Exploiting Pf phage superinfection to lower Pseudomonas aeruginosa virulence via evolutionary tradeoffs

PROJECT SUMMARY Many clinically relevant pathogens have bacteriophage (phage) genomes integrated in their chromosome (prophages), which can have large effects on the bacteria’s phenotype and fitness. Since phage fitness is tied to bacterial host fitness, phages can become fitter by decreasing their burden on their host. However, when

bacteria are infected by multiple phages (i.e., superinfection), competition for host resources may select phages that are more competitive against other phages, even at the increased burden to their host. The objective of this proposal is to understand and learn to exploit the evolutionary tradeoff between phage intracellular

competitiveness and bacterial fitness during superinfection. Understanding this tradeoff will give better insight into how prophages influence their bacterial host’s phenotype and fitness, and potentially pave way for a novel approach in phage therapy that utilizes such tradeoffs to make bacterial infections easier to treat.

We propose to use Pseudomonas aeruginosa (Pa) and its prophage, Pf phage, as a model system for better understanding the evolutionary tradeoff between phage competitiveness and bacterial fitness. More than half of Pa carry Pf prophages. Furthermore, cystic fibrosis (CF) patients who are chronically infected with Pa were more

likely to have Pa that have Pf prophages than acutely infected patients. This hints that Pf phages are an integral part of Pa evolutionary history and pathogenesis. The first part of this project aims to understand whether Pa virulence factor production is correlated with the number of Pf prophages that Pa carries in its chromosome.

From a previously funded study, we have a collection of >100 Pa clinical isolates from 33 CF patients that carry zero, one, or two Pf prophages. Using this collection and lab Pa strains, we will test for correlations between Pf copy number and the production of virulence factors like pyocyanin and pyoverdine. In the second aim, we will

superinfect Pa lab strain PA14 with Pf phage that has a mutation in the prophage repressor gene. This Pf phage mutant replicates quickly and at high populations within the host cell, creating an environment that favors selection for defective interfering (DI) phages that lack capsid genes. These DI phages are cheaters that exploit

full-length phages for public resources, like capsid, to selfishly propagate. Pf capsid is tied to clinically relevant phenotypes of Pa, such as biofilm robustness and antibiotic tolerance. Thus, the loss of capsid genes is not only a way Pf phages become more competitive against other Pf phages but can affect host fitness as well. We plan

to evolve PA14 infected with this selfish Pf phage under biofilm and antibiotic selection to test whether capsid genes become lost over time, undermining biofilm stability and antibiotic tolerance. Completion of this project will provide valuable information on the influence prophages have on their bacterial

host’s phenotype and fitness. Exploiting the evolutionary tradeoff between phage competitiveness and host fitness may potentially pave way for a novel approach in phage therapy, analogous to a gene drive, that exploits such tradeoffs to make bacterial infections easier to treat.