Comparative genomic provides insight into the virulence and genetic diversity of Vibrio parahaemolyticus associated with shrimp acute hepatopancreatic necrosis disease

Abstract

Acute hepatopancreatic necrosis disease (AHPND) is an important shrimp disease of economic importance which causes mass mortality of cultivated penaeid shrimps in Southeast Asian countries, Mexico and South America. This disease was originally caused by Vibrio parahaemolyticus (VP_AHPND) which is reported to harbour a transferable plasmid carrying the virulent PirAB-like toxin genes (pirAB^vp). However, little is known about the pathogenicity of VP_AHPND. To extend our understanding, comparative genomic analyses was performed in this study to identify the genetic differences and to understand the phylogenetic relationship of VP_AHPND strains. Seven Vibrio parahaemolyticus strains (five VP_AHPND strains and two non-VP_AHPND strains) were sequenced and 31 draft genomes of V. parahaemolyticus were retrieved from NCBI database and incorporated into the genomic comparison to elucidate their genomic diversity. The study showed that the genome sizes of the VP_AHPND strains were approximately 5 Mbp. Ten sequence types (STs) were identified among the VP_AHPND strains using in silico-Multilocus Sequence Typing analysis (MLST) and ST 970 was the predominant ST. Phylogenetic analysis based on MLST and single nucleotide polymorphisms (SNP) showed that the VP_AHPND strains were genetically diverse. Based on the comparative genomic analysis, several functional proteins were identified from diiferent categories associated with virulence-related proteins, secretory proteins, conserved domain proteins, transporter proteins, and phage proteins. The CRISPR analysis showed that VP_AHPND strains contained less number of CRISPRs elements than non-VP_AHPND strains while six prophages regions were identified in the genomes, suggested the lack of CRISPR might promote prophage insertion. The genomic information in this study provide improved understanding of the virulence of these VP_AHPND strains.

Keywords: AHPND; Comparative genomics; Phylogenetic tree; VP(AHPND); Virulence.