Functional profiling of ESKAPE viromes uncovers resistance-limiting phage-host dynamics

ESKAPE pathogens drive clinical antibiotic resistance and intractable infections, severely compromising antimicrobial therapies. Bacteriophages are promising alternatives to antibiotics, yet their diversity, function and ecological impacts in ESKAPE pathogens remain poorly defined, hindering phage therapy translation. Here, we integrated 11,947 high-quality ESKAPE genomes with global metagenomic viral data to construct a comprehensive non-redundant virome of 14,496 ESKAPE-associated viruses, including four unreported viral clades. We found pervasive competition among mobile genetic elements (MGEs) in the ESKAPE mobilome, where nested MGE architectures empower low-mobility antibiotic resistance genes (ARGs) with horizontal transfer ability to fuel resistance dissemination. Unlike ARG-rich MGEs, ESKAPE phages carry minimal ARGs and antagonize plasmids to constrain ARG propagation, confirming their biosafety for therapy. We further revealed distinct phage-host arms races, typically virulent phages enrich anti-defense genes to evade bacterial immunity, and novel viruses hijack host methyltransferases targeted by CRISPR–Cas systems. This study establishes a systematic ESKAPE virome resource, demonstrates phages’ dual roles in targeting resistant pathogens and curbing resistance spread, and provides mechanistic support for phage therapy clinical application.