Genomic and functional characterization of six novel phages targeting multidrug-resistant Escherichia coli: promising candidates for clinical phage therapy

Abstract

Antimicrobial resistance in multidrug-resistant Escherichia coli has severely compromised the efficacy of conventional antibiotics, particularly in hospital-acquired infections. Bacteriophage therapy offers a targeted approach, yet the rapid emergence of phage-resistant mutants during monotherapy limits its durability. However, phage cocktail therapy can overcome this issue. In this study, we isolated and characterized six novel lytic bacteriophages from hospital wastewater that specifically infect MDR E. coli clinical isolates. All six phages exhibited strictly lytic lifestyles, and genomic analysis confirmed the absence of lysogeny, virulence, or antibiotic-resistance genes. They are promising candidates for phage cocktail therapy. Stability assays demonstrated that the phages maintained activity under various temperature and pH conditions. Adsorption kinetics showed rapid binding to host cells, and one-step growth curves indicated efficient lytic replication with short latent periods and high burst sizes. Moreover, the phages consistently reached high titers (1010–1012 PFUs/mL) and demonstrated potent activity against preformed biofilms of MDR E. coli strains. Phylogenetic analyses placed these phages within distinct clusters, supporting their genetic diversity. Together, these findings expand current understanding of the biology and diversity of E. coli-targeting phages and provide a robust foundation for the rational design of phage cocktails aimed at overcoming persistent MDR E. coli infections.