Enhanced preservation of the human intestinal microbiota by ridinilazole, a novel <i>Clostridium difficile</i>-targeting antibacterial, compared to vancomycin

<div><p>Ridinilazole, a novel targeted antibacterial being developed for the treatment of <i>C</i>. <i>difficile</i> infection (CDI) and prevention of recurrence, was shown in a recent Phase 2 study to be superior to vancomycin with regard to the primary efficacy measure, sustained clinical response (SCR), with the superiority being driven primarily by marked reductions in the rates of CDI recurrence within 30 days. Tolerability of ridinilazole was comparable to that of vancomycin. The current nested cohort study compared the effects of ridinilazole and vancomycin on fecal microbiota during and after treatment among participants in the Phase 2 study. Changes in the microbiota were assessed using qPCR and high-throughput sequencing on participants’ stools collected at multiple time-points (baseline [Day 1], Day 5, end-of-treatment [EOT; Day 10], Day 25, end-of-study [EOS; Day 40], and at CDI recurrence). qPCR analyses showed profound losses of <i>Bacteroides</i>, <i>C</i>. <i>coccoides</i>, <i>C</i>. <i>leptum</i>, and <i>Prevotella</i> groups at EOT with vancomycin treatment, while ridinilazole-treated participants had a modest decrease in <i>C</i>. <i>leptum</i> group levels at EOT, with levels recovering by Day 25. Vancomycin-treated participants had a significant increase in the Enterobacteriaceae group, with this increase persisting beyond EOT. At EOT, alpha diversity decreased with both antibiotics, though to a significantly lesser extent with ridinilazole (p <0.0001). Beta diversity analysis showed a significantly larger weighted Unifrac distance from baseline-to-EOT with vancomycin. Taxonomically, ridinilazole had a markedly narrower impact, with modest reductions in relative abundance in Firmicutes taxa. Microbiota composition returned to baseline sooner with ridinilazole than with vancomycin. Vancomycin treatment resulted in microbiome-wide changes, with significant reductions in relative abundances of Firmicutes, Bacteroidetes, Actinobacteria, and a profound increase in abundance of Proteobacteria. These findings demonstrate that ridinilazole is significantly less disruptive to microbiota than vancomycin, which may contribute to the reduced CDI recurrence observed in the Phase 2 study.</p></div

Comparison of bacterial group median quantities at each timepoint within treatment arms.

<p>Comparison of bacterial group median quantities at each timepoint within treatment arms.</p

Comparison of alpha diversity measures between baseline and end-of-treatment (EOT) within each treatment arm (horizontal), and between treatment arms (vertical).

<p>Comparison of alpha diversity measures between baseline and end-of-treatment (EOT) within each treatment arm (horizontal), and between treatment arms (vertical).</p

Taxa to the genus level with ≥2-fold change in relative abundance from baseline to end of treatment (EOT) with vancomycin or ridinilazole.

<p>Taxa to the genus level with ≥2-fold change in relative abundance from baseline to end of treatment (EOT) with vancomycin or ridinilazole.</p

Beta diversity between participants receiving ridinilazole or vancomycin and normal controls.

<p>Principal co-ordinate analysis was performed between samples at baseline and EOT from participants receiving ridinilazole or vancomycin in the vegan package in R on weighted Unifrac distances generated in QIIME. For another comparator, healthy controls are also shown. Ellipses represent 95% confidence interval of each cluster. Abbreviations: RDZ, ridinilazole; VAN, vancomycin; PC1, first Principal co-ordinate; PC2, second principal co-ordinate.</p

Effects of vancomycin and ridinilazole on relative abundance of taxa at baseline vs end-of-therapy.

<p>Cladograms were generated by LEfSe showing taxa with significantly higher relative abundance at baseline in red, and those with significantly higher relative abundance at end-of-therapy (EOT) in green. The phylogenetic tree is represented by concentric rings with phyla located at the innermost ring and subsequent taxonomic levels descend outwards to the species level. Panel A: Ridinilazole; Panel B: Vancomycin.</p

Microbiota levels belonging to different taxonomic groups measured by qPCR in samples from study participants and 14 healthy controls.

<p>Red circles represent participants treated with ridinilazole and blue circles represent participants treated with vancomycin. Bolded bars represent the median of all samples at that time point.</p