LB15. SER-109, an Investigational Microbiome Therapeutic, Reduces Abundance of Antimicrobial Resistance Genes in Patients with Recurrent Clostridioides difficile Infection (rCDI) after Standard-of-Care Antibiotics

Abstract

Background. The gastrointestinal microbiota is the first line of defense against colonization with antimicrobial resistant (AR) bacteria, particularly in vulnerable hosts with frequent antibiotic exposure. In a double‐blind Phase 3 trial of rCDI patients, SER‐109, an orally formulated consortia of purified Firmicutes spores, was superior to placebo in reducing CDI recurrence at week 8 post clinical resolution on standard‐of‐care (SoC) antibiotics. Overall recurrence rates were lower in SER‐109 vs placebo (12.4% vs 39.8%, respectively) relative risk, 0.32 [95% CI, 0.18‐0.58; p< 0.001 for RR< 1.0; p< 0.001 for RR< 0.833]. This is a post‐hoc analysis examining the impact of SER‐109 on antimicrobial resistance genes (ARGs) abundance in the intestinal microbiota compared to placebo. Methods. Subjects with rCDI received SoC antibiotics, then were randomized 1:1 to SER‐109 or placebo at baseline. Of 182 subjects, 140 who had paired stool samples at baseline and 1‐week post‐treatment were included in this analysis. ARG abundances and taxonomic profiles were generated from whole metagenomic shotgun sequencing. t‐tests were used to compare changes in ARG abundance from baseline; mixed linear models were used to associate ARG and taxon abundances across time points. Results. ARG abundance was reduced overall by week 1, with a significantly greater decrease in SER‐109 subjects vs. placebo at week 1 (Fig. 1). Proteobacteria relative abundance were positively correlated with ARG abundance across all samples (Fig. 2), with the Enterobacteriaceae family associated with the abundance of 95 ARGs (all p < 0.05). Enterococcaceae relative abundance was associated with glycopeptide AR abundance (p < 0.001). At week 1, Proteobacteria relative abundance was significantly decreased from baseline in SER‐109 subjects vs. placebo (p < 0.001). Enterobacteriaceae and Enterococcaceae relative abundances were also decreased from baseline in SER‐109 subjects vs. placebo (p < 0.001 and p = 0.007, respectively). Conclusion. SER‐109 was associated with significantly greater reduction of ARGs and AR bacteria abundances compared to placebo at 1 week post treatment. These findings support a potential role of microbiome therapeutics in rapid decolonization of AR bacteria with implications for infection prevention.