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. Issue 17 (7th October 2019)

• Record Type: Journal Article
• Authors: Yan, Chrystine Zou Yi; Austin, Christopher M; Ayub, Qasim; Rahman, Sadequr; Gan, Han Ming
• Is Part Of: FEMS microbiology letters. Volume 366:Issue 17(2019)
• Publication Date: 2019-10-07
• Subjects: multi-locus sequence typing -- shrimp -- whole-genome sequencing -- phylogenomics -- comparative genomics; Microbiology -- Periodicals; 579
• DOI: 10.1093/femsle/fnz211
• Languages: English
• ISSNs: 0378-1097

Abstract

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 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. Abstract : The draft genomes of 40 Vibrio parahaemolyticus collected from Malaysian shrimp aquaculture farms were assembled and analyzed, providing the first comprehensive insight into the genomic diversity of V. parahaemolyticus in Malaysia.