Prophage-Derived Endolysin E1 Synergizes with Meropenem Against Acinetobacter baumannii

Carbapenem-resistant Acinetobacter baumannii (CRAB) is classified as a critical priority pathogen by the World Health Organization, and new therapeutic alternatives are urgently needed. In this study, we performed genomic mining of 27,531 A. baumannii genomes and identified 5144 prophage-derived endolysin candidates. Four highly prevalent candidates (E1–E4) were recombinantly expressed and functionally evaluated against A. baumannii. Among them, E1 exhibited the strongest bactericidal activity against reference strains ATCC 19606 and CMCC 25001, with a minimum inhibitory concentration in the micromolar range. E1 effectively disrupted preformed biofilms (>60% reduction) and remained stable under a broad range of temperatures (4–60 °C), pH values (6–8), and NaCl concentrations (up to 500 mM). Structural analysis indicated that E1 adopts a canonical lysozyme-like fold with key residues for peptidoglycan binding, and its lytic activity in vitro relied on 1 mM EDTA-mediated outer membrane permeabilization. In a murine peritoneal infection model, combination therapy with E1 and meropenem (each at 1 × MIC) significantly increased the survival rate to 66.7% and reduced bacterial loads in blood and multiple organs. This study demonstrates that prophage-derived endolysin E1 acts synergistically with meropenem against A. baumannii, supporting E1 as a promising candidate for developing combination therapies against CRAB.