Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes

Abstract

The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.

A Review of the Functional Annotations of Important Genes in the AHPND-Causing pVA1 Plasmid

“…This results in an out-of-frame insertion of pirA vp and further affects the downstream gene expression of pirB vp [50]. Furthermore, whole-genome sequencing of 40 V. parahaemolyticus isolated from shrimp hepatopancreas and aquaculture water in Malaysia indicated that pirAB vp genes are prone to deletion [51]. Taken together, these results demonstrate the importance of this DNA transposon in the transfer, deletion, and mutation of the pirAB vp -containing gene cluster.…”

Vibrio parahaemolyticus: Exploring its Incidence in Malaysia and the Potential of Streptomyces sp. as an Anti-Vibrio Agent

“…The high seafood consumption in Malaysia puts Malaysians at risk of foodborne diseases from seafood, given there is an increased risk of transmission and/or exposure to V. parahaemolyticus. Moreover, the foodborne pathogen has been frequently isolated from various sources such as seafood and the water environments in Malaysia [39,43,44,[61][62][63] (Table 1).…”

“…A quick search was performed across three databases, Embase, Medline, Scopus, and Google Scholar, using the keywords: "prevalence OR incidence OR occurrence AND Vibrio parahaemolyticus AND Malaysia" to determine relevant original articles published between 2005 and 2023. Results from the search found that V. parahaemolyticus are most commonly isolated from seafood such as shellfish [39,41,43,62,[68][69][70][71][72][73][74][75][76] , shrimps [42,63,[68][69][70][77][78][79][80][81] , squids [68,69,72] , fishes [40,44,61,69,72,75,[82][83][84][85][86][87][88][89][90] , and sea cucumber [91] . The pathogen has also been isolated from vegetables [92,93] and environmental sources such as seawater [44,94] , coastal waters…”

“…Results from the search found that V. parahaemolyticus are most commonly isolated from seafood such as shellfish [39,41,43,62,[68][69][70][71][72][73][74][75][76] , shrimps [42,63,[68][69][70][77][78][79][80][81] , squids [68,69,72] , fishes [40,44,61,69,72,75,[82][83][84][85][86][87][88][89][90] , and sea cucumber [91] . The pathogen has also been isolated from vegetables [92,93] and environmental sources such as seawater [44,94] , coastal waters [73,74,95] , and water from shrimp farms [63,…”

“…Blood clams [68,69] Fish [40,44,69,72,75,[82][83][84][85][86][87][88][89][90] Oyster [69] Prawn [69] Sea cucumber [91] Shellfish [39,41,43,62,[70][71][72][73][74][75][76] Short mackerels [61] Shrimps [42,63,[68][69][70][77][78][79][80][81] Squids [68,69,72] Surf clams [68] Vegetables Cabbage [92,93] Carrot [92,93] Cucumber [92,93] Four-winged bean…”