Investigating Co-evolutionary Phage Training for Enhanced Therapeutic Potential: A Genomic and Molecular Insights on Phage-Host Interactions

Abstract

Due to the rise of multi-drug-resistant bacterial infections, phage therapy has been a promising solution to tackle the problem of antibiotic resistance. However, bacteria quickly gain resistance against phages by modifying its outer membrane receptors though spontaneous mutations. This study investigates co-evolutionary dynamics between lytic phage PBM-2 and its host Avian pathogenic Escherichia coli (APEC), focusing on origin of bacterial resistance, phage counter adaptation and bacterial suppression. This research aims to detect and characterize mutations in bacterial receptors and phage receptor binding proteins (RBPs) using whole genome sequencing to investigate the patterns of bacterial resistance and phage counter adaptations. Co-evolutionary phage training experiments were conducted for 28 days involving untrained phage and 8 days involving trained phage to assess the origin of resistance and prolonged suppression of bacteria by phages. Trained phages and co-evolved bacterial isolates of different timepoints were subjected to whole genome sequencing for mutation analysis and molecular docking of bacterial receptors and phage RBPs. The results revealed that the host bacteria quickly emerged resistance by modifying its receptors ompF, ompA, Maltoporin and FhuA though spontaneous mutations and untrained phages were unable to suppress bacterial growth. However, trained phages were able to suppress bacterial growth for a long period of time and delayed bacterial resistance by modifying its Tail fiber protein though mutations. The infectivity and resistance profiling revealed that phages of later timepoints evolved to regain the ability to infect bacterial cells. In conclusion, this study provides insights into phage-bacteria interactions on molecular and genomic level highlighting key genetic changes influencing resistance and infectivity of bacteria and phage respectively. These findings are helpful to optimize phage therapy strategies against multi-drug-resistant bacterial infections.