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

The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused byVibrio parahaemolyticusharboring the pVA plasmid containing thepirAVpandpirBVpgenes which code forPhotorhabdusinsect-related (Pir) toxin. The limited genomic resource forV. parahaemolyticusstrains 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. parahaemolyticusfrom 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 ofV. parahaemolyticusthat harbor thepirABVpgenes. The recovery of pVA plasmid backbone devoid ofpirAVporpirABVpin someV. parahaemolyticusisolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of AsianV. 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.