Defining omic-signatures in recurrent Clostridium difficile infection

摘要 艰难梭菌感染(CDI)是一种最普遍、最具破坏性的与医疗保健相关的疾病。 感染。在标准的抗生素治疗之后，高达25%的CDI患者会发展成一种或多种 反复发作。持续或反复发作很难治疗，对患者来说是一个巨大的困难。 粪便微生物区系移植治疗复发性CDI的高成功率为我们提供了强有力的洞察 恢复正常肠道微生物区系的重要性。然而，到目前为止，还没有微生物或“基因组” (微生物组、后基因组、代谢组学)艰难梭菌复发的预测因子。这项提议的目标是 确定与艰难梭菌相关的微生物谱和“基因组”特征的时间动力学 复发。我们的假设是，没有出现艰难梭菌复发的患者都有一个可识别的集合 肠道微生物区系中的微生物、基因和粪便代谢物。其基本原理是，一旦时间 与艰难梭菌复发相关的微生物和“基因组”特征的动力学被很好地定义，候选 微生物或“组”生物标记物可以被前瞻性地验证，最终允许开发 预防CDI复发的策略。特定的先发制人疗法(例如，微生物组操作)然后可以 根据该微生物区系的微生物组成、基因或代谢物而形成的。这部小说 该方法为预防CDI复发提供了一种创新的方法。我们将通过以下方式来检验假设 具体目标如下：1)纵向测定受试者肠道微生物区系的组成和结构 在CDI之后，2)确定艰难梭菌肠道微生物区系的元基因组，3)进行全球代谢组学 使用LC-HRMS和GC-MS进行分析，包括胆固醇和胆汁酸代谢物，以确定关键 艰难梭菌肠道微生物区系中的代谢产物。这种方法是创新的，因为它将利用 无偏见、独立于培养的16S rRNA深度测序、元基因组和代谢组学方法 用创新的计算技术和多元统计方法识别肠道中的“基因组”特征 与艰难梭菌复发相关的微生物区系。这项拟议的研究意义重大，因为有 几乎没有关于肠道微生物区系、基因组特征和艰难梭菌复发之间关系的数据。这 该提案将定义可以在未来研究中验证的“体型”签名，最终导致新的 基于“OMIC”特征的复发性CDI一级预防策略。

ABSTRACT Clostridium difficile infection (CDI) is one of the most prevalent and devastating healthcare-associated infections. Following standard antibiotic therapy, up to 25% of individuals with CDI develop one or more recurrences. Persistent or repeated episodes are difficult to treat and are a significant hardship for patients. The high success rate of fecal microbiota transplant for recurrent CDI provides powerful insight into the importance of restoring normal gut microbiota. However, to date, there are no microbiological or “omic” (microbiomic, metagenomic, metabolomic) predictors of C. difficile recurrence. The objective of this proposal is to determine temporal dynamics of microbial profiles and “omic” signatures associated with C. difficile recurrence. Our hypothesis is that patients who do not develop a C. difficile recurrence share an identifiable set of microbes, genes, and fecal metabolites in the gut microbiota. The rationale is that once the temporal dynamics of microbial and “omic” signatures associated with C. difficile recurrence are well defined, candidate microbial or “omic” biomarkers can be validated prospectively, ultimately allowing the development of strategies to prevent recurrent CDI. Specific preemptive therapy (e.g. microbiome manipulation) may then be developed on the basis of microbial compositions, genes, or metabolites of that microbiota. This novel approach offers an innovative method for preventing recurrent CDI. We will test the hypothesis by pursuing the following Specific Aims: 1) Determine the composition and structure of gut microbiota longitudinally in subjects following CDI, 2) Determine the metagenome of C. difficile gut microbiota, and 3) Perform global metabolomic analyses using LC-HRMS and GC-MS, including cholesterol and bile acid metabolites, to determine key metabolites in C. difficile gut microbiota. The approach is innovative because it will utilize a combination of unbiased, culture-independent 16S rRNA deep sequencing, metagenomic, and metabolomic approach and innovative computational techniques and multivariate statistical methods to identify “omic” signatures in gut microbiota associated with C. difficile recurrence. The proposed research is significant because there are virtually no data on the relationship between gut microbiota, omic signatures and C. difficile recurrence. This proposal will define “omic” signatures that can be validated in future studies, ultimately leading to novel strategies based on “omic” profiles for primary prevention of recurrent CDI.