Characterization of broad-host-range bacteriophages targeting multidrug-resistant E. coli and Shigella spp.: in vitro potential

Background: Bacteriophage therapy is a promising strategy for treating multidrug-resistant bacteria, such as Escherichia coli, involved in urinary tract infections (UTIs), and Shigella spp., the main culprit in diarrheal diseases in children. Given these pathogens’ propensity for antibiotic resistance, phages offer a viable alternative, though challenges remain. Methods: A collection of 327 E. coli and 26 Shigella clinical isolates was tested for prophage induction with mitomycin C to exclude inducible phages prior to host range assessment. Six lytic bacteriophages were evaluated for their ability to lyse pathogenic isolates through double-layer plaque assays and bacterial growth kinetics at different multiplicities of infection (MOIs). Phage morphology was analysed by transmission electron microscopy (TEM), and genomes were sequenced and annotated. Results: Most bacterial isolates were susceptible to at least one phage, with only 2.7% (8/297) resistant to all six. Phage FM10 was the most effective against E. coli, lysing 88.5% of isolates, while LF2 demonstrated the highest efficacy against Shigella spp., lysing 96% of isolates, followed by DP16. LF2 and DP16 inhibited the growth of antibiotic-resistant Shigella spp. isolates in 72 h, either alone or in combination. Whole-genome sequencing confirmed genome sizes between 163–169 kb and the absence of genes related to lysogeny, toxins, or antibiotic resistance. Phylogenetic and TEM analyses classified all six phages within the Straboviridae family. No significant correlation was found between antibiotic resistance and phage susceptibility (ρ = − 0.007, p = 0.91). Conclusions: The identified lytic bacteriophages exhibit broad activity against clinical isolates of E. coli and Shigella spp., including antibiotic resistant strains, without carrying undesirable genetic elements. These findings support their potential use as safe biocontrol or therapeutic agents, contributing to the reduction of antibiotic use and the preservation of microbiota diversity in future phage therapy applications. Supplementary information: The online version contains supplementary material available at 10.1186/s12866-025-04672-3.