Undetected Drug resistance and Tolerance in lesions of recurrent TB

复发性结核病灶中未检测到的耐药性和耐受性

• 批准号: 10656341
• 负责人: Faramarz Valafar
• 金额: $ 69.83万
• 依托单位: SAN DIEGO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10656341
• 关键词: Adherence; Antibiotic Therapy; Antibiotics; Antigens; Automobile Driving; Awareness; Bacillus; Bacteria; Biological; Catalogs; Cells; Characteristics; Clinical; Communities; DNA Methylation; Day Surgery; Detection; Development; Diagnostic; Differentiation Antigens; Disease; Drug Tolerance; Drug resistance; Elements; Ensure; Epigenetic Process; Excision; Failure; Genes; Genetic Recombination; Genetic Variation; Genome; Genomic approach; Genomics; Genotype; Goals; Heterogeneity; Human; Immune; In Vitro; Infection; Lesion; Liquid substance; Lung; Lung infections; Methods; Methylation; Mycobacterium tuberculosis; Nature; Necrosis; Operative Surgical Procedures; Patient-Focused Outcomes; Patients; Penetration; Persons; Pharmaceutical Preparations; Pharmacotherapy; Phenotype; Population; Predisposition; Prevalence; Process; Protocols documentation; Proxy; Recurrence; Reporting; Resected; Resistance; Sampling; Sequence Analysis; Site; Solid; South Africa; Specific qualifier value; Sputum; Technology; Testing; Therapeutic; Time; Transposase; Treatment Failure; Tuberculosis; Vaccines; Variant; World Health Organization; bacterial community; chemotherapy; comparative; comparative genomics; drug repurposing; epigenomics; genomic biomarker; human pathogen; knowledgebase; lung lesion; methylation biomarker; methylome; methylomics; mosaic; new therapeutic target; next generation; novel; novel diagnostics; novel therapeutics; novel vaccines; outcome prediction; pathogen; pressure; prognostic; rational design; resistance mechanism; resistant strain; superinfection; tuberculosis chemotherapy; tuberculosis diagnostics; tuberculosis treatment; vaccine development

Tuberculosis (TB) kills nearly 1.5 million people in the world. Despite powerful chemotherapeutics, surviving bacteria often go undetected by standard diagnostics, persist in lung lesions, and continue to make patients ill, even after declaration of microbiological “cure” as specified by criteria from the World Health Organization. This project’s objective is to characterize the “(epi)genomic” (genomic and epigenomic) composition of Mycobacterium tuberculosis (Mtb) in patients who require surgical intervention for treatment of tuberculosis (TB), directly at the site of infection, and to create a knowledgebase that helps explain failure of chemotherapy and standard diagnostics. Are these failures due to undetected resistant strains absent in the sputum? Were there persister cells in pulmonary lesions that tolerated the drug pressure? Did drugs not reach bacteria within the lesion in sufficient concentrations? Or were persistent or resistant bacilli in the sputum that went undetected by standard diagnostics? Answering these questions will enable the development of new and more sensitive diagnostics, inform development of novel therapeutics that to more effectively penetrate lesions and target the surviving bacteria, or target all bacterial subpopulations, and enable rational design and development of a vaccine with a more comprehensive understanding of genomic variability of this pathogen in the context of human infection. Mtb is an obligate human pathogen, yet treatment decisions hinge on phenotypic testing and genomic characterization of bacteria isolated from sputum and grown in vitro as a proxy for the Mtb communities driving infection in the lungs. Inconsistencies between the sputum and lung bacterial communities have been hypothesized as reasons behind the mischaracterization of the disease. In this project, we investigate this hypothesis and, additionally, aim to determine whether there are additional bacteria in the sputum that can inform development of novel methods to provide more comprehensive diagnostics. In this process, we will also determine whether persistence or superinfection played a role in treatment failure, and how frequently. To reach these goals, this project will study bacteria residing within pulmonary lesions excised from 200 patients who failed traditional treatment. For the first time, we will directly sequence, and de novo assemble genomes and methylomes of Mtb in pulmonary lesions and sputum, and determine the distinguishing genomic and epigenetic characteristics of each subpopulation in these flora. We will detect hidden resistance or persistence, and, through differential culturing, identify whether bacteria have been damaged by antibiotic treatment and whether they are all detected by standard diagnostics. Our existing project has identified novel rapid diversifying mechanisms that allows the bacterial community to withstand immune and drug pressures. As part of this project, we will investigate the prevalence and nature of these mechanisms in the lung. This will inform new paths to development of more effective and novel therapeutics and vaccines.

尽管有强大的化疗药物，结核病 (TB) 仍导致世界上近 150 万人死亡。 标准诊断方法常常无法检测到细菌，它们持续存在于肺部病变中，并继续使患者患病， 即使在世界卫生组织标准规定的微生物“治愈”声明之后。 该项目的目标是表征“（表观）基因组”（基因组和表观基因组）的组成 需要手术干预治疗结核病的患者中存在结核分枝杆菌 (Mtb) （结核病），直接在感染部位，并创建一个有助于解释化疗失败的知识库 这些失败是否是由于痰液中不存在未检测到的耐药菌株所致？ 肺部病变中是否存在能够耐受药物压力的持久细胞？药物是否无法到达其中的细菌？ 或者痰液中是否存在持续存在或耐药的杆菌？ 未被标准诊断检测到？回答这些问题将有助于开发新的和更多的产品。 敏感的诊断，为新疗法的开发提供信息，以更有效地穿透病变并 针对存活的细菌，或针对所有细菌亚群，并实现合理的设计和 开发一种疫苗，更全面地了解该病原体的基因组变异性 人类感染的背景。 结核分枝杆菌是一种人类固有病原体，但治疗决策取决于表型测试和基因组 从痰液中分离并在体外生长的细菌的特征，作为 Mtb 群落的代表 导致肺部感染。痰液和肺部细菌群落之间存在不一致。 在这个项目中，我们对此进行了调查。 假设，此外，旨在确定痰中是否还有其他细菌可以 在此过程中，我们还将通知开发新方法以提供更全面的诊断。 确定持续性或重复感染是否导致治疗失败以及发生频率。 为了实现这些目标，该项目将研究 200 例肺病灶中存在的细菌。 传统治疗失败的患者，我们将首次直接测序，从头组装。 肺部病变和痰液中 Mtb 的基因组和甲基化组，并确定区分基因组 我们将检测这些菌群中每个亚群的隐藏耐药性和表观遗传特征。 持久性，并通过差异培养，鉴定细菌是否被抗生素破坏 治疗以及它们是否都可以通过标准诊断检测到。 快速多样化机制使细菌群落能够承受免疫和药物压力。 作为该项目的一部分，我们将研究这些机制在肺部的普遍性和性质。 为开发更有效和治疗性的小说和疫苗提供新途径。