Pathogen-phage geomapping to overcome resistance.

Abstract

The rise of antibiotic resistance has renewed interest in bacteriophages as therapeutic alternatives. However, coevolution 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 16 S rRNA sequencing to identify reservoirs where bacterial hosts co-exist with their phage predators. This strategy, which we term geographical phage mapping (geΦmapping), pinpoints ecological 'hotspots' for targeted phage hunting. We further developed a portable phage hunting device (ΦHD) that generates highly enriched phage concentrates directly from these reservoirs. By integrating geΦmapping with high-throughput enrichment, we constructed the RΦ 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.