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

项目摘要 转移健康的肠道微生物群是治疗难治性GI感染患者的有效方法。 最近，FDA批准了第一个粪便微生物群产品，以防止复发的梭菌dif- ficile感染（CDI），为寻求改变肠道微生物组的其他临床试验打开了大门。虽然效果- 毒力微生物的传播是粪便微生物群转移的已知风险， （FMT）。建议筛查供体样本和患者监测以减轻这些风险，但它们 既不标准，也不全面。举个例子，在2019年，Day Zero Diagnostics（DZD） 在两项研究中起着至关重要的作用，最终表明传播确实发生了。因此，FDA更新了 指南包括（1）对FMT患者的不良事件进行更彻底的随访和（2）延长捐赠者 筛选然而，目前还没有物种不可知服务可以评估供体样本的安全性， 协助FMT药物警戒。为了解决这一差距，DZD建议建立epiXact-FMT -样品制备 和生物信息学管道，旨在提供与FMT安全相关的明确答案。 DZD专注于通过全基因组测序（WGS）分析传染病传播- 基于方法。在微生物群转移的情况下，测序具有评估微生物群转移的安全性的潜力。 供体样本，但受样本复杂性和物种丰度与其感染潜力的限制。在 在第一阶段，DZD提出创新样品制备、深度测序和SNV分析， 宏基因组供体样品的菌株水平分辨率，其包含整个复制的基因组序列， 人类肠道微生物群。 这一工作流程可立即用于解决疑似供体-患者传播。通过测量 从感染患者分离的细菌与测序的相同物种之间的基因组相关性 在复杂的宏基因组供体样本中，DZD可以快速确定患者的感染是否与 供体因此，epiXact-FMT可直接用于FMT相关不良反应的回顾性分析。 事件和药物警戒。 微生物群转移的未来在于通过全面筛选供体样本来确保其安全性 并明确定义了安全的微生物组成和丰度。在这个第一阶段开发的工作流程亲- 通过建立一种方法， 具有菌株水平分辨率的宏基因组样品中的病原体（或物种）检测。未来，DZD将 专注于采用epiXact-FMT作为通用工作流程，评估宏基因组样本的安全性 临床使用。

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.