Whole Genome Sequencing of Drug Resistant Tuberculosis in India: Genotype-Phenotype Correlation, Clinical Impact of Resistance, and Sequencing Directly from Sputum

项目总结/摘要 结核病（TB）是全球主要的传染病杀手，印度占全球病例的25%， 印度孟买的耐多药结核病（耐多药结核病，对利福平和异烟肼耐药）。依赖 标准化的治疗方案意味着大多数印度结核病不进行药物敏感性测试（DST） 这导致有效药物的延迟使用，45%的耐多药结核病患者的结果很差。 在一个前瞻性的耐多药结核病患者队列中， 在进行的一项研究中，患者报告的症状出现和耐多药结核治疗之间的平均时间为6个月。其中四 是在诊断之后，但在全面的电阻测试完成之前。在这段时间里， 进展和传播仍在继续，而患者接受的药物没有帮助，许多人遭受严重的 副作用.耐多药结核病治疗项目需要快速、全面的DST，这在印度可以实现 全基因组测序（WGS）K23以患者为导向的职业发展奖 将允许接受者发展研究事业，通过 在一个实施方案中，本发明提供了在临床群组中对患者样品进行WGS和最小抑菌浓度（MIC）测试的组合。 该科学计划将通过评估培养的结核病标本的WGS来评价耐多药结核病的DST， 二线DST方法与基于MIC的DST和标准DST方法的比较; 通过MIC鉴定的低水平耐药、通过WGS鉴定的异质耐药和药代动力学的影响 MDR-TB患者队列中纵向结局的参数;以及 直接从痰液中提取结核分枝杆菌DNA作为DST培养WGS的替代方法这些 目标嵌套在IRB批准的200名成人和青少年患者的纵向队列中， 在孟买的一家私人多专科转诊医院接受治疗。这项指导性研究将培训申请人 生成和分析数据，优化结核病DST，缩短耐多药结核病个体化治疗的时间。 申请人是约翰霍普金斯大学传染病专业的医生， 致力于在资源有限的环境中开展以患者为导向的研究。他花了两年时间开发了一种临床 他在孟买的一群耐多药结核病患者中生活过，并参加了NIH Fogarty全球健康奖学金。他 长期目标是发展WGS数据解释和临床应用于MDRTB的专业知识 最终目标是将WGS转化为有用的临床诊断工具。这K23将有助于技能 开发WGS、MIC和药代动力学数据的生成、分析和解释。培训 将包括正式的课程，监督数据分析，实验室工作，并由一个团队指导， 队列研究、生物信息学、WGS、分枝杆菌学、临床药理学和MDR-TB方面的专业知识 治疗总的来说，这个K23的活动将提供一个独立的职业生涯作为临床 研究人员能够设计、测试和传播新的个性化耐多药结核病治疗方法。

Project Summary / Abstract Tuberculosis (TB) is the primary infectious disease killer worldwide, with 25% of global cases in India and 12% of India's multidrug-resistant TB (MDR-TB, resistant to rifampin and isoniazid) in Mumbai. Reliance on standardized treatment regimens means drug susceptibility testing (DST) is not performed for most Indian TB patients at diagnosis, resulting in delayed use of effective drugs, and poor outcomes for 45% of MDR-TB patients. In a prospective cohort of MDR-TB patients cared for at the specialty referral center where this K23 will be conducted, the average patient reports 6 months between symptom onset and MDR-TB treatment. Four of these are after diagnosis, but before comprehensive resistance testing is completed. This is time during which disease progression and transmission continue, while patients receive drugs that don't help and many suffer significant side effects. MDR-TB treatment programs need rapid, comprehensive DST, which can be achieved in India through whole genome sequencing (WGS). This K23 Mentored Patient-Oriented Career Development Award will allow the recipient to develop a research career pursuing more comprehensive, rapid diagnosis through the combination of WGS and minimum inhibitory concentration (MIC) testing of patient samples in a clinical cohort. This scientific plan will evaluate DST for MDR-TB through an assessment of WGS of cultured TB specimens as a method of second-line DST in comparison to MIC-based DST and standard DST methods; an assessment of the impact of low-level resistance identified by MIC, hetero-resistance identified by WGS, and pharmacokinetic parameters on longitudinal outcomes in a cohort of MDR-TB patients; and an assessment WGS of Mycobacterium tuberculosis DNA directly from sputum as an alternative to culture-based WGS for DST. These aims are nested in an IRB-approved longitudinal cohort of 200 adult and adolescent patients initiating treatment for MDR-TB at a private multispecialty referral hospital in Mumbai. This mentored research will train the applicant to generate and analyze data optimizing DST for TB and shortening time to individualized therapy for MDR-TB. The applicant is an Infectious Diseases-trained physician at Johns Hopkins University with a longstanding commitment to patient-oriented research in resource-limited settings. He has spent 2 years developing a clinical cohort of MDR-TB patients in Mumbai, where he has lived through an NIH Fogarty Global Health Fellowship. His long-term goals are to develop expertise in the interpretation and clinical application of WGS data to MDRTB with the ultimate goal of translating WGS into a useful clinical diagnostic tool. This K23 will facilitate skill development in the generation, analysis, and interpretation of WGS, MIC, and pharmacokinetic data. Training will include formal coursework, supervised data analysis, laboratory work, and mentorship by a team with expertise in cohort studies, bioinformatics, WGS, mycobacteriology, clinical pharmacology, and MDR-TB treatment. Collectively, the activities of this K23 will provide a pathway to an independent career as a clinical investigator able to design, test, and disseminate novel personalized approaches to the therapy of MDR-TB.