Rapid Detection of TB from Blood using Cell-Free DNA and CRISPR

使用无细胞 DNA 和 CRISPR 快速检测血液中的结核病

• 批准号: 10620065
• 负责人: Richard S Garfein
• 金额: $ 79.52万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-17 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10620065
• 关键词: Address; Adult; Affinity; Aftercare; Arkansas; Binding; Biological Assay; Biological Markers; Blood; Blood Tests; Blood specimen; COVID-19; California; Cessation of life; Child; Childhood; Clinical; Clinical Research; Clinical Sensitivity; Clustered Regularly Interspaced Short Palindromic Repeats; Collaborations; Communicable Diseases; Cryopreservation; DNA; DNA Binding; Detection; Diagnosis; Diagnostic; Diagnostic Sensitivity; Diagnostic Specificity; Disease; Drug resistance in tuberculosis; Extinction; Fluorescence; Goals; Growth; HIV; Immunocompromised Host; Laboratories; Lateral; Lung diseases; Mexico; Microscopy; Molecular; Monitor; Mycobacterium tuberculosis; Nonlinear Dynamics; Pakistan; Paper; Patient-Focused Outcomes; Patients; Pediatrics; Performance; Persons; Pharmaceutical Preparations; Pilot Projects; Predisposition; Process; Proteins; Reader; Reference Standards; Reporter; Reporting; Research; Resource-limited setting; Risk; Sampling; Sensitivity and Specificity; Signal Transduction; South Africa; Specificity; Sputum; Testing; Triage; Tuberculosis; Tuberculosis diagnosis; United States National Institutes of Health; Universities; accurate diagnosis; biobank; cell free DNA; co-infection; cohort; cost; cross reactivity; detection assay; detection limit; diagnostic criteria; innovation; isothermal amplification; lateral flow assay; molecular diagnostics; mortality; non-tuberculosis mycobacteria; novel; nuclease; peripheral blood; point-of-care diagnostics; prospective; rapid detection; rapid diagnosis; rapid test; technology platform; transmission process; tuberculosis diagnostics; tuberculosis treatment

Project Summary While >90% of TB cases are curable, treatment is dependent on diagnostics based exclusively on the detection of Mycobacterium tuberculosis (Mtb) in patient sputum, despite the limitations of sputum as a diagnostic sample. Sputum is difficult to process, almost impossible to obtain from patients with paucibacillary TB, such as people living with HIV (PLWH) and children and is not diagnostic for patients with extrapulmonary TB. A low- cost, rapid test using blood instead of sputum could transform TB diagnosis for ALL patients and reduce the current diagnostic gap between patients with and without HIV co-infection. Most active TB disease (ATB) is still diagnosed with sputum smear microscopy, despite its low sensitivity and specificity. This lack of diagnostic rigor contributes to the ongoing underdiagnosis of ~3 million TB cases/year, resulting in continued transmission and poor patient outcomes, especially among PLWH in whom mortality is highest. Our long-term goal is to transform TB diagnosis with a blood test that accurately distinguishes patients with ATB from latent TB infection (LTBI), and other pulmonary disorders regardless of co-infection with HIV. The objective of this study is to demonstrate the analytical and clinical performance of a novel assay for rapid diagnosis and treatment monitoring of ATB that exploits the precise molecular affinity of CRISPR and promiscuous nuclease activity of Cas12a to detect ultra-low concentrations of Mtb cell free DNA (cfDNA) circulating in blood. Preliminary analytical studies indicate assay detection limits of <1fg/µL of Mtb cfDNA in blood and no cross-reactivity with non-tuberculosis mycobacteria (NTM) DNA. Preliminary clinical studies including adults and children with presumptive TB, as well as samples from a diagnostically challenging cohort of symptomatic immunocompromised children living with HIV, demonstrated high diagnostic sensitivity and specificity in a pooled adult and pediatric group (>90%), and high diagnostic sensitivity (85%) in children. We will achieve our proposed objective through the following specific aims: AIM 1: Validate a lateral flow version of the CRISPR-TB assay for low resource settings. Our current working assay requires a PCR step and fluorescence reader. Preliminary studies indicate we can significantly simplify this workflow using isothermal amplification and a novel lateral flow (LF) strip for detection of Mtb cfDNA. We will expand on our pilot studies to validate the existing LF assay using contrived and clinical samples. AIM 2: Define the dynamics of the Mtb cfDNA signal for treatment monitoring. Preliminary studies indicate the Mtb cfDNA signal decreases to extinction after treatment initiation but can have non-linear dynamics. We will define the variability and trajectory of the Mtb cfDNA signal in biobanked serial samples from 34 patients treated for drug resistant TB over a year, and 50 prospectively collected patients with drug susceptible TB treated over six months. AIM 3: Determine the clinical sensitivity and specificity of the CRISPR-TB assay in field settings. We will prospectively collect and test blood samples from 450 patients at risk for TB in TB-endemic field settings with high (South Africa), medium (Pakistan) and low (Mexico) HIV burden.

