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: 10454640
• 负责人: Faramarz Valafar
• 金额: $ 70.54万
• 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/10454640
• 关键词: Adherence; Antibiotic Therapy; Antibiotics; Antigens; Automobile Driving; Awareness; Bacillus; Bacteria; 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; Immunotherapeutic agent; In Vitro; Infection; Lesion; Liquid substance; Lung; Lung infections; Methods; Methylation; Microbiology; Mosaicism; Mycobacterium tuberculosis; Nature; Necrosis; Operative Surgical Procedures; Patient-Focused Outcomes; Patients; Persons; Pharmaceutical Preparations; Pharmacotherapy; Phenotype; Play; Population; Prevalence; Process; Protocols documentation; Proxy; Recurrence; Resected; Resistance; Role; Sampling; Sequence Analysis; Site; Solid; South Africa; Specific qualifier value; Sputum; Technology; Testing; Time; Transposase; Treatment Failure; Tuberculosis; Vaccines; Variant; World Health Organization; bacterial community; base; chemotherapy; comparative; comparative genomics; epigenomics; genomic biomarker; human pathogen; knowledgebase; lung lesion; methylation biomarker; methylome; methylomics; 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.

结核病（TB）杀死了世界近150万人。尽管有强大的化学治疗药，但生存 细菌通常不会被标准诊断剂发现，持续存在于肺部病变中，并继续使患者疾病， 即使在世界卫生组织标准指定的微生物“治愈”宣布之后。 该项目的目标是表征“（EPI）基因组”（基因组和表观基因组）组成 需要手术干预以治疗结核病的患者的结核分枝杆菌（MTB） （TB），直接在感染部位，并创建一个有助于解释化学疗法失败的知识基础 和标准诊断。这些失败是否是由于痰液中未发现的抗性菌株而引起的？是 肺部病变中有持久的细胞耐受药物压力？药物是否未到达细菌 足够浓度的病变？或在痰中持续或抗性杆菌 未被标准诊断的发现？回答这些问题将使新的以及更多 敏感诊断，为新疗法的开发提供信息，以更有效地渗透病变和 靶向幸存的细菌，或针对所有细菌亚群，并实现理性设计和 开发疫苗，对这种病原体的基因组变异性有更全面的了解 人类感染的背景。 MTB是一种强制性的人类病原体，但治疗决定取决于表型测试和基因组 从痰中分离并在体外生长的细菌作为MTB群落的代理 在肺部驾驶感染。痰液和肺细菌群落之间的不一致已经存在 假设是该疾病错误示例化的原因。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 告知新方法的开发，以提供更全面的诊断。在此过程中，我们还将 确定持久性或超染料是否在治疗失败中起作用，以及频率的频率。 为了实现这些目标，该项目将研究居住在肺部病变内的细菌 传统治疗失败的患者。我们将第一次直接序列，然后从头组装 肺部病变和痰中MTB的基因组和甲基组，并确定区别基因组 这些菌群中每个亚群的表观遗传特征。我们将发现隐藏的阻力或 持久性，并通过差异培养，确定细菌是否已被抗生素损害 治疗以及是否都通过标准诊断检测到它们。我们现有的项目已经确定了小说 快速多元化的机制，使细菌群落能够承受免疫压力和药物压力。 作为该项目的一部分，我们将研究这些机制在肺中的普遍性和性质。这会 为开发更有效和新颖的疗法和疫苗的开发提供新的道路。