Genomic characterization and phage cocktail suppression of a multidrug-resistant Vibrio sinaloensis isolate from diseased shrimp

Abstract

ABSTRACT Vibrio sinaloensis has been reported in association with disease events in aquaculture, yet its genomic features and non-antibiotic suppression strategies remain largely unexplored. Here, we report genomic characterization of a multidrug-resistant V. sinaloensis strain, ZZ006, isolated from diseased shrimp and evaluate phage-mediated suppression of this strain in vitro. The ZZ006 genome harbors multiple putative virulence-associated secretion systems and antimicrobial resistance genes, suggesting chromosomal carriage of traits potentially relevant to host association and antimicrobial tolerance. Using this isolate and its phage-resistant derivatives as hosts, we isolated and characterized three novel bacteriophages (VS1, VS2, VS3) with complementary infection strategies. Their combined application efficiently suppressed ZZ006 growth in vitro and reduced the emergence of phage-resistant populations compared with individual phages. Whole-genome resequencing of cocktail-resistant isolates revealed recurrent mutations in pilus- and pseudopilin-associated genes, consistent with receptor-level phage resistance. This study provides genomic characterization of an aquaculture-associated V. sinaloensis isolate and establishes an in vitro framework for phage cocktail suppression and resistance-evolution analysis, supporting future evaluation of phage-based biocontrol in aquaculture-relevant settings. IMPORTANCE Vibrio sinaloensis has been detected in diseased aquaculture animals, and multidrug-resistant isolates may complicate disease management. By integrating genomic analysis with experimental phage therapy, this work characterizes a multidrug-resistant V. sinaloensis isolate from diseased shrimp and evaluates in vitro phage-mediated suppression of this isolate and its phage-resistance evolution. These findings offer actionable solutions for mitigating antibiotic resistance and enhancing sustainability in aquaculture systems. Vibrio sinaloensis has been detected in diseased aquaculture animals, and multidrug-resistant isolates may complicate disease management. By integrating genomic analysis with experimental phage therapy, this work characterizes a multidrug-resistant V. sinaloensis isolate from diseased shrimp and evaluates in vitro phage-mediated suppression of this isolate and its phage-resistance evolution. These findings offer actionable solutions for mitigating antibiotic resistance and enhancing sustainability in aquaculture systems.