Unraveling Phage-Bacteria Interactions: Phage Resistance and Defense System Dynamics in Cystic Fibrosis P. aeruginosa Isolates and the Statistical Methods for Assessing Network Nestedness

With a long history of co-evolution, the mechanisms underlying interactions between bacteria and their viral predators, phages, remain poorly understood. A deeper understanding of these mechanisms would enable better design of phages for antimicrobial therapy, known as phage therapy. This work investigated the factors driving bacterial immunity to phages, known as phage resistance, from empirical, bioinformatic, and statistical perspectives. Empirically, the mechanisms underlying phage resistance in Pseudomonas aeruginosa, a major pathogen in Cystic Fibrosis (CF) lung infections, were characterised. Genetic variation in receptor biosynthesis genes associated with resistance breadth, while the defence system repertoire associated with resistance specificity. Bioinformatically, the pan-immune system of 456 clinical P. aeruginosa isolates from a previous longitudinal CF study was characterised. Despite most systems being localised to variable genomic regions, signatures of horizontal gene transfer were rare, and defence system repertoires remained mostly unchanged over time, suggesting a broad but stable pan-immune system. Statistically, the methods for determining nestedness in phage-bacteria infection networks (PBINs) were evaluated. An alternative null model more accurately classified nested and non-nested PBINs, indicating that previous nestedness analyses may need revisiting. Overall, this thesis suggests complementary roles for receptor modification and defence system carriage in P. aeruginosa phage resistance, proposes that the theory of frequent horizontal defence system transfer does not apply to clinical CF P. aeruginosa isolates and recommends a more robust approach for analysing PBIN nestedness.