Whole genome and phylogenomic insights into Vibrio parahaemolyticus from Pacific White Shrimp reveal resistance and virulence traits in Bangladeshi aquaculture

Abstract

The fisheries sector of Bangladesh has significantly contributed to the national economy and provided livelihoods for millions of rural households. However, disease outbreaks and contamination of fish by Vibrio species pose significant hurdles to production and trade. This study analyzed the whole genomes of V. parahaemolyticus (SU37A and SU91A) isolates from Pacific white shrimp using the Nanopore sequencing platform. Subsequent de novo genome assemblies of the strains revealed high-quality, genome profiles. Further annotation identified multiple antimicrobial resistance genes ( vanT, vanY, tet, adeF , and CARB-18 ) in the strains, conferring resistance to various antibiotic classes. Mobile genetic elements were located adjacent to key regulatory genes associated with antibiotic resistance, indicating potential acquisition and dissemination of resistance phenotypes among the strains. Most of the identified virulence-associated genes are related to regulatory and stress response functions ( rpoS , rpoE , crp , hfq , arcA ), which facilitate adaptation to nutritional scarcity, oxidative stress, and host immune responses. Functional subsystem analysis demonstrated a high degree of metabolic adaptability. Phylogenomic analysis showed that the SU91A clustered with the clinical strain 3148−98, while the SU37A aligned with the non-clinical strain 11−2, suggesting potential zoonotic characteristics. These findings contribute to understanding the pathophysiology of this opportunistic bacterium during infection and elucidate the molecular factors that enable V. parahaemolyticus to adapt and persist in diverse environments.