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.
Highlights
Acute hepatopancreatic necrosis disease (AHPND), known as early mortality syndrome, is an emerging shrimp disease that has caused more than 60% reduction in shrimp (Litopenaeus vannamei) production worldwide, with global economic losses estimated to be up to USD $1 billion annually (FAO, 2013)
In 2017, only five genomes of Malaysian V. parahaemolyticus associated with shrimp aquaculture environment were reported (Foo et al, 2017) followed closely by only two additional pVa-harbouring V. parahaemolyticus genomes a year later, each presented as a single genome report (Devadas et al, 2018, Devadas et al, 2018)
We attempt to overcome this shortcoming by sequencing an additional 40 V. parahaemolyticus isolates from deceased shrimps and rearing water collected from three Malaysian shrimp aquaculture farms
Summary
Acute hepatopancreatic necrosis disease (AHPND), known as early mortality syndrome, is an emerging shrimp disease that has caused more than 60% reduction in shrimp (Litopenaeus vannamei) production worldwide, with global economic losses estimated to be up to USD $1 billion annually (FAO, 2013). V. parahaemolyticus strains identified the presence of a 70-kb pVa plasmid containing the pirABVp genes in the virulent strain that code for binary toxins with structural similarity to the Bacillus Cry insecticidal toxin-like proteins (Lee et al, 2015). This binary toxin induces cell death through pore formation in shrimp cell membranes leading to tissue degradation and digestive organ dysfunction (Lai et al, 2015, Lee et al, 2015, Han et al, 2016). Current genomic sampling suggests that most of AHPND-causing Vibrio spp. belong to the species V
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