Defined microbial communities for the treatment of recurrent C. difficile infection

 描述(由申请人提供)：艰难梭菌感染(CDI)是抗生素相关性腹泻的主要原因，也是最常见的医院感染。由于频繁的感染，潜在的严重并发症，以及很高(高达30%)的复发机会，CDI的治疗费用估计为每年10-50亿美元。一旦CDI复发，许多患者就会陷入抗生素治疗和复发的恶性循环。虽然粪便微生物区系移植(FMT)在治疗CDI方面显示出有效的效果(~90%的成功率)，但也存在潜在的风险。在动物模型中，微生物区系导致肥胖、糖尿病、癌症和心血管疾病等慢性疾病的能力要求更好地了解移植群落对人类健康的长期影响。在儿童和年轻人中尤其如此，FMT不仅被越来越多地用于CDI，而且还被用于包括炎症性肠病在内的其他疾病。用明确的、最小的纯菌株群落治疗CDI是FMT的一种替代方案，可以消除这些风险。到目前为止，10、12或33种菌株的鸡尾酒疗法已被证明对有限的人类有效。 审判。虽然这些研究很有希望，但由于缺乏严格的临床前测试来证明所有菌株的有效性/必要性并探索它们对人类健康的长期影响，这些研究受到了限制。 这项研究的总体目标是确定人类来源的、定义的微生物群落，这些微生物群落对于治疗复发性CDI是安全有效的。为此，我们开发了两种CDI的临床前模型，即人类粪便微型生物反应器阵列(MBRA)和人源化微生物区系小鼠(HMb小鼠)的复发疾病模型。这些模型的独特优势在于，无论是在中等吞吐量的MBRA中还是在宿主环境中，人类来源的菌株都可以与人类来源的微生物群落进行测试。目的1.建立明确的群落以抑制艰难梭菌在人类粪便MBRAs和反复发生艰难梭菌病的HMbb小鼠模型中的入侵。在R21阶段，我们的MBRA模型将用于快速筛选许多菌株组合，以确定能够对抗CDI的最小群落。成功的社区将在HMB小鼠身上进行测试，以确定哪些社区成功的可能性最高。目的2.优化社区对CDI的疗效。目的3.评估确定的社区移植的安全性和长期效果。在R33阶段，社区将针对有效性、安全性和在工业环境中生产的能力进行优化。将通过基因组测序/注释、抗生素耐药性分析以及与小鼠模型的长期关联研究来评估菌株的潜在危害，以确定对宿主健康和生理的影响。对人体组织的具体影响将通过人体肠样模型进行评估。这项研究的最终产品将是一种或多种明确的菌株鸡尾酒，这些菌株在治疗CDI方面已被证明有效，可接受的安全概况，以及已被证明可用于工业规模生产的方案。

 DESCRIPTION (provided by applicant): Clostridium difficile infection (CDI) is the primary cause of antibiotic associated diarrhea and the most common nosocomial infection. Due to frequent infection, potential for serious complications, and high (up to 30%) chance of recurrence, CDI treatment costs are estimated at $1-5 billion per year. Once CDI recurs, many patients get into a vicious cycle of antibiotic therapy and relapse. Although Fecal Microbiota Transplants (FMT) have demonstrated effectiveness in treating CDI (~90% success rate), there are also potential risks. The ability of the microbiota to contribute to chronic diseases such as obesity, diabetes, cancer, and cardiovascular disease in animal models demands that the long-term effects of transplanted communities on human health be better understood. This is especially true in children and young adults, where FMT is increasingly being used not only for CDI but also other ailments including inflammatory bowel disease. Treatment of CDI with defined, minimal communities of pure strains is one alternative to FMT that could negate these risks. Thus far, treatment cocktails of 10, 12 or 33 strains have proven effective in limited human trials. Although promising, these studies were limited by their lack of rigorous pre-clinical testig to demonstrate the effectiveness/necessity of all strains and to probe their long-term impacts on human health. The overall goal of this research is to identify human derived, defined microbial communities that are safe and effective for the treatment of recurrent CDI. To this end, we have developed two pre-clinical models of CDI, a human fecal Mini BioReactor Array (MBRA) and humanized microbiota mouse (HMbmouse) model of recurrent disease. The unique strengths of these models are that human-derived strains can be tested against human- derived microbial communities, either in medium-throughput MBRAs or in the context of a host. Aim 1. Develop defined communities to suppress C. difficile invasion in human fecal MBRAs and the HMbmouse model of recurrent C. difficile disease. In the R21 phase, our MBRA model will be used to rapidly screen many combinations of strains to identify minimal communities capable of combatting CDI. Successful communities will be tested in HMbmice to identify those with the highest likelihood for success. Aim 2. Optimization of communities for efficacy against CDI. Aim 3. Assess the safety and long-term effects of defined community transplantation. In the R33 phase, communities will be optimized for effectiveness, safety, and capability of being produced in industrial settings. The potential hazards of strains will be evaluated through genome sequencing/annotation, antibiotic resistance profiling, and long-term association studies with murine models to determine the impact on host health and physiology. Specific impacts on human tissue will be evaluated with human enteroid models. The final products of this research will be one or more defined cocktails of strains with proven effectiveness in treating CDI, acceptable safety profiles, and proven protocols for industrial-scale production.