Date of Award


Degree Type


Degree Name

Master of Science (MS)


Bioinformatics & Computational Biology


The rising rate of antibiotic-resistant bacteria is a global health concern, and the Pseudomonas aeruginosa is estimated to be a leader in serious threats. Bacteriophages, or viruses that infect bacteria, have gained renewed interest in Western Medicine as an alternative to antibiotics. Phage therapy of P. aeruginosa infections has primarily focused on obligately lytic phages. However, prophages, or phages in the lysogenic life cycle, are estimated to far outnumber obligately lytic phages. In theory, these prophages can be genetically modified to be obligately lytic and thus ideal candidates for phage therapy. To date there has not been a comprehensive analysis on the diversity of P. aeruginosa-infecting prophages. Furthermore, genetic engineering of P. aeruginosa-infecting prophages has yet to be explored.Here I present a 2-fold study including a comprehensive analysis of the prevalence and diversity of prophages within all publicly available P. aeruginosa genomes paired with the engineering of 2 P. aeruginosa-infecting temperate phages. 6,852 high confidence prophages were identified from 5,383 genomes of P. aeruginosa with 68% of the genomes containing at least 1 high confidence prophage. While 57% of the predicted prophages displayed sequence similarity to publicly available phage genomes, novel prophages were discovered. There was extensive diversity observed among the prophages, including diversity within the widely conserved integrase and C repressor coding regions " the two genes responsible for prophage entering and persisting through the lysogenic life cycle. Two P. aeruginosa phages, Dobby and D3112, were engineered to become obligately lytic phages. This engineering included removal of Dobby's integrase and D3112's C repressor producing phage strains eDobby and eD3112, respectively. To our knowledge, this is the first instance of a P. aeruginosa-infecting temperate phage being engineered to remove the C repressor for production of an obligately lytic phage. Both the ancestral and engineered strains were capable of infecting clinical P. aeruginosa isolates. Furthermore, both eDobby and eD3112 were able to kill and debilitate P. aeruginosa ATCC 15692 at MOIs of 1 and 10. This study has identified numerous additional prophage candidates, which can be engineered using the approach presented here, for phage therapy of P. aeruginosa infections.

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.