Enhancing bacteriophage function with coevolution and synthetic biology

Project Summary/Abstract: Antimicrobial resistance (AMR) poses a growing threat to human health, with nearly 5 million deaths worldwide attributed to AMR bacterial infections in 2019. There is a growing critical need for innovative treatments for AMR infection, and phage therapy, which uses naturally occurring viruses that attack bacteria, is emerging as a potentially powerful treatment modality. Phage therapy is limited by the ability of bacteria to evolve resistance to phages, but phages have the capacity to evolve counter-resistance. We do not fully understand the diversity of ways that phage can evolve to overcome a wide variety of bacterial resistance strategies. The overall objective of this proposal is to use experimental evolution in the laboratory to identify genetic changes in phages that are responsible for enhanced phage function, and to engineer phages that have optimized traits to suppress bacterial growth. The experiments in specific aim 1 will examine the genetic and functional patterns underlying enhanced phage function when phage T2 is evolved alongside a variety of diverse clinical isolates of Escherichia coli. The experiments in specific aim 2 will identify the causative mutations in evolved phages, their optimal combinations, and the associated mechanisms of action. This work will contribute new insights to phage-bacteria interactions that will assist in the design of engineered phage therapies, as well as collections of genetically and functionally characterized evolved and engineered phages with enhanced antibacterial function. This proposal is designed to support the career development of the candidate, who will expand expertise in the microbiology of bacteria and phages, microbial genomics, and experimental methods in synthetic biology. The proposed work is expected to identify new mechanisms that phages can exploit to overcome bacterial resistance, providing the groundwork for the candidate to develop independent lines of research.