CRISPR detection of circulating cell-free Mycobacterium avium complex (MAC) DNA for rapid diagnosis and monitoring of MAC pulmonary disease

PROJECT SUMMARY/ABSTRACT Nontuberculous mycobacteria (NTM) are opportunistic environmental pathogens that are present in soil and water. NTMpulmonary infections, most commonly due to Mycobacterium avium complex (MAC), may result in chronic, debilitating pulmonary disease (MAC-PD). Treatment, when necessary, consists of 3-4 antibiotics for 14+ months. MAC-PD disproportionately impacts the elderly and women, and those with underlying lung diseases. The prevalence of MAC-PD is increasing, a trend that will likely continue due to aging populations and increased comorbidities. Our lack of disease biomarkers poses significant diagnostic and therapeutic challenges. In contrast with its well-studied cousin tuberculosis (TB), with NTM it is difficult to discern colonization vs. disease caused by these organisms and determine when treatment is necessary or successful. For many patients it is difficult to obtain sufficient respiratory sputum samples to culture for diagnosis or to monitor for microbiologic response during therapy. There is a critical need for non-invasive biomarkers to monitor disease activity and treatment response, in order to limit sputum induction or bronchoscopy procedures and exposure to computed tomography scan radiation. Furthermore, treatment is frequently initiated to improve the patient's symptoms but there is scant data on the correlation of measures of patient-reported outcomes with biomarkers of MAC-PD. The Hu lab has developed an ultra-sensitive CRISPR diagnostic assay using a portable CRISPR-based test to rapidly detect TB cell-free DNA (cfDNA) directly from blood samples. The test allows early TB diagnosis and precisely quantifies TB cfDNA for rapid assessment of disease severity or anti-mycobacterial treatment efficacy. We have preliminary data to suggest this approach can be applied to MAC-PD; accordingly, we seek to evaluate a cfDNA CRISPR-based diagnostic assay (CRISPR-NTM) to diagnose MAC-PD and measure treatment response. We will conduct Aims 1 and 2, analytical and clinical validation of the CRISPR-NTM in patients with MAC-PD during Years 1-2. Aim 2 will use established NTM Biobanks associated with our NTM Clinical Trial Network (OHSU Coordinating Center) to identify a retrospective cohort of patients with MAC-PD and uninfected controls with and without chronic underlying lung disease. During Years 1-4, for Aim 3, we will further utilize our NTM Clinical Trial Network to prospectively collect longitudinal blood samples from patients starting treatment for MAC-PD (NTM-TREAT) from our 1) ongoing pragmatic clinical trial (MAC2v3) and 2) non-MAC2v3 clinic patients representing a broader “real-world” patient population. We will also enroll a pilot cohort at treatment completion (NTM-TRACK), who are subsequently monitored for microbiologic relapse/re-infection. During Years 3-5 we will complete Aim 3 to evaluate the potential for CRISPR-NTM to monitor microbiologic treatment response and relapse/re-infection. Ultimately, the identification of a biomarker for pulmonary MAC-PD and other clinically relevant NTM species will optimize diagnosis and monitoring, and facilitate therapeutic decision-making.