Infection dynamics and virulence potential of clinical Pseudomonas aeruginosa isolates in a human airway epithelium model system

Persistent bacterial infections constitute an increasing health problem, often associated with antibiotic resistance. However, despite extensive antibiotic treatment, Pseudomonas aeruginosa persists for decades in people with cystic fibrosis (pwCF), remaining susceptible. Host-pathogen interactions during infection may, therefore, be a major contributing factor to treatment failure. Using an infection model based on human airway epithelial cells, cultured at the air-liquid interface (ALI), we simulated the infection process of P. aeruginosa to investigate the colonization dynamics and virulence potential during infection in ALI models from non-CF and CF donors, and the BCi-NS1.1 cell line. Infections by reference strains and clinical isolates from pwCF revealed four infection clusters based on virulence, epithelial damage, and localization within the epithelium, in a strain-specific manner regardless of the type of ALI model or clonal lineage. Modulator treatment to restore CFTR channel function did not change infection patterns in CF ALI models. Dual RNA-seq revealed that bacterial colonization of ALI models significantly upregulated host inflammatory pathways, dependent on the strains virulence. Simultaneously, while bacterial gene expression was similar in non-CF and BCi-NS1.1 ALI models, CF models promoted differential regulation in a type III secretion mutant. Altogether, our results profile key infection dynamics occurring in pwCF and provide ground knowledge on the interplay between the airway epithelium and P. aeruginosa.