Phenotypic and Genomic Characterization of Novel Straboviridae Bacteriophages Targeting Multidrug-Resistant Salmonella enterica subspecies enterica Serovar Enteritidis

Salmonella enterica serovar Enteritidis is a leading cause of foodborne zoonoses worldwide. The rapid emergence of multidrug-resistant (MDR) strains has compromised traditional antimicrobial therapies, necessitating the development of biosafe alternatives such as bacteriophages. This study aimed to isolate and comprehensively characterize novel lytic bacteriophages targeting multidrug-resistant Salmonella enterica subspecies enterica serovar Enteritidis isolates from Lebanon. In this study, four novel Salmonella phages, EDA02, EDA03, EDA05, and EDA06, were isolated from wastewater and poultry effluents in Lebanon. The isolates were characterized using host range profiling, one-step growth kinetics, and physicochemical stability assays. Comprehensive whole-genome sequencing (WGS) and phylogenetic analyses were performed to assess their genomic safety and taxonomic placement. Phages EDA03 and EDA06 exhibited the broadest intra-serovar lytic activity within the tested panel, infecting up to 72% and 67% of the MDR isolates, respectively. One-step growth analysis revealed latent periods of 30–40 min, with burst sizes ranging from 6.0 to 150 phages/infected cell. All four phages demonstrated robust stability across pH 4.7–10.3 and temperatures from 4 °C to 50 °C. WGS revealed genome sizes ranging from 42.3 kb to 108.8 kb, with no identified genes associated with lysogeny, virulence, or antimicrobial resistance. Phylogenomic analysis assigned all isolates to the family Straboviridae, with <95% intergenomic similarity to their closest RefSeq relatives, supporting their classification as novel species. The isolated phages demonstrate substantial lytic activity and environmental resilience under the tested conditions. Their complementary lytic profiles, environmental resilience, and genomic safety support their further evaluation as biocontrol candidates. This study represents the first genomic and phenotypic characterization of anti-Salmonella Enteritidis phages from Lebanon. These findings support the development of phage-based interventions for food safety and antimicrobial resistance mitigation in resource-limited settings.