Comparative Genomic Analysis of Seven Vibrio alginolyticus Strains Isolated From Shrimp Larviculture Water With Emphasis on Chitin Utilization

Abstract

The opportunistic pathogen Vibrio alginolyticus is gaining attention because of its disease-causing risks to aquatic animals and humans. In this study, seven Vibrio strains isolated from different shrimp hatcheries in Southeast China were subjected to genome sequencing and subsequent comparative analysis to explore their intricate relationships with shrimp aquaculture. The seven isolates had an average nucleotide identity of ≥ 98.3% with other known V. alginolyticus strains. The species V. alginolyticus had an open pan-genome, with the addition of ≥ 161 novel genes following each new genome for seven isolates and 14 publicly available V. alginolyticus strains. The percentages of core genes of the seven strains were up to 83.1–87.5%, indicating highly conserved functions, such as chitin utilization. Further, a total of 14 core genes involved in the chitin degradation pathway were detected on the seven genomes with a single copy, 12 of which had undergone significant purifying selection (dN/dS < 1). Moreover, the seven strains could utilize chitin as the sole carbon-nitrogen source. In contrast, mobile genetic elements (MGEs) were identified in seven strains, including plasmids, prophages, and genomic islands, which mainly encoded accessory genes annotated as hypothetical proteins. The infection experiment showed that four of the seven strains might be pathogenic because the survival rates of Litopenaeus vannamei postlarvae were significantly reduced (P < 0.05) when compared to the control. However, no obvious correlation was noted between the number of putative virulence factors and toxic effects of the seven strains. Collectively, the persistence of V. alginolyticus in various aquatic environments may be attributed to its high genomic plasticity via the acquisition of novel genes by various MGEs. In view of the strong capability of chitin utilization by diverse vibrios, the timely removal of massive chitin-rich materials thoroughly in shrimp culture systems may be a key strategy to inhibit proliferation of vibrios and subsequent infection of shrimp. In addition, transcontinental transfer of potentially pathogenic V. alginolyticus strains should receive great attention to avoid vibriosis.

Comparative Genomic Analysis of Shrimp-Pathogenic Vibrio parahaemolyticus LC and Intraspecific Strains with Emphasis on Virulent Factors of Mobile Genetic Elements

“…For example, strains FORC_023, AM51552, TJA114, and 2210633 resided in a subclade but came from Korea, the USA, China, and Japan, respectively. Similar to the results reported for V. harveyi and V. alginolyticus [17,28], the transcontinental spread of V. parahaemolyticus through the seafood trade or human activity also occurs frequently. In contrast, there was a relatively clear divergence in the two kinds of pathogenic strains regarding the accessory genome, i.e., 11 out of the 14 shrimp-pathogenic strains and seven of the 11 human-pathogenic strains separately clustered together, suggesting that the pathogenicity of V. parahemolyticus is closely associated with dispensable genes.…”

“…DNA extraction, genome sequencing, gene prediction, and functional annotation of the LC strain were performed as previously described [17]. The assembled contigs were subjected to a built-in plasmid database using data downloaded from NCBI (https: //ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/, accessed on 10 July 2023).…”

Insights into Chitin-Degradation Potential of Shewanella khirikhana JW44 with Emphasis on Characterization and Function of a Chitinase Gene SkChi65

“…Although chitin can be utilized by numerous bacteria, genome-wide investigations have been conducted mainly in vibrios [2,[36][37][38]. In this study, the genome of Sh.…”

“…Therefore, JW44 harbors the complete equipment needed for the degradation of chitin and its derivatives. However, some enzymes, including chitinase A and β-Nacetylhexosaminidase, are encoded by more than one gene, thus suggesting gene versatility in the chitin degradation pathway, although the chitinolytic ability is considered to be highly conserved across diverse bacterial genera [29,37,38].…”

Application of Fragmented Extracellular Self-DNA (esDNA) Concept as an Alternative Prophylactic Approach against Vibrio parahaemolyticus and Vibrio harveyi Infection in Brine Shrimp Artemia

“…The rapid development of aquaculture in recent decades requires increasing supply of fingerlings as one of the most critical factors for commercial success of the industry [10]. However, there are two bottlenecks in larviculture industry: disease outbreaks [11,12] and proper feed at the early larvae stage when larvae deplete yolk reserve and need to shift the feeding process from endogenous to exogenous system (Pan et al, 2022). Therefore, the combination of diseases control and viable phytoplankton and zooplankton is important, not only to provide more bio-available nutrients, but also to trigger higher responses to the pathogens [13,14].…”