria.
• Therapeutic approaches that decolonize AMR gut bacteria would be valuable.
• In a previous analysis, RBX2660, an investigational standardized microbiota-restoration therapy in clinical development for preventing rCDI decreased vancomycin-resistant enterococci colonization.
• Herein, we assessed the total AMR gene profile before and after treatment in fecal samples from RBX2660 treatment responders in a Phase 2 rCDI trial.

Methods

• PUNCH Open Label™ (NCT02589847) – prospective, multicenter, open-label Phase 2 study assessing the efficacy and safety of RBX2660 treatment of recurrent CDI.
  • PATIENT POPULATION: multi-recurrent CDI (≥ 2 recurrent episodes at enrollment)
  • TREATMENT: two doses of RBX2660 administered 7 ± 2 days apart
  • EFFICACY: absence of CDI recurrence at 8 weeks after last study treatment
  • FAILURE: documented recurrence, including positive laboratory diagnosis for C. difficile
  • CONTROL GROUP: historical chart review of patients who only received antibiotic therapy for rCDI
• Analysis included 66 longitudinally matched samples from 22 treatment responsive participants, including before treatment (BL) and 7 ± 3 and 30 ± 10 days after treatment. Sample set represents 17 trial sites from US and Canada.
• All samples were frozen without stabilizers after collection, extracted, and sequenced using a shallow shotgun method.
• Sequencing reads were compared to a proprietary database of gene sequences annotated as related to antimicrobial resistance (CosmosID)
• ≥ 40% sequencing coverage of an AMR gene was considered positive identification in each sample.
• AMR gene coverage for participant samples were compared to Human Microbiome Project (HMP) data for which comparable sequencing depth was simulated.

RBX2660 is Efficacious & Durable

• 119 of 149 RBX2660-treated participants (80%) were responders at 8 weeks after treatment
• 57 of 110 patients (52%) in the historical control group were recurrence free 8 weeks after antibiotic treatment
• Only 3 of 109 evaluable primary RBX2660 responders reported reinfection at 6 months
• 97% of RBX2660-treated 8-week responders who were evaluable at 6 months remained recurrence free
• Follow up ongoing to 24 months

RBX2660 Shifts Microbiome Composition

• Participants were dysbiotic at study entry, with decreased Bacteroidia and Clostridia and overabundance of Gammaproteobacteria and Bacilli
• Bacteroidia, Clostridia increased and Gammaproteobacteria, Bacilli decreased after treatment; durable to 6 months after treatment
• Based on shallow-shotgun sequencing data

Antimicrobial Resistance Genes (AMR) Analysis

• Prior to treatment (BL) rCDI participants had significantly higher abundance of antimicrobial resistance (AMR) genes than the HMP healthy population
• After treatment (7 and 30 days), participants’ had decreased AMR gene abundance, not significantly different from HMP

Conclusions

• In a Phase 2 open label trial, RBX2660 was 80% effective for preventing rCDI, with durable response to at least 6 months.
• Responding participants’ microbiomes resolved toward a healthier composition after treatment.
• In a 22-participant subgroup analysis, there was a significant decrease in antimicrobial resistance genes from before to after successful response to RBX2660.