EpiXact-FMT: A metagenomic, pharmacovigilance assay for microbiota therapeutics safety

PROJECT SUMMARY The transfer of healthy intestinal microbiota is an effective treatment for patients with refractory GI infections. Recently, FDA approved the first fecal microbiota product to prevent the recurrence of Clostridium dif- ficile infections (CDI), opening doors to other clinical trials seeking to modify intestinal microbiome. While effec- tive and generally safe, the transmission of virulent organisms is a known risk of fecal microbiota transfer (FMT). Screening of donor samples and patient surveillance are recommended to mitigate these risks, but they are neither standardized, nor comprehensive. Case-in-point, in 2019, Day Zero Diagnostics (DZD) played a crucial role in two studies, conclusively showing that transmissions do occur. As a result, FDA updated its guidelines to include (1) a more thorough follow-up of adverse events in FMT patients and (2) extended donor screening. However, there is currently no species-agnostic service that can assess donor sample safety and assist in FMT pharmacovigilance. To address this gap, DZD proposes to build epiXact-FMT – a sample prep and bioinformatic pipeline designed to provide definite answers related to FMT safety. DZD specializes in the analysis of infectious disease transmissions through whole genome sequencing (WGS)- based approaches. In the case of microbiota transfer, sequencing has the potential to assess the safety of a donor sample, but is limited by sample complexity and relating species abundance to its infectious potential. In this Phase I, DZD proposes to innovate sample preparation, deep sequencing, and SNV analysis to achieve strain-level resolution of metagenomic donor sample, which contains the genomic sequences of the entire rep- ertoire of human gut microbiota. This workflow is of immediate use for resolving suspected donor-to-patient transmissions. By measuring the genomic relatedness between the bacteria isolated from an infected patient and the same species sequenced in the complex metagenomic donor sample, DZD can rapidly determine if a patient's infection is linked to the donor. Therefore, epiXact-FMT can be directly applied in the retrospective analysis of FMT-related adverse events and pharmacovigilance. The future of microbiota transfer lies in ensuring its safety by comprehensively screening the donor samples and clearly defining a safe microbial composition and abundance. The workflow developed in this Phase I pro- posal will serve as a foundation for future prospective donor sample screening by establishing a method of pathogen (or species) detection in metagenomic samples with strain-level resolution. In the future, DZD will focus on adopting epiXact-FMT to serve as a general workflow, assessing the safety of metagenomic samples for clinical use.