Establishment and characterization of a newPseudomonas aeruginosainfection model using 2D airway organoids and dual RNA sequencing

Abstract

AbstractPseudomonas aeruginosais a Gram-negative bacterium that is notorious for infections in the airway of cystic fibrosis (CF) subjects. Often, these infections become chronic, leading to higher morbidity and mortality rates. Bacterial quorum sensing (QS) coordinates the expression of virulence factors and the formation of biofilms at a population level. QS has become the focus of attention for development of alternatives to antimicrobials targetingP. aeruginosainfections. However, a better understanding of the bacteria-host interaction, and the role of QS in infection, is required. In this study, we set up a newP. aeruginosainfection model, using 2D airway organoids derived from healthy and CF individuals. Using dual RNA-sequencing, we dissected their interaction, focusing on the role of QS. As expected,P. aeruginosainduced epithelial inflammation. However, QS signaling did not affect the epithelial airway cells. The epithelium influenced several infection-related processes ofP. aeruginosa, including metabolic changes, induction of type 3 and type 6 secretion systems (T3SS and T6SS), and increased expression of antibiotic resistance genes, includingmexXYefflux pump and several porins. Interestingly, the epithelium influenced the regulation by QS of the type 2 (T2SS) and T6SS. Finally, we compared our model within vivo P. aeruginosatranscriptomic datasets, from samples directly isolated from the airways of CF subjects. This shows that our model recapitulates important aspects ofin vivoinfection, like enhanced denitrification, betaine/choline metabolism, increased antibiotic resistance, as well as an overall decrease of motility-related genes. This relevant infection model is interesting for future investigations, helping to reduce the burden ofP. aeruginosainfections in CF.