Diversity of environmental and clinical Pseudomonas aeruginosa isolates

Abstract

Background and AimsThe bacterium Pseudomonas aeruginosa is a versatile environmental organism which is capable of persisting within a diverse range of habitats. For people with cystic fibrosis (CF), P. aeruginosa is the most common bacterial species isolated from respiratory secretions and infection is associated with poor health outcomes and decreased life expectancy.Molecular-based epidemiological studies have shown that patients with CF can harbour indistinguishable genotypes (shared strains) of P. aeruginosa that have not been isolated from natural or commonly encountered environments sources. It is speculated that these shared strains are acquired by person-to-person transmission and have become highly niche-adapted to the CF airway. However, the specific mechanisms relating to the transmission, host adaptation and persistence of these strains remain uncertain.By thoroughly characterising P. aeruginosa isolates from a defined cohort of patients this thesis aims to determine the prevalence and diversity of strains among adults with CF, and using phenotypic and genomic methods, to explore the key differences pertaining to adaptation between shared and unique strains of P. aeruginosa strains sourced from a range of ecological settings. MethodsLongitudinal analysis of respiratory pathogens from adults with CF was undertaken to determine the prevalence of P. aeruginosa and other major CF pathogens. Univariate analysis was conducted to determine change in prevalence over time.P. aeruginosa isolates at two time points from adults with CF underwent single nucleotide polymorphism (SNP) based genotyping to assess the incidence and prevalence of shared strains. Statistical analyses was undertaken to find associations between acquisition of shared strains and health outcomes.Bacterial motility and adhesion was determined for clinical (CF, non-CF and animal) and environmental P. aeruginosa isolates. Each assay was performed under varied atmospheric conditions. Regression analysis was performed to assess an association between genotype and phenotype.iii CF and environmental P. aeruginosa isolates were grown a dynamic flow cell system to allow for the development and visualisation of biofilm structures. Following incubation and staining, three dimensional images were captured and resulting data analysed using Comstat software.Mixed effects models were used to compare relevant biofilm parameters.Bioinformatic analysis was performed on CF and environmental P. aeruginosa isolates.Genetic variants associated with phenotypic characteristics were identified. ResultsThe prevalence of significant airway pathogens declined over the study period. For paediatric patients at the time of transition, this decline was correlated with an improvement in lung function. Interestingly, the prevalence of chronic P. aeruginosa infection remained stable.While the proportion of patients harbouring the shared strain AUST-02 declined over time, there was a marked increase in those infected with the AUST-06 strain. In contrast, the prevale...