The evolution and adaptation of clinical Pseudomonas aeruginosa isolates from early cystic fibrosis infections

Pseudomonas aeruginosa is a major cause of morbidity and mortality in cystic fibrosis (CF) patients. P. aeruginosa infects the CF airways and establishes chronic infections that can last for a lifetime during which P.aeruginosa evolves in order to adapt to the environment.In this PhD thesis, we investigated the evolution of two convergent lineages of P. aeruginosa isolated from the early stages of infection in two CF patients using both transcriptomic and proteomic methods. Both lineages harbour sequential mutations in a specific regulatory system, the retS-gacS-gacA-rsmA-rsmYZ signalling pathway, which reciprocally regulates the expression of genes attributed to chronic and acute infection states. Additionally, we investigate the effects of the evolution not caused by the mutations in this regulatory system through allelicre placements in the clinical isolates.We show that the initial stages of infection with P. aeruginosa is subject to temporal and differential expression of virulence factors caused by mutations in the retS-gacS-gacA-rsmA-rsmYZ signalling pathway. Initially, a mutation in retS causes a switch to a chronicinfection mode characterised by the expression of the Type VI secretion system (T6SS) and induction of the phenazine biosynthesis operons. The effects of the retS-mutation are reversed with a later mutation in either gacS or gacA, which lowers the expression of the T6SS and the phenazine biosynthesis operons and instead leads to high expression of the Type III secretion system (T3SS). This suggests that the current dogma of this regulatory system does not adequately explain the biological significance of this system, as the opposite mutation pattern would be expected if this dogma were true. Furthermore, we show that the residual evolution caused by other mutations also has an effect on the expression of virulence factors.