SafePhage: Engineering synthetic phages with intrinsic biocontainment

Rising levels of antimicrobial resistance worldwide threaten our healthcare systems and the global economy, which both rely on a ready supply of cheap and effective antimicrobial drugs to treat infections and prevent infections occurring in routine care. Phage therapy is a promising alternative to traditional chemical antibiotics for treating multidrug resistant bacterial infections that has proven to be lifesaving as a last-line treatment. However, conventional phage therapy faces multiple barriers to widespread use and commercialization. A promising emerging alternative is to use synthetic phages in place of natural phages building on recent advances in synthetic genomics technologies in Manchester that enable the rapid design/build of genomes from scratch. Synthetic phage therapy has a number of key advantages, including but not limited to: (i) Precise control over phage genomic contents to improve safety; (ii) Programmable specificity of the targeted bacterium leaving beneficial microbes intact; (iii) Directing phages to specific host niches or cell types; (iv) Adding bacteria-killing toxins to more effectively clear bacterial pathogens; (v) Adding genes or modifications to evade bacterial immunity systems. Synthetic phage therapy, therefore, has the potential to be transformative, offering both safer and more effective treatments for patients, as well as far greater ability to produce protectable IP and thus commercially viable phage-based products for companies. To deliver on this transformative potential, however, we must first overcome a major barrier: preventing unwanted release of synthetic phages outside the clinic. In this project, we focus on developing a foundational technology that will be essential for the safe use of synthetic phage therapy in humans and animals: the development of genome safeguarding technologies for synthetic phages that will ensure their long-term biosecurity and biocontainment, preventing their unintended release and/or misuse by third parties. Such safety mechanisms are inherent to all mature technologies and, here, must be robust to the evolution of escape mutants whilst not negatively impacting treatment effectiveness. Our interdisciplinary project combines synthetic genomics to design and build synthetic phages, evolutionary microbiological experiments to test how different biocontainment strategies affect phage escape and bacterial resistance evolution, together with tests of how biocontainment affects the efficacy of synthetic phage therapy to treat infections in both in vitro and in vivo models of respiratory infection. We believe that genome safeguarding technologies will be foundational for the entire synthetic phage technologies industry (which stretches far beyond phage therapy into diverse fields and other biotechnologies) and will be essential for the widespread commercialization and adoption of synthetic phage therapy worldwide. Our project will place UK at the forefront of the fast-growing global phage-based technologies industry and ensure the UK has a leading role in setting the global standards for safe use of synthetic phages.

OVERVIEW:
We propose an ambitious, interdisciplinary research programme including synthetic genomics, microbiology, molecular biology, evolutionary biology, infection biology and respiratory immunology, to develop and validate genome safeguarding technologies for synthetic phage therapy, which will be foundational for the fast-growing global synthetic phage-based technologies and therapeutics sectors.

APPROACH:
We will use our synthetic genomics platform to design and build engineered phage genomes with different configurations of built-in genome safeguarding in our well-established yeast-based genome foundry. In tandem, we will develop genetically engineered bacterial reboot hosts for efficient production of these synthetic phages from episomes, which will also introduce key epigenetic modifications enabling evasion of common bacterial immunity systems. We will use our established high-throughput evolutionary screening methods to quantify rates of phage escape mutation and how these vary among different configurations of genome safeguarding, and to quantify the dynamics and mechanisms of bacterial resistance evolution and how these are affected by phage genome safeguarding and the toxin-gene-cargo of synthetic phages. Finally, we will test how synthetic phage biocontainment strategies affect treatment of Pseudomnas infections, by quantifying the efficacy of synthetic phage therapies in our established in vitro (respiratory tract-mimicking media) and in vivo (mouse respiratory infection) infection models.

OUTCOMES:
Our Mission Award project will develop a series of new genome safeguarding technologies for synthetic phages alongside experimental validation of their robustness and efficacy in the lab and relevant infection environments. Together this programme of research will substantially advance the technology readiness level of synthetic phage biocontainment, from TRL3 to TRL6.