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 利福平耐药结核病 (RR-TB) 是与抗菌药物相关的死亡主要原因之一 反抗。目前全球推荐的新型全口服含贝达喹啉 RR-TB 治疗方案将缩短 治疗并改善结果。但由于生长缓慢，缺乏及时的药敏数据 结核分枝杆菌的发病率和对高防护生物实验室的需求是扩大规模的主要障碍 贝达喹啉和其他新的和重新利用的药物。 Xpert MTB/RIF Ultra 和其他商业分子 TB 测试可以识别利福平耐药性，但不能告知完整的治疗方案，因为它们是有限的 仅分析少量遗传位点（即“热点”）。靶向下一代测序（NGS） 能够快速对整个基因进行测序，无需培养，因此可以改变 RR-TB 的临床 管理。然而，实现近患者临床应用有两个主要瓶颈：（1）复杂的、 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 Illumina 平台的要求。我们与全球结核病诊断领导者 Cepheid 合作 通过利用超声处理、微流体和热循环仪功能来解决这些障碍 现有的 Xpert Ultra 试剂盒已在 180 多个国家/地区使用，以统一经过审查的直接样本到答案 首次配备纳米孔基因测序平台的系统。 Xpert CartSeq，一种开创性的试剂盒 - 基于测序的解决方案适用于较低水平的医疗保健，实现稳健的 DNA 提取和 复杂的文库制备，同时最大限度地减少用户差异并降低技术技能要求。 通过本提案中详述的开发，我们的目标是促进 NGS 在高风险领域的临床应用。 负担设置。