A modular system to create designer phages in E. coli

The Erwin Schrödinger project A modular system to create E. coli-based designer phage factories, led by Noa Wolff, will address bacteriophage design as an alternative to antibiotics at the University of Edinburgh. As the spread of antibiotic resistance continues, new treatment options must be explored to prevent increasing mortality rates due to bacterial infection. Examples of prominent resistant pathogens are Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and various Enterobacter species, which are summarized by the acronym ESKAPE and can cause a multitude of diseases, such as pneumonia. Bacteriophages, being viruses that infect bacteria exclusively, are a promising option to eliminate resistant pathogens, as they do not infect human cells at all. However, there are several problems associated with this solution. First, bacteriophages are host-specific down to the strain level. Therefore, a phage would only infect one strain of a pathogen, while there are usually many strains that cause the respective disease. Treating a Klebsiella pneumoniae-caused pneumonia by a therapeutic phage would thus be possible in special cases only. Second, direct elimination of pathogens by phages is controversially discussed, as they propagate in enormous copy numbers using the host pathogens metabolism and thus reach uncontrolled doses. Another concern is the potential rapid endotoxin release from the host cell upon lysis. Third, most bacteriophage genomes contain a multitude of uncharacterised genes, which impedes the admission of phage-based medications. Phages transfer antibiotic resistances themselves, and the influence of unknown genes, whose products are released upon host cell lysis, is uncertain. In the course of this project, phage genomes will be analysed and unknown genes will be excluded. A minimal genome will be created to facilitate admission and to prevent unexpected side effects. Thereupon, the host specificity will be broadened via directed evolution, so that all strains of a pathogenic bacterial species will be infected. Last, the transfection of viral DNA carrying different killer genes will be tested. In this scenario, the pathogens will be eliminated via the expression of these genes instead of uncontrolled lysis, which should prevent adverse therapeutic effects. The created artificial designer phages will be produced after each intermediate step and their effect will be tested. Finally, at the University of Vienna, an inhalation spray will be developed for the treatment of acute lung infections caused by resistant strains of Pseudomonas aeruginosa und Klebsiella pneumoniae.