Journal
FEMS MICROBIOLOGY LETTERS
Volume 366, Issue 17, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/femsle/fnz211
Keywords
multi-locus sequence typing; shrimp; whole-genome sequencing; phylogenomics; comparative genomics
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Funding
- Ministry of Higher Education [FRGS/1/2016/STG05/MUSM/03/1]
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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 pirA(Vp) and pirB(Vp) 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 pirAB(Vp) genes. The recovery of pVA plasmid backbone devoid of pirA(Vp) or pirAB(Vp) 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.
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