Analysis of Pseudomonas aeruginosa transcription in an ex vivo cystic fibrosis sputum model

Chronic Pseudomonas aeruginosa lung infections are a distinctive feature of cystic fibrosis (CF) pathology, especially for adults with CF. Even with the advent of highly effective modulator therapies, which have dramatically improved clinical outcomes, many patients continue to experience chronic infections that can limit the positive impact of these drugs. Characterizing P. aeruginosa transcription in the CF lung and identifying the biological factors that drive gene expression could yield novel strategies to eradicate infection. However, the vast majority of studies measure P. aeruginosa gene expression in laboratory culture models, which may not fully reproduce the transcriptional profile active in the CF lung environment. To more accurately reproduce this profile, we employed an ex vivo sputum model in which laboratory strain PAO1 was incubated in sputum from CF donors. We compared PAO1 gene expression in the spike-in model to artificial sputum medium (ASM), and determined the top differentially expressed genes, functional terms, and correlated gene sets that are uniquely characteristic of incubation in real CF sputum compared to ASM. Many of the most differentially active transcriptional features in real CF sputum were related to zinc and iron acquisition, suggesting that P. aeruginosa transcription in the CF lung is characterized by a metal restriction response that laboratory models of CF sputum do not adequately represent. Future studies should consider the use of an ex vivo sputum model or amending ASM with factors that induce metal restriction.