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央的诊断和治疗来改善人类健康 神经系统感染，包括脑膜炎和脑炎，未鉴定出病原体 在多达50％的案件中。这些感染与明显的发病率和死亡率有关。因此，快速 准确的诊断对于适当的患者管理和改善结果至关重要。很遗憾， 由于可能引起中枢神经系统感染的各种生物，因此当前的护理标准 诊断方法遭受较长的周转时间和高的假负率。宏基因组接下来 - 生成测序（MNG）已成为传染性的有望通用检测方法 疾病，使病毒，细菌和真菌病原体的同时鉴定和表征 直接来自临床样品中存在的DNA/RNA。然而，尽管分子的采用越来越高 临床微生物学实验室的诊断，MNGS的成本，周转时间， 以及生产和分析数据所需的技术专长。我们正在开发的产品 解决所有这些障碍。伽利略One - CSF是一个样本与回答平台，包括所有 直接检测和报告临床相关病原体所需的试剂，控制，协议和软件 来自脑脊液（CSF）样品在〜24小时内。该平台包含了几个专有 技术，包括库的制备模块，该模块减少了丰富的人类序列和 定量生物信息学管道增加了对序列变体的敏感性。这个多合一的捆绑包 允许实验室在自己的实验室中轻松评估和采用MNG，而无需广泛 基因组学或生物信息学专业知识。在我们的阶段I等效工作中，我们使用了贡献样本 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 使用我们的Galileo One Workflow，图书馆并检测CSF中的一组代表性病原体 最初在血浆上验证。因此，我们准备进入产品的开发阶段 发展过程。在第二阶段，我们将对伽利略进行分析和初步临床验证 一个 - CSF平台，CSF特异性套件控制的完整开发，并对贡献进行Beta测试 和我们的合作者临床样本。该产品将是验证的第一个部署的MNGS平台 CSF，使我们能够利用基于NGS的传染病诊断的不断增长的市场， 预计到2027年将达到$2.1B。GalileoOne - CSF将授权最终用户，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 当前用于检测中枢神经系统感染的工具差距。