Pathogen-Phage Geomapping to Overcome Resistance

Abstract

The rise of antibiotic resistance has renewed interest in bacteriophages as therapeutic alternatives. However, co-evolution of phage and bacteria will naturally give rise to phage-resistant pathogens, complicating phage therapy efforts. A critical bottleneck in the production of phage therapeutics is the discovery of virulent phages against resistant pathogens. Conventional methods for discovery are time-consuming, biased, and laborious, limiting the potential for identifying suitable phage candidates. To overcome these limitations, we combined small-volume environmental sampling with 16S rRNA sequencing to identify reservoirs where bacterial hosts co-exist with their phage predators. This strategy, which we term geographical phage mapping (ge{Phi}mapping), pinpoints ecological "hotspots" for targeted phage hunting. We further developed a portable phage hunting device ({Phi}HD) that generates highly enriched phage concentrates directly from these reservoirs. By integrating ge{Phi}mapping with high-throughput enrichment, we constructed the R{Phi} library, a diverse collection of novel phages. We captured and isolated 36 new phages targeting extremely-resistant organisms across various ESKAPE pathogens when conventional phage hunting and experimental evolution approaches failed.