A molecular method for bacterial infection monitoring in bronchiectasis by RNA quantification

Culture-based methods are the standard-of-care for diagnosing bacterial infections in people with (pw) bronchiectasis (BE), but are prone to contamination, are poorly reproducible and can be associated with lengthy time-to-results. Molecular methods such as quantitative PCR (qPCR) offer a quicker, more sensitive, and more reproducible alternative. However, utility of qPCR in this setting depends on the type of nucleic acid targeted. As DNA is relatively stable, assays targeting this molecule may not adequately differentiate viable from dead bacteria. RNA molecules tend to be less stable after cell death offering a potential means to detect only viable bacteria. We have developed RNA targeting qPCR assays for use in detection and monitoring of bacterial infection in pwBE. These assays were successfully tested on sputum; the Pseudomonas aeruginosa assay showed 100% concordance with culture in positive (20/20) and negative (10/10) samples, and the quantity of RNA measured using our test correlated with quantitative culture (range: 1.6-9 Log₁₀ CFU/g). We present data comparing results from our test with quantitative culture and clinical outcome. In addition, we have compared results from the same samples run on our test and on the BIOFIRE Pneumonia panel (bioMerieux), a CE-IVD that provides a semi-quantitative measure of bacterial infection through targeting DNA. We conclude that our RNA-based molecular test is a quantitative alternative to culture that could be used to monitor infection resolution and treatment response, including in the context of eradication treatment. Our test also represents a convenient alternative to quantitative culture for use in the clinical trial setting.