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WHO、CDC、FDA和NIH公认为是一个 当今社会面临的最严重的公共卫生威胁。万古霉素耐药肠球菌（VRE）， 产超广谱β-内酰胺酶/碳青霉烯酶肠杆菌科（ESBL-E/CRE），和 艰难梭菌是特别感兴趣的，因为它们不成比例地影响免疫功能低下和 重症患者。CDC已将VRE指定为严重威胁，ESBL-E/CRE和C。艰难 紧急威胁。这些病原体中的每一种都能够定殖并感染肠道， 抗生素保护肠道微生物组是感染的主要风险因素。最重要的假设是 免疫功能低下患者多药耐药菌定植和感染的动态观察 程序（ESTITE）是患者对医院获得、肠道定植和随后的 病原体的感染主要取决于功能性微生物-病原体相互作用， 疾病进展和临床结果。重要的是，我们认为鸟枪宏基因组学数据 推断代谢潜力不足以预测和解释定植的易感性， 微生态失调患者中的感染，以及基因组学、宏基因组学、代谢组学和 元蛋白质组学对于阐明病原体、微生物组和 主持人为了使这种多组学方法成为可能，功能基因组学核心（FGC）将提供一个中心的 资源用于此应用程序中包含的所有三个项目，为整个项目提供设施和专业知识 基因组测序、宏基因组学、元蛋白组学和代谢组学。此外，利用强大的 在FGC内的生物信息学基础设施，我们将提供现有的分析应用程序 管道和疾病分类器-以及新型管道的开发-将集成和 便利对每个项目产生的数据进行综合分析。为例 已经建立了一个高吞吐量的管道，用于生成和注释参考质量完全循环 细菌染色体和伴随的质粒，以及伴随的元蛋白质组学数据， 将92%的蛋白质标记定位到了来源基因上总的来说，为了实现 在P01申请中，FGC将承担三个目标：i）协调纯微生物的转移， 从研究地点到FGC的分离物和患者粪便样品; ii）完整的基因组，宏基因组， 每个项目的元蛋白质组学和代谢组学过程;以及iii）协助分析和整合 每个项目产生的多组学数据。FGC提供了一种独特的、无与伦比的能力， 联合收割机多种组学数据类型，以创建一个真正的多组学评估之间的复杂相互作用 VRE、ESBL-E/CRE和C.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。 EQUIPITE程序。

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.