Genomic Characterization and Identification of Virulence Associated Genes of Isolated V. nigripulchritudo

Abstract

Vibrio nigripulchritudo (family Vibrionaceae) is an emerging pathogenic bacterium that causes vibriosis in penaeid shrimps. V. nigripulchritudo strains were isolated from the mass mortality that occurred in white-leg shrimp Penaeus vannamei in a closed aquarium in Tokyo, Japan in 2018. Those isolated bacterial colonies were identified and confirmed as V. nigripulchritudo by Sanger sequencing with 16S rRNA and hemolysin genes. Compared to other Vibrio pathogens, whole genome sequencing and annotation of V. nigripulchritudo are yet to be done. Therefore, Illumina and Nanopore whole genome sequencing technology was used to create hybrid genomic assemblies of the isolated strains (TUMSAT V.nig1, TUMSAT V.nig2 & TUMSAT V.nig3). The genome consisted of two circular chromosomes (I and II) with either one or two plasmids. The size of chromosome I ranged from 4.02 to 4.07 Mb with an average GC content of 46 % while the number of predicted coding sequences (CDSs) ranged from 3,563 to 3,644. The size of chromosome II ranged from 2.16 to 2.18 Mb, with an average GC content of 45.5 %, and the number of predicted CDSs ranged from 1,970 to 1,987. Numerous virulence-related genes are identified in either chromosome I or chromosome II related to adherence, antiphagocytosis, chemotaxis and motility, iron uptake, quorum sensing, secretion systems, and toxins. The presence of antimicrobial resistance genes suggests that the V. nigripulchritudo strains have multi-drug resistance. The presence of prophages and genomic islands indicates that this bacterium can acquire new genetic information through horizontal gene transfer. The comparative genomic analysis based on whole-genome proteome data of five V. nigripulchritudo genomes (three isolated strains with two reference genomes) showed that the resulting tree split into three clusters. With the findings of the annotated genomic features related to virulence factors and mobile genetic elements, the present study would be important for the prevention and control of vibriosis in penaeid shrimps.