Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial

Abstract

Background. Intestinal microbiota restoration can be achieved by complementing a subject’s perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic resistant genes (ARGs) and organisms (AROs). In this study, we investigated fecal specimens from a multicenter, randomized, double-blind, placebo-controlled phase 2b study of microbiota-based investigational drug RBX2660. Patients were administered either placebo, 1 dose of RBX2660 and 1 placebo, or 2 doses of RBX2660 via enema and longitudinally tracked for changes in their microbiome and antibiotic resistome.Results. All patients exhibited significant recovery of gut microbiome diversity and a decrease of ARG relative abundance during the first 7 days post-treatment. However, the microbiome and resistome shifts towards average configurations from unperturbed individuals were more significant and longer-lasting in RBX2660 recipients compared to placebo. We quantified microbiome and resistome modification by RBX2660 using a novel ‘transplantation index’ metric. We identified taxonomic and metabolic features distinguishing the baseline microbiome of non-transplanted patients and taxa specifically enriched during the process of transplantation. We elucidated the correlation between resistome and taxonomic transplantations and post-treatment dynamics of patient-specific and RBX2660-specific ARGs. Whole genome sequencing of AROs cultured from RBX2660 product and patient samples indicate ARO eradication in patients via RBX2660 administration, but also, to a lesser extent, introduction of RBX2660-derived AROs.Conclusions. Through shotgun metagenomic sequencing, we elucidated the effects of RBX2660 in the microbiome and resistome. Antibiotic discontinuation alone resulted in significant recovery of gut microbial diversity and reduced ARG relative abundance, but RBX2660 administration more rapidly and completely changed the composition of patients’ microbiome, resistome, and ARO colonization by transplanting RBX2660 microbiota into the recipients. Although ARGs and AROs were transmitted through RBX2660, the resistome post-RBX2660 more closely resembled that of the administered product—a proxy for the donor—than an antibiotic perturbed state.Trial registration: NCT02299570. Registered 19 November 2014, https://clinicaltrials.gov/ct2/show/NCT02299570

A randomized controlled trial of Lactobacillus rhamnosus GG on antimicrobial-resistant organism colonization

“…28 Analyses of stool specimens from the RBX2660 phase 2b double-blinded, placebo-controlled, randomized trial using metagenomic sequencing found that RBX2660 reduced ARO colonization and more rapidly restored the microbiota compared to placebo. 29 MRT administered for CDI has also been associated with reductions in urinary tract infections. 30 Notably, a detailed cased report in which RBX2660 was administered for treatment of recurrent antimicrobial-resistant Klebsiella pneumoniae UTIs suggests that decolonization may not be the mechanism by which MRT interacts with ARO.…”

“…31 Notably, potential risks are associated with MRT administration for ARO colonization, including transferring new resistant organisms or genes to the recipient. 29 Additional study is needed to better understand the mechanisms, benefits, and harms of MRT when administered for ARO colonization before adoption into clinical practice. 22 Probiotics overall are safe, but it is also important to consider the potential for organisms in probiotic formulations to cause infections, particularly in immunocompromised patients who may be at risk of gut microbiota disruption due to other factors.…”

What is unknown in using microbiota as a therapeutic?

“…These include FMT-based products derived from donor stool, such as frozen stool capsules, lyophilized microbes, bacterial consortia, or purified spores isolated from stool. 80 They have been tested for treating recurrent CDI 81,82 and other conditions 83,84 with variable successes. Other non-FMT-based approaches have been developed, such as direct strategies to enrich certain beneficial bacteria by probiotics, to deplete harmful bacteria by antibiotics, or indirect strategies to change the gut microbiota through prebiotics or personalized nutrition.…”

Safety of fecal microbiota transplantation for Clostridioides difficile infection focusing on pathobionts and SARS-CoV-2

“…A study investigating fecal specimens from 66 recipients and the RBX2660 product in a multicenter, randomized, double-blind, placebo-controlled phase IIb study showed that RBX2660 not only shifted the taxonomic structure of the intestinal microbiome in the recipient group, but it also lead to dynamic changes in their antibiotic resistance patterns. 69 Besides decreasing the overall antibiotic resistance in the microbiome, it also simultaneously introduced RBX2660-origin antibiotic-resistant genes (ARGs) in a dose-dependent manner. This emphasizes the importance of screening fecal transplant samples for medically important ARGs via highly sensitive molecular methods.…”