Bacterial quantification assay to detect and monitor Pseudomonas aeruginosa infection in patients with bronchiectasis

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Abstract Background Pseudomonas aeruginosa (PA) is the most commonly detected pathogen in bronchiectasis. The clinical standard of care for pathogen detection is culture, which has low sensitivity. Early detection and improved monitoring could be used to enhance eradication and long-term suppressive treatments. Methods A novel bacterial quantification assay (BQA) targeting ribosomal RNA for the detection of viable PA was developed. The BQA sensitivity and specificity in patient samples was assessed utilising culture (n=57); as well as BioFire pneumonia panel (n=111) and 16S rRNA gene sequencing (n=62). The potential clinical impact of the BQA in clinical settings was explored using two international patient cohorts. Results The BQA detected PA in 100% of samples where PA was identified by other methods. The BQA quantification was positively correlated with quantitative culture (r=0.42; p<0.001) and BioFire (r=0.68; p<0.001). The BQA identified PA in an additional 23-44% of cases. To evaluate if this increased detection had clinical implications, we tested sputum samples considered to be PA negative by culture in patients who subsequently tested positive for PA. The BQA detected PA in 8/20 patient samples 8-484 days prior to primary detection by culture. In patients considered to have successful PA eradication by culture, the BQA detected PA in 13 samples from 27 patients who went on to relapse. Conclusions The BQA is a highly sensitive detection and quantification method for PA. The BQA demonstrated improved detection and treatment monitoring compared to culture, identifying patients who went on to either isolate a first PA or relapse.

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