Microevolution of the two most abundant Pseudomonas aeruginosa clones PA14 and C in cystic fibrosis lungs

The opportunistic pathogen Pseudomonas aeruginosa frequently colonizes the airways of patients suffering from cystic fibrosis. Strains of this species often cause chronic infections and stayin the lungs for many years. During that time of adaption to the different niches in the lung, challenges by the host's immune system or antibiotics, confrontation with other colonizing P. aeruginosa strains or bacterial species etc. the strains undergo a microevolution in the lung habitat causing the rise of different variants or 'ecotypes' of the original colonizing strain. In order to identify the respective genomic changes we sequenced the genomic DNA of sets of three sequential isolates each from the airways of two CF patients. Over many years isolates had been obtained from these patients belonging to the same major clonal lineage within the species P. aeruginosa (clone PA14 for one patient, clone C for the other), indicating that the subsequent isolates indeed represent such variants arisen from the original colonizer by microevolution. Each set of isolates (RN3, RN6, RN43, and NN2, NN11, NN80, respectively) comprises a so-called early isolate (first isolate of the persisting clonal lineage), a middle isolate (obtained 16 ? 22 month after the early isolate and a late isolate from more than 12 years later. Thus the screening for genomic differences between these isolates allows monitoring the bacterial microevolution in a cystic fibrosis lung habitat for two different cases over a long time course.