A Novel Approach for Predicting Phage Therapy Outcomes Prior to Treatment: Characterization of Bacterial Immune Systems

Overview

The rapid rise of antibiotic resistant bacteria, coupled with stagnating antibiotic discovery, makes once-treatable infections increasingly lethal. Bacteriophage (phage) therapy offers a promising alternative. However, it is currently only approved for compassionate use in the USA due to its inconsistent efficacy. This is caused by bacteria's diverse immune systems that can block phage infection, producing unpredictable outcomes. Characterizing these immune systems is therefore essential to ensure reliable treatment effectiveness. Using model E. coli strains, each engineered to express a distinct immune system, this study examined 33 bacterial immune systems using plate reader assays. These assays measured lysis timing and population survival of strains following exposure to serial dilutions of T7 bacteriophage. Based on these results, immune system susceptibility was determined, and 10 representative systems were selected for further characterization using solid plaque assays. These assays quantified burst size and efficiency of plating (EOP). Together, these experiments revealed a wide spectrum of immune system susceptibility and abortive infection (Abi) mechanisms. These findings establish a predictive framework for phage therapy. By linking bacterial immune systems to therapeutic outcomes, this study allows one to determine whether phage therapy will succeed or if phage engineering, insertion of immune evasion proteins, is required. This approach transforms phage therapy from a last-resort option into a predictable, reliable, and scalable treatment. Characterization of bacterial immunity paves the way for phage therapy's broad clinical use against life-threatening antibiotic resistant infections.