Proteomic characterisation of three independent series of sequential cystic fibrosis strains in an International Pseudomonas aeruginosa reference panel indicates positive selection in late infection strains

Pseudomonas aeruginosa is a frequent cause of chronic opportunistic infections in people with cystic fibrosis (CF). It is a highly diverse and adaptable Gram-negative bacterium that thrives in many environments. It is well recognised that P. aeruginosa adapts over time of colonisation to facilitate chronic infection including loss of virulence factors, however proteomic analyses of the adaptation to chronic infection have been limited. We previously collated and characterised an international panel of P. aeruginosa strains from different clinical presentations and geographical regions. Within this panel were three series of sequential isolates from people with CF, comprising eight strains in total which present an excellent opportunity to seek potential conserved adaptations that may be involved in driving chronic colonisation in the CF lung. We compared the proteomes of all eight strains (early versus respective late) to examine whether there were any changes in the proteomes over time of colonisation that were common to the three series of chronic P. aeruginosa infection isolates from three different patients. We identified 11 proteins that showed increased abundance in late isolates from all three patient series, many of which are reported to be involved in virulence, regulation of virulence or response to hypoxia and include cystic fibrosis inhibitory factor repressor (CifR), WspR, two two-component response regulators (PA2572 and PA3702), and transcriptional regulator (PA2551). Moreover, we identified three proteins (PA2572, PA3819 and PA5028) that showed increased abundance in all five late isolates from three people with CF. The probability of this being a random event is 5.06 x 10 ^-53 and consequently is very strong evidence of positive selection. The increased abundance of PA2573 and PA3819 appears to improve the fitness P. aeruginosa to antibiotics and oxidative stress. Overall, despite the diversity within this species, there appear to be common mechanisms of adaptation in the cystic fibrosis lung.