Eco-Evolutionary Approach to Isolate, Evolve, and Characterize Broad-Host- Range Bacteriophages to Inform Solutions for Antimicrobial Resistance (360G-Wellcome-344078_Z_26_Z)

This project will develop an eco-evolutionary framework for discovering, evolving, and characterizing bacteriophages (phages) capable of infecting a wide range of clinically relevant bacteria bearing antibiotic resistance plasmids. By focusing on plasmid-dependent phages (PDPs), which target the conjugative plasmids responsible for disseminating antibiotic resistance genes, we seek to reduce the spread of multidrug resistance at its source. Starting from phage-rich environmental samples (wastewater, rivers), we will build an isolation pipeline that depletes somatic phages and enriches for PDPs by sequential exposure to diverse plasmid-bearing hosts. We will then systematically broaden host range using stepwise experimental evolution guided by evolutionary distance metrics derived from protein-structure prediction and protein language model embeddings of plasmid-encoded pilus proteins and phage receptor-binding proteins. Phage infectivity dynamics will be quantified using high-throughput assays, and deep sequencing will identify genetic changes underpinning expanded infectivity. Finally, long-term coevolution in continuous culture will test how broadened-host-range PDPs and multiple distinct bacterial species adapt reciprocally, and whether outcomes converge (e.g. predictable receptor-binding modifications) or diverge (host-specific trajectories). Ultimately, this work aims to deepen mechanistic insight into phage-bacteria coevolution and inform phage-based interventions that could limit the spread of antibiotic resistance. Keywords: antimicrobial resistance; plasmid-dependent phages; conjugative plasmids; experimental evolution