Functional Genomics Core

摘要(功能基因组学核心) 抗菌素耐药性(AMR)及其影响已被世界卫生组织、美国疾病控制与预防中心、美国食品和药物管理局和美国国立卫生研究院视为一体 当今社会面临的最重要的公共卫生威胁。耐万古霉素肠球菌(VRE)， 产超广谱β-内酰胺酶/碳青霉烯酶肠杆菌科(ESBL-E/Cre)，以及 艰难梭菌特别令人感兴趣，因为它们不成比例地影响免疫受损和 重病患者。疾控中心已将VRE列为严重威胁，ESBL-E/CRE和艰难梭菌 作为紧急威胁。这些病原体中的每一种都能够定居并感染肠道，破坏肠道 通过抗生素保护肠道微生物群是感染的主要危险因素。最重要的假设是 免疫低下患者多药耐药病原菌定植和感染的动态研究 计划(炸药)是患者对医院内获取、肠道定植和随后的 病原体感染严重依赖于功能微生物群-病原体的相互作用，这种相互作用决定了 疾病进展和临床结果。重要的是，我们假设猎枪元基因组学数据 用推测的代谢潜力不足以预测和解释对移居和 基因组学、元基因组学、代谢组学和 代谢蛋白质组学是阐明病原体、微生物组和细菌之间复杂相互作用的必要条件。 主持人。为了实现这种多组学方法，功能基因组核心(FGC)将提供一个中央 为此应用程序中包含的所有三个项目提供资源，为 基因组测序，元基因组学，元蛋白质组学和代谢组学。此外，利用强大的 生物信息学基础设施安置在FGC内，我们将提供现有分析应用程序 管道和疾病分类器-以及新型管道的开发-将整合和 促进对每个单独项目产生的数据进行全面分析。作为一个例子，我们 已经建立了一条高通量的管道，用于参考质量完全循环的生成和注释 细菌染色体和伴随的质粒，以及伴随的代谢蛋白质组数据 将92%的蛋白质签名映射回源基因。总体而言，为了实现下列科学目标 在这项P01申请中，FGC将承担三个目标：i)协调纯微生物 从研究地点到FGC的分离株和患者粪便样本；ii)完整的基因组、后基因组、 每个项目的代谢组学和代谢组学过程；以及iii)协助分析和整合 在每个项目下生成的多组体数据。FGC提供了独特且无与伦比的能力 组合多种组学数据类型，以创建真正的多组学评估 VRE、ESBL-E/Cre和艰难梭菌、肠道微生物组和宿主代谢组，促进了这一目标的实现 爆炸性的计划。

ABSTRACT (Functional Genomics Core) Antimicrobial resistance (AMR) and its impact have been recognized by the WHO, CDC, FDA, and NIH as one of the most important public health threats facing society today. Vancomycin-resistant enterococci (VRE), extended spectrum β-lactamase/carbapenemase-producing Enterobacteriaceae (ESBL-E/CRE), and Clostridiodes difficile are of particular interest as they disproportionately affect immunocompromised and severely ill patients. The CDC has designated VRE as a serious threat and both ESBL-E/CRE and C. difficile as urgent threats. Each of these pathogens is able to colonize and infect the gut, with disruption of the protective gut microbiome by antibiotics a leading risk factor for infection. The overarching hypothesis of the DYNamics of colonizAtion and infection by Multidrug-resIstant paThogens in immunocompromisEd patients program (DYNAMITE) is that patient susceptibility to nosocomial acquisition, gut colonization, and subsequent infection by pathogens is critically dependent on functional microbiota-pathogen interactions that determine disease progression and clinical outcomes. Importantly, we posit that shotgun metagenomics data coupled with inferred metabolic potential is not enough to predict and interpret susceptibility to colonization and infection in a dysbiotic patient, and a combination of genomics, metagenomics, metabolomics, and metaproteomics is necessary to elucidate the complex interplay between the pathogen, the microbiome, and the host. To enable this multi-omic approach, the Functional Genomics Core (FGC) will provide a central resource to all three projects contained within this application, providing facilities and expertise for whole genome sequencing, metagenomics, metaproteomics, and metabolomics. Additionally, leveraging the robust bioinformatics infrastructure housed within the FGC, we will provide the application of existing analytical pipelines and disease classifiers–as well as the development of novel pipelines—that will integrate and facilitate the comprehensive analyses of the data generated for each individual project. As an example, we have built a high-throughput pipeline for the generation and annotation of reference-quality fully circularized bacterial chromosomes and accompanying plasmids, and with accompanying metaproteomics data have mapped 92% of protein signatures back to the source gene. Overall, to achieve the scientific goals outlined in this P01 application, the FGC will undertake three aims: i) coordinate the transfer of pure microbiological isolates and patient stool samples from the study sites to the FGC; ii) complete genomic, metagenomic, metaproteomic, and metabolomic processes of each project; and iii) assist in the analysis and integration of the multi-omic data generated under each project. The FGC provides a unique and unparalleled ability to combine multiple omics data types to create a truly multi-omic assessment of the complex interplay between VRE, ESBL-E/CRE, and C. difficile, the gut microbiome, and the host metabolome, facilitating the goals of this DYNAMITE program.