Unveiling co-infection in cystic fibrosis airways: Transcriptomic analysis of Pseudomonas aeruginosa and Staphylococcus aureus dual-species biofilms

Staphylococcus aureus and Pseudomonas aeruginosa are the most prevalent pathogens that colonize structurally abnormal airways such as those in Cystic Fibrosis (CF) and other chronic obstructive lung diseases. Although these bacteria seem to succeed one another, CF patients acquire coinciding P. aeruginosa and S. aureus pulmonary infections, being co-infection usually associated with decreased lung function and increased frequency of pulmonary exacerbations. In addition, P. aeruginosa and S. aureus pathogens adopt a biofilm mode of growth, which contributes to high tolerance to antibiotic treatment and the recalcitrant nature of these chronic coinfections, leading to significant patient morbidity and mortality. Interactions between P. aeruginosa and S. aureus have been widely studied and it is commonly admitted that P. aeruginosa outcompetes S. aureus, perhaps outcompeting S. aureus for limited nutrients or producing anti-staphylococcal compounds, having S. aureus a minimal contribution to the overall course of the infection. However, the molecular mechanisms behind these interactions are largely unknown. Herein, we decided to characterize the full transcriptome of these dual-species biofilms, to unveil important molecular interactions that can occur between these two bacterial species that are relevant for the pathogenesis of the entire consortia. Our data provide novel insights into the role of interspecies interactions in the pathogenesis of P. aeruginosa and S. aureus co-infections and will contribute to future studies by the research community. Briefly, transcriptional profiles of P. aeruginosa and S. aureus were obtained after 24-h of growth as dual-species biofilms and compared to the respective single-species biofilms, using high-throughput RNA-sequencing (RNA-seq) from six independent biological samples, pooled into two independent RNA-sequencing libraries (pool of 3 independent samples/libraries). Please note that the dual-species biofilm raw data were aligned with either S. aureus or P. aeruginosa genomes and then compared with S. aureus or P. aeruginosa single biofilms data.