A novel cartridge-based sequencing solution for decentralized M. tuberculosis resistance detection

一种新型的基于盒的测序解决方案，用于分散结核分枝杆菌耐药性检测

• 批准号: 10719138
• 负责人: Soumitesh Chakravorty
• 金额: $ 73.04万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-07 至 2028-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10719138
• 关键词: Acceleration; Address; Antimicrobial Resistance; Bar Codes; Biological Assay; Biological Containment; Calibration; Capital; Cause of Death; Cells; Characteristics; Clinical; Clinical Management; Clinical Trials; Clinical assessments; Complex; Containment; Country; Cytolysis; DNA; Data; Decentralization; Detection; Development; Diagnostic; Drug Targeting; Drug resistance in tuberculosis; Evaluation; Fluoroquinolones; Funding; Genes; Genetic; Goals; Growth; HIV; Health Status; Healthcare; Hot Spot; Industry Standard; Infrastructure; Investments; Laboratories; Length; Libraries; Linezolid; Longevity; Methods; Microfluidics; Molecular; Mycobacterium tuberculosis; Oral; Patient-Focused Outcomes; Patients; Pharmaceutical Preparations; Pharmacotherapy; Phenotype; Philippines; Predisposition; Preparation; Pyrazinamide; Pyrazinamide resistance; Reagent; Recommendation; Reference Standards; Regimen; Research; Resistance; Resistance profile; Rifampicin resistance; Sampling; Sensitivity and Specificity; South Africa; Specimen; Speed; Sputum; System; Technical Expertise; Technology; Testing; Time; Treatment Protocols; Treatment outcome; Tuberculosis; United States National Institutes of Health; biobank; clinical application; cost; drug repurposing; genome sequencing; genomic locus; improved; improved outcome; industry partner; ineffective therapies; nanopore; next generation sequencing; novel; portability; preservation; primary outcome; product development; programs; prospective; prototype; public health emergency; public health relevance; sample collection; scale up; secondary outcome; sequencing platform; success; tuberculosis diagnostics; tuberculosis drugs; tuberculosis treatment; whole genome

A novel cartridge-based sequencing solution for decentralized M. tuberculosis resistance detection Rifampin-resistant tuberculosis (RR-TB) is one of the principal causes of death associated with antimicrobial resistance. Newer all oral bedaquiline-containing RR-TB regimens, now recommended worldwide, will shorten treatment and improve outcomes. However, the lack of timely drug susceptibility data due to the slow growth rate of M. tuberculosis and the need for high containment biological laboratories are major barriers to scale-up of bedaquiline and other new and repurposed drugs. Xpert MTB/RIF Ultra and other commercial molecular TB tests can identify rifampin resistance, but cannot inform complete treatment regimens because they are limited to analyzing only a small number of genetic loci (i.e., “hot spots”). Targeted next-generation sequencing (NGS) is able to sequence entire genes rapidly without need for culture, and therefore could transform RR-TB clinical management. Achieving near-patient clinical application, however, has two major bottlenecks: (1) a complex, unstandardized workflow for preparing clinical samples for NGS, and (2) the cost and infrastructure requirements of industry-standard Illumina platforms. Partnering with global TB diagnostics leader Cepheid, we address these barriers by utilizing the ultrasonication, microfluidics, and thermocycler capabilities of the existing Xpert Ultra cartridge, already in use in over 180 countries, to unite a vetted direct-sample-to-answer system with a nanopore gene sequencing platform for the first time. Xpert CartSeq, a pioneering cartridge- based sequencing solution suitable for lower levels of healthcare, achieves robust DNA extraction and sophisticated library preparation while minimizing user variability and mitigating technical skill requirements. Through its development as detailed in this proposal, we aim to catalyze the clinical application of NGS in high burden settings.

一种基于墨盒的新型测序溶液，用于分散结核分枝杆菌耐药性检测 抗利福平的结核病（RR-TB）是用抗菌剂的印刷品之一 阻力。 但是，由于速度增长而缺乏及时的药物敏感性数据 结核分枝杆菌的发生率和对高贡献生物实验室的需求是扩大规模的主要障碍 Bedaquiline和其他新的和再利用的药物。 测试可以识别利福平的抵抗力，但不能为完整的治疗提供信息，因为它们是有限的 仅分析少量的遗传基因座（即“热点”）。 能够快速对整个基因进行测序，而无需培养，因此可以临床 管理，实现近乎敏感的临床应用有两个主要的瓶颈：（1） 为NGS准备临床样本的非标准化工作流程，以及（2）成本和基础设施 行业标准的Illumina平台与全球结核病诊断领导者合作 通过利用超声波，微流体和热圈能力来解决障碍 现有的Xpert Ultra墨盒，在180多个国家 /地区使用的Allyady，以审查样本到对面的样本 首次具有纳米孔基因测序平台的系统。 基于适用于医疗水平水平的基于的测序解决方案，可实现可靠的DNA提取和 精致的图书馆准备，同时最大程度地减少用户可变性并减轻技术技能要求。 通过此提案中详细的开发，我们旨在促进NGS的临床应用 负担设置。