Patients suffering from cystic fibrosis (CF) are affected by dysfunctions of exocrine glands. The defect or limited function of a certain transporter protein results in aberrantly composed secretions produced in the guts, stomach and pancreas and also in the airways. The secretions are more viscous and impair the function of the affected organs. In the airways of CF patients, mucosal tissue is not sufficiently supplied with water and thus more prone to bacterial infection. Airways of 80 % of adult patients are permanently colonised by the bacterium P. aeruginosa. The bacteria cannot be cleared by the immune system of CF patients and establish a chronic infection accompanied by increasing damage of the airway tissue and drastic reduction of the lung function. The chronic P. aeruginosa infection thereby determines the clinical status and the further course of the disease for 90 % of the CF patients overall.

The aim of this project is to analyse the contribution of genome variations of the pathogens as well as of the human hosts to the severity of the disease courses, which can vary significantly from between patients. For P. aeruginosa, characteristics of the initially colonising strains are involved, but also genome variations introduced during the chronic infection. This microevolution within the CF airways can modify bacterial phenotypes and apparently contributes to the adaption of the bacterial lifestyle to the CF lung habitat, to increased resistance against mechanisms of the host immune system and also against antimicrobial treatment. Therefore, the long-term objective of the project is to characterize genomic variation between the hosts and the bacterial microevolution during the courses of the chronic infection, and to look for eventual associations between them. The identification of CF-specific bacterial microevolution events and consequential habitat adaptation strategies could reveal targets for new treatment strategies for chronically infected CF patients.

In addition, phylogenetic trees (based on shared or individual occurrences of the detected genome variations) were constructed for each of the twelve sets of sequential isolates which display the respective modes of microevolution. Overall, the detected genome variations, their presumed effects and the detected microevolution modes are questioned for associations with the severity of the patients’ clinical courses and for the occurrence of common CF-specific traits.

The twelve subsets of sequential isolates are also analysed by competitive fitness experiments. Studying the competitive growth of the isolates in nutrient-rich and nutrient-poor medium shall reveal the abilities of the bacteria to thrive under these conditions after different time spans of adaptation to the CF lung habitat. The results should also display the influence of adaptation and specialisation to an unusual host under continuous pressure of the immune system on the global fitness of P. aeruginosa and on their ability to thrive afterwards in other environments.

For the fitness experiments the respective sequential isolates are cultivated together in liquid culture, and samples are taken at different time points. The portions of the individual isolates are determined from amplicon sequencing data by utilisation of isolate-specific trains detected by the previous genome sequencing as markers.

These collections contained P. aeruginosa CF isolates from other hospitals as well as isolates from other habitats (isolates from COPD patients, from acute infections, environmental isolates). Strains displaying notable mutations shall be examined individually afterwards for fitness traits and for changes in protein functions encoded by the affected genes and subsequent phenotypic changes.

The influence of the genetic background of the CF patient on the course of the chronic P. aeruginosa infection shall be analysed by examining the genomes of the twelve patients from which the sequential bacterial isolates have been chosen for detailed analysis. Genome variations associated with either the mild or the severe clinical courses are candidates for potential modifiers of the severity of the chronic infection and shall be tested for occurrence in other CF patients. The modulator candidates shall be screened in large patient cohorts for whom DNA has been deposited in the European-Canadian unified CF DNA biobank storing samples of several thousand patients from Germany, Switzerland and Canada. Modifiers confirmed in the large patient cohorts would then represent novel biomarkers for the severity of chronic P. aeruginosa infection in CF.