In the lungs, this this website is characterized by the production of a thickened dehydrated mucus layer, which provides an environment
suitable for colonization by pathogens . Although many species are able to colonize the CF lung, including Staphylococcus aureus and Haemophilus influenzae, P. aeruginosa will eventually dominate in the majority of patients. Initial P. aeruginosa infections may be cleared by antibiotics, however biofilm formation allows persistence that is associated with antibiotic resistance and chronic infection . Strains of P. aeruginosa associated with CF infections are likely to contain and/or express genes that confer functional traits allowing initial colonization of the CF lung mucosa as well as the ability to out-compete other pathogens. Contrary to the dogma that CF patients acquire unique P. aeruginosa from an environmental source , it has now become evident that person-to-person
transmissible strains may circulate within CF clinics [7–11]. Such strains have been found in the United Kingdom and see more Europe (Manchester epidemic strain [MA], Liverpool epidemic strain [LES] [10, 11] and Clone C ), as well as Canada  and Australia (Australian epidemic strain 1 [AES-1] ). Increasing evidence suggests that transmission between patients occurs via a cough-associated aerosol route [14, 15]. The majority of epidemic strains display evidence of increased virulence in CF patients  and transmission to patients with non-CF bronchiectasis, or even otherwise healthy relatives, has been detected . Little is known however, about the mechanisms underlying transmissibility and pathogenesis of epidemic P. aeruginosa. Isolates from initial infection tend to be non-mucoid and motile, but over time GBA3 the organism undergoes genotypic and phenotypic changes that promote persistence, including conversion
to mucoidy, loss of motility and reduced type III secretion consistent with biofilm formation . Whole genome sequencing of two clonally related isolates collected from a CF patient 7.5 years apart  (early infection and chronic infection) showed loss of function in virulence genes required for O-antigen biosynthesis, type III secretion, twitching motility, exotoxin A regulation, multi-drug Foretinib cell line efflux, phenazine biosynthesis, quorum sensing (QS) and iron acquisition. Horizontal gene transfer and recombination in gene islands, large chromosomal inversions and gene loss are important in P. aeruginosa evolution [19, 20], and phenotypic traits may also be acquired from infecting bacteriophage. P. aeruginosa Clone C carries a plasmid and genomic islands with sequences substantially different from the P. aeruginosa reference clone PAO1 that may confer enhanced colonization and survival . Adaptation by P. aeruginosa to the CF lung is also accelerated by the host immune response and nutrient limitation, including oxidative stress and iron availability, as well as antibiotic challenge.