Genomic and biological characterization of three lytic phages targeting Vibrio parahaemolyticus and their application in a raw salmon model

ABSTRACT Vibrio parahaemolyticus is a major seafood-borne pathogen that poses substantial threats to food safety and aquaculture. However, effective and food-compatible strategies for controlling this pathogen along the seafood supply chain remain limited. In this study, three novel lytic bacteriophages (Z5, Z44, and Z109) that infect V. parahaemolyticus were isolated from seafood-market wastewater and characterized with respect to their biological properties, genomic features, and bactericidal activity under food-relevant conditions. All three phages exhibited siphovirus-like morphologies and short latent periods (~10 min), with Z5 and Z44 showing high burst sizes (267–688 plaque-forming units [PFU]/cell). The three phages showed stability across a wide range of temperatures (4°C–60°C) and pH values (4–10), supporting their compatibility with seafood processing and cold-chain storage. Phylogenetic analyses indicated that Z5 and Z44 represent novel species within the family Queuovirinae , whereas Z109 belongs to the genus Mardecavirus . Genomic analyses confirmed the absence of known antibiotic resistance genes or virulence factors, supporting their genetic safety for food applications. Predicted interactions between phage- and host-encoded anti-restriction and defense systems likely influence phage lytic efficacy and killing patterns. Specifically, Z5 and Z44 encode a putative 7-deazaguanine DNA modification pathway that may enhance resistance to host restriction-modification systems. Conversely, the presence of prophage-related regions in the host genome may contribute to the reduced killing efficacy of Z109 at high phage doses. In a salmon model, all three phages significantly reduced V. parahaemolyticus at 25°C and 4°C, demonstrating effective biocontrol in a food matrix. In addition, the phages strongly inhibited biofilm formation, although their capacity to disrupt mature biofilms was limited. Collectively, these results indicate that Z5, Z44, and Z109 are promising candidates for the biocontrol of V. parahaemolyticus contamination in seafood systems. IMPORTANCE Bacterial infections in aquaculture and seafood pose significant challenges to food safety, with Vibrio parahaemolyticus being a major seafood-borne pathogen. Bacteriophages are promising alternatives to antibiotics, but their effectiveness may be influenced by phage-encoded counter-defense strategies and host-encoded antiphage defense systems. In this study, we characterized three novel lytic phages and observed distinct killing patterns under different infection conditions. In a raw salmon model, these phages effectively reduced V. parahaemolyticus , demonstrating their practical biocontrol potential. Genome analysis identified putative phage-encoded DNA modification genes and host prophage-associated defense genes that may help explain these differences. These findings highlight the importance of considering both phage and host genomic features when optimizing phage-based strategies for controlling V. parahaemolyticus in aquaculture and seafood systems.