Pilot 18 – Cell-free Bacterial DNA to Identify Mycobacterial Lung Pathogens in CF

P.I.: Stephen Salipante, MD, PhD
Associate Professor, Immunology

Much remains unknown about the nature and impact of infectious organisms in the CF lung, and robust biomarkers for assessing patient health are critically needed. Recent work suggests that bacterial cell-free DNA, highly fragmented nucleic acids released from decomposing microbes, can be detected in patient blood during fulminant infections such as sepsis. I have developed novel, ultrasensitive methods for recovering bacterial cell-free DNA from human blood using hybridization capture and next-generation sequencing. My initial results suggest that, using these methods, lung pathogens cultured from CF patients’ sputa can be identified from their cell-free DNA. I will use this approach to test the hypothesis that bacterial cell-free DNA can non-invasively enumerate pathogens present in the lungs of chronically-infected CF patients, and can be used to diagnose nontubercular mycobacterial bacteria (NTM) disease in affected CF patients. The objectives of this study are to begin developing, validating, and exploring the utility of bacterial cell-free DNA as a biomarker of pulmonary health in CF patients, with a special focus on nontubercular mycobacterial bacteria (NTM) disease. In Aim 1, we will develop a hybridization capture panel capable of speciating NTM by expanding our existing 16s rRNA capture panel to include hsp65 and rpoB genes, which provide species-level discrimination within that taxon. In Aim 2, we will optimize methods for recovering and sequencing bacterial cell-free DNA from human blood, and will subsequently validate the ability of bacterial cell-free DNA to identify pathogenic organisms from CF patients with NTM by comparing sequencing results to concurrent sputum culture results. In Aim 3, we will evaluate cell-free bacterial DNA as a diagnostic tool for nontubercular mycobacterial (NTM) disease. NTM is rapidly becoming a major complication in CF patients, but there remain significant challenges in the diagnosis of primary disease, measuring treatment response, differentiating active and indolent infection, and more. We will evaluate the ability of our approach in sensitively and specifically identifying NTM disease from cell-free bacterial DNA, by examining parameters including bacterial species composition and bacterial cell-free DNA abundance per unit blood.