Preventing Emergence of Antibiotic Resistant High-Risk Clones of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a devastating hospital pathogen, which plays a prominent role in the ongoing antimicrobial resistance crisis. To understand this pathogen, it is necessary to closely examine the genetic factors (virulence factors) that enable this bacteria to cause infection and disease. A particular virulence factor, called the lipopolysaccharide (LPS) is displayed on the surface of most bacterial pathogens and it has been the subject of scientific scrutiny for well over a century. A part of this molecule, called the O-Specific Antigen, has historically been used to differentiate bacteria (serotyping). The composition of the OSA (serotype) is very diverse in P. aeruginosa and plays a major role in its interactions with host and environment.

Previous studies into the evolution of the highly successful multi-drug resistant (MDR) clone type ST111 was found to involve recombinant exchange (serotype switch) of the the genes that determine OSA structure. But we do not understand how this affects the fitness of this pathogen. The focus of this thesis is to identify and characterize the factors that that has enabled the success of MDR P. aeruginosa, with specific focus on the OSA.

From a genomics perspective, a new method is developed to discover serotype switching from whole-genome sequencing data. This also enables us to provide a first estimate of serotype switching prevalence in high-risk epidemic clones of P. aeruginosa. We further contribute with several high-quality ST111 genomes to further our understanding of this important clone.

We then present a new recombinant cloning method to clearly investigate the specific contribution of different OSA structures to various clinically relevant properties. We characterize the ability of serotype switched strains, engineered to express different serotypes for adhesion, virulence, and susceptibility to bacteriophages and pyocins. We show that the ST111 serotype switch to O12 provides it with a substantial fitness advantage across these parameters. Further study of almost the entire OSA diversity, known to P. aeruginosa, is similarly addressed and it reveals that the OSA composition represents distinct bacterial phenotypes. Using bacteriophages and pyocins, we can show how the OSA can be targeted to overcome the limitations normally associated with drug resistance. Overall, the results and materials presented in this thesis holds great promise in furthering the development of novel antimicrobials that can control this pathogen.