项目摘要 虽然90%以上的结核病例是可以治愈的，但治疗依赖于完全基于检测的诊断。 尽管痰液作为诊断手段存在局限性，但患者痰液中结核杆菌（Mtb）的检测 sample.痰液很难处理，几乎不可能从少杆菌结核病患者那里获得，例如 艾滋病毒感染者（PLWH）和儿童，不能诊断为肺外结核患者。一个低- 使用血液而不是痰液进行快速检测可以改变ALL患者的结核病诊断， 减少目前合并感染和未合并感染艾滋病毒的患者之间的诊断差距。最活跃的结核病 尽管敏感性和特异性较低，但ATB仍然通过痰涂片显微镜进行诊断。这 缺乏诊断的严谨性导致每年约300万结核病例的诊断不足， 艾滋病毒/艾滋病继续传播和病人预后不良，特别是在死亡率最高的艾滋病毒携带者和艾滋病患者中。我们 长期目标是通过准确区分ATB患者的血液检测来改变结核病诊断 潜伏性TB感染（LTBI）和其他肺部疾病，无论是否与HIV合并感染。的 本研究的目的是证明一种新的快速检测方法的分析和临床性能。 利用CRISPR的精确分子亲和力进行ATB的诊断和治疗监测， Cas 12 a的混杂核酸酶活性检测超低浓度的Mtb细胞游离DNA（cfDNA） 在血液中循环。初步的分析研究表明，Mtb cfDNA的测定检测限<1fg/µL， 与非结核分枝杆菌（NTM）DNA无交叉反应。初步临床研究 包括患有推定结核病的成人和儿童，以及来自诊断具有挑战性的队列的样本 有症状的免疫功能低下的儿童感染艾滋病毒，表现出较高的诊断敏感性， 在成人和儿童组中具有特异性（>90%），在儿童中具有高诊断灵敏度（85%）。我们 将通过以下具体目标实现我们提出的目标：AIM 1：侧流版本 的CRISPR-TB测定。我们目前的工作测定需要PCR步骤， 荧光读数器。初步研究表明，我们可以大大简化这一工作流程， 扩增和用于检测Mtb cfDNA的新型侧向流动（LF）条。我们将扩大我们的试点研究 使用人工样本和临床样本验证现有LF检测。目标2：确定结核分枝杆菌的动力学 用于治疗监测的cfDNA信号。初步研究表明，Mtb cfDNA信号降低至 治疗开始后消失，但可能具有非线性动力学。我们将定义可变性， 来自34名接受耐药TB治疗的患者的生物库系列样品中Mtb cfDNA信号的轨迹 50名前瞻性收集的药物敏感结核病患者接受了6个月以上的治疗。目标3： 确定CRISPR-TB测定在现场环境中的临床灵敏度和特异性。我们将 前瞻性地收集和检测结核病流行现场环境中450名有结核病风险的患者的血液样本， 高（南非）、中（巴基斯坦）和低（墨西哥）艾滋病毒负担。