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: 10560552
• 负责人: Stephane Gourguechon
• 金额: $ 93.11万
• 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/10560552
• 关键词: Academic Medical Centers; Acceleration; 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; Libraries; Manufacturer; Marketing; 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; bioinformatics pipeline; clinically relevant; commercial application; commercial launch; commercialization; cost; detection method; disease diagnostic; effective therapy; empowerment; 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.

抽象的 这项研究最终将通过改善中枢神经系统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，其致病病原体尚未确定 在高达 50% 的病例中，这些感染与显着的发病率和死亡率相关； 不幸的是，准确的诊断对于适当的患者管理和改善结果至关重要。 由于可引起中枢神经系统感染的微生物种类繁多，目前的护理标准 诊断方法存在周转时间长和假阴性率高的问题。 世代测序（mNGS）已成为一种有前途的传染性通用检测方法 疾病，能够同时识别和表征病毒、细菌和真菌病原体 然而，尽管越来越多地采用分子技术。 临床微生物学实验室的诊断中，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。 Galileo ONE – CSF 是一个从样本到答案的平台，涵盖了所有这些障碍。 直接检测和报告临床相关病原体所需的试剂、控制、方案和软件 大约 24 小时内从脑脊液 (CSF) 样本中提取该平台包含多项专有技术。 技术，包括减少丰富人类序列的文库制备模块和 定量生物信息学管道，可提高序列变异的敏感性。 允许实验室在自己的实验室中轻松评估和采用 mNGS，而不需要大量的 在我们的第一阶段等效工作中，我们使用了基因组学或生物信息学专业知识。 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样本 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，该工作流程是 最初在血浆上进行了验证，因此，我们已准备好进入该产品的开发阶段。 在第二阶段的开发过程中，我们将对伽利略进行分析和初步临床验证。 ONE – CSF 平台，完成 CSF 特定试剂盒对照的开发，并对人为进行 beta 测试 以及与我们的合作者合作的临床样本，该产品将是第一个经过验证的部署 mNGS 平台。 CSF 使我们能够利用基于 NGS 的传染病诊断不断增长的市场， 预计到 2027 年将达到 $2.1B。 Galileo ONE – CSF 将为最终用户提供支持，其中包括 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 目前检测中枢神经系统感染的工具存在差距。