|Microevolution of Pseudomonas aeruginosa in cystic fibrosis airways|
P. aeruginosa causes a wide range of infections in humans that can vary from local to systemic, subacute to chronic, and superficial and self-limiting to life-threatening . Chronic airway infections with P. aeruginosa are regularly seen in patients with advanced stages of chronic obstructive pulmonary disease [2,3] and individuals suffering from the autosomal recessive trait cystic fibrosis . The chronic infections of the stomach with Helicobacter pylori  and of the cystic fibrosis airways with P. aeruginosa  are the only cases of infections with extracellular bacteria in humans where the causative agent persists in its niche for decades and does not disseminate into other organs. These two scenarios provide a unique opportunity to monitor the genome evolution of a human pathogen in a disease habitat over many years.
The cystic fibrosis clinics in Copenhagen and Hanover have regularly collected P. aeruginosa from the airways of all their patients who became chronically colonized in the 1970s and 1980s [6,7]. The analysis of these unique strain collections taken from numerous patients should provide a comprehensive insight into the microevolution of P. aeruginosa during the chronic infection of cystic fibrosis airways. Therefore we are currently investigating the genome evolution of P. aeruginosa in contrasting CF-patient cohorts with a very mild or very severe course of their infection (our own unpublished data) by whole genome sequencing and phenotyping. Exopolysaccharide biosynthesis, antimicrobial resistance and global regulators of lifestyle and metabolism were found to be common functional categories whose genes were hit by mutations in all P. aeruginosa clones, irrespective of the severity of infection in the cystic fibrosis host. Microevolution, however, was not uniform in the patients' lungs. For example, the P. aeruginosa clone inhabiting the most severely affected lungs generated progeny with stop mutations or drastic amino acid changes in key genes of lifestyle, whereas the P. aeruginosa clone that has persisted in a patient with normal lung function had diverged into co-existing clades which, accumulated benign, probably modifying amino acid substitutions, but no stop mutations.
Phenotypic diversity of sequential isolates of clonal complexes PA14 and C during more than 20 years of colonization of CF airways. Isolates were characterized by eight bioassays on agar plates. From top to bottom: 1, colony morphotype; 2, autolysis; 3, haemolysis; 4, casein degradation; 5, siderophore secretion; 6, twitching motility; 7, swarming motility; 8, swimming motility. Dichotomous characters (1, 2) are designated by different colours (1) or white/grey (2). Five different observed colony morphologies were represented by five different colours. Isolates showing autolysis are marked in grey, others in white. Continuous characters are designated by normalized colour intensity (3, red; 4, green; 5, magenta; 6, red; 7, blue; 8, orange) ranging from zero (white) to maximal activity within the lineage (strongest colour intensity). Data for the individual isolates are either shown at their position in the clone PA14 (A) or shown at their position in the clone C dendrograms (B). Squares or triangles above strains indicate the presence of the large deletion in RN isolates (A); stars indicate a hypermutable strain in the NN lineage (B) .