Development and validation of a sample-to-answer metagenomics workflow for comprehensive pathogen detection in central nervous system infections

开发和验证用于中枢神经系统感染中全面病原体检测的样本到答案宏基因组学工作流程

• 批准号: 10384637
• 负责人: Stephane Gourguechon
• 金额: $ 99.77万
• 依托单位: ARC BIO, LLC
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-02-02 至 2024-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10384637
• 关键词: Academic Medical Centers; Acute; Address; Adopted; Adoption; American; Bacteria; Bioinformatics; Biological Assay; Biotechnology; Businesses; Central Nervous System Infections; Cerebrospinal Fluid; Characteristics; Clinical; Clinical Microbiology; Communicable Diseases; Computer software; Contracts; DNA; DNA sequencing; Data; Detection; Development; Diagnosis; Diagnostic; Diagnostic Procedure; Diagnostic tests; Differential Diagnosis; Encephalitis; Future; Genomics; Goals; Health; Hour; Human; Infection; Instruction; Laboratories; Lead; Libraries; Manufacturer Name; Meningitis; Metagenomics; Microbe; Mission; Modeling; Morbidity - disease rate; Organism; Outcome; Parasites; Pathogen detection; Patients; Performance; Pharmacologic Substance; Phase; Physicians; Plasma; Preparation; Process; Prognosis; Protocols documentation; RNA; Reagent; Recording of previous events; Reporting; Research; Research Personnel; Sales; Sampling; Sensitivity and Specificity; Small Business Innovation Research Grant; Symptoms; Technical Expertise; Technology; Testing; Time; Universities; Validation; Variant; Virus; Work; accurate diagnosis; base; bioinformatics pipeline; clinically relevant; commercial application; commercialization; cost; detection method; disease diagnostic; effective therapy; fungus; improved; improved outcome; ineffective therapies; manufacturing process; metagenomic sequencing; microbial; molecular diagnostics; mortality; next generation sequencing; pathogen; pathogenic bacteria; pathogenic fungus; pathogenic virus; product development; rapid diagnosis; sequencing platform; standard of care; targeted treatment; tool; user-friendly

ABSTRACT This research will ultimately advance human health by improving the diagnosis and treatment of central nervous system infections including meningitis and encephalitis, where the causative pathogen is not identified in up to 50% of cases. These infections are associated with significant morbidity and mortality; therefore, rapid and accurate diagnosis is crucial for appropriate patient management and to improve outcomes. Unfortunately, due to the variety of organisms that can cause central nervous system infections, current standard of care diagnostic methods suffer from long turnaround times and high false negative rates. Metagenomic next- generation sequencing (mNGS) has emerged as a promising universal detection method for infectious disease, enabling the simultaneous identification and characterization of viral, bacterial, and fungal pathogens directly from the DNA/RNA present in clinical samples. However, despite the increasing adoption of molecular diagnostics in clinical microbiology labs, mNGS has not become widespread due to its cost, turnaround time, and the technical expertise required to produce and analyze the data. The product we are developing addresses all of these obstacles. Galileo ONE – CSF is a sample-to-answer platform that includes all of the reagents, controls, protocols, and software required to detect and report clinically relevant pathogens directly from a cerebrospinal fluid (CSF) sample in ~24 hours. This platform incorporates several proprietary technologies, including a library preparation module that reduces abundant human sequences and a quantitative bioinformatics pipeline that increases sensitivity for sequence variants. This all-in-one bundle allows labs to easily evaluate and adopt mNGS in their own laboratories without the need for extensive genomics or bioinformatics expertise. During our Phase I-equivalent work, we used contrived samples to assess the feasibility of using CSF as a sample type; the results show that we can generate high-quality libraries and detect a representative set of pathogens in CSF using our Galileo ONE workflow, which was initially validated on plasma. Therefore, we are ready to move into the development phase of the product development process. In Phase II, we will perform analytical and preliminary clinical validation of the Galileo ONE – CSF platform, complete development of CSF-specific kit controls, and perform beta testing on contrived and clinical samples with our collaborators. This product will be the first deployed mNGS platform validated for CSF, enabling us to take advantage of the growing market for NGS-based infectious disease diagnostics, which is expected to reach $2.1B by 2027. Galileo ONE – CSF will empower end users, who include researchers, reference laboratories, and pharma/biotech partners, to adopt metagenomics to address the current gap in tools for detecting central nervous system infections.

摘要 这项研究最终将通过改善中枢神经系统疾病的诊断和治疗来促进人类健康。 神经系统感染，包括脑膜炎和脑炎，其中致病病原体尚未确定 在高达50%的情况下。这些感染与显着的发病率和死亡率相关;因此，迅速 准确的诊断对于适当的患者管理和改善结果至关重要。不幸的是， 由于可引起中枢神经系统感染的微生物种类繁多， 诊断方法的缺点是周转时间长和假阴性率高。宏基因组学下一步- 第二代测序（mNGS）已经成为一种有前途的通用检测方法， 疾病，能够同时识别和表征病毒，细菌和真菌病原体 直接从临床样品中存在的DNA/RNA中提取。然而，尽管越来越多地采用分子生物学， 在临床微生物实验室的诊断中，mNGS由于其成本，周转时间， 以及生成和分析数据所需的技术专业知识。我们正在开发的产品 解决所有这些障碍。Galileo ONE - CSF是一个样本到答案的平台， 直接检测和报告临床相关病原体所需的试剂、对照品、方案和软件 脑脊液（CSF）样本在约24小时内。该平台集成了多个专有 技术，包括减少丰富的人类序列的文库制备模块和 定量生物信息学管道，增加了对序列变异的敏感性。这个一体化的包裹 允许实验室在自己的实验室中轻松评估和采用mNGS，而无需进行广泛的 基因组学或生物信息学专业知识。在我们的第一阶段等效工作中，我们使用人造样本， 评估使用CSF作为样本类型的可行性;结果表明，我们可以生成高质量的 库，并使用我们的Galileo ONE工作流程检测CSF中的一组代表性病原体， 最初在血浆中验证。因此，我们准备进入产品的开发阶段 发展过程在第二阶段，我们将对Galileo进行分析和初步临床验证。 ONE - CSF平台，完成CSF特异性试剂盒质控品的开发，并对人工 和临床样本。该产品将是第一个经过验证的部署mNGS平台， CSF，使我们能够利用不断增长的市场，为基于NGS的传染病诊断， 预计到2027年将达到21亿美元。Galileo ONE - CSF将为终端用户提供支持， 研究人员，参考实验室和制药/生物技术合作伙伴，采用宏基因组学来解决 目前在检测中枢神经系统感染的工具方面存在差距。