Genomic and evolutionary features of nine AHPND positive Vibrio parahaemolyticus strains isolated from South American shrimp
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ABSTRACT:
PROVIDER: PRJEB53801 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR9880130_1.fastq.gz | Fastqsanger.gz | |||
| ERR9880130_2.fastq.gz | Fastqsanger.gz | |||
| ERR9880131_1.fastq.gz | Fastqsanger.gz | |||
| ERR9880131_2.fastq.gz | Fastqsanger.gz |
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Project description:Vibrio parahaemolyticus is a bacterial pathogen that becomes lethal to Penaeus shrimps when acquiring the pVA1-type plasmid carrying the PirABvp genes, causing acute hepatopancreatic necrosis disease (AHPND). This disease causes significant losses across the world, with outbreaks reported in Southeast Asia, Mexico, and South America. Virulence level and mortality differences have been reported in isolates from different locations, and whether this phenomenon is caused by plasmid-related elements or genomic-related elements from the bacteria remains unclear. Here, nine genomes of South American AHPND-causing V. parahaemolyticus (VPAHPND) isolates were assembled and analyzed using a comparative genomics approach at (i) whole-genome, (ii) secretion system, and (iii) plasmid level, and then included for a phylogenomic analysis with another 86 strains. Two main results were obtained from our analyses. First, all isolates contained pVA1-type plasmids harboring the toxin coding genes, and with high similarity with the prototypical sequence of Mexican-like origin, while phylogenomic analysis showed some level of heterogeneity with discrete clusters and wide diversity compared to other available genomes. Second, although a high genomic similarity was observed, variation in virulence genes and clusters was observed, which might be relevant in the expression of the disease. Overall, our results suggest that South American pathogenic isolates are derived from various genetic lineages which appear to have acquired the plasmid through horizontal gene transfer. Furthermore, pathogenicity seems to be a multifactorial trait where the degree of virulence could be altered by the presence or variations of several virulence factors. IMPORTANCE AHPND have caused losses of over $2.6 billion to the aquaculture industry around the world due to its high mortality rate in shrimp farming. The most common etiological agent is V. parahaemolyticus strains possessing the pVA1-type plasmid carrying the PirABvp toxin. Nevertheless, complete understanding of the role of genetic elements and their impact in the virulence of this pathogen remains unclear. In this work, we analyzed nine South American AHPND-causing V. parahaemolyticus isolates at a genomic level, and assessed their evolutionary relationship with other 86 strains. We found that all our isolates were highly similar and possessed the Mexican-type plasmid, but their genomic content did not cluster with other Mexican strains, but instead were spread across all isolates. These results suggest that South American VPAHPND have different genetic backgrounds, and probably proceed from diverse geographical locations, and acquire the pVA1-type plasmid via horizontal gene transfer at different times.
| S-EPMC10433878 | biostudies-literature
Project description:Vibrio parahaemolyticus is a Gram-negative bacterium commonly found in marine and estuarine environments. Acute hepatopancreatic necrosis disease (AHPND) caused by this bacterium is an ongoing problem among shrimp farming industries. V. parahaemolyticus proteins PirA and PirB have been determined to be major virulence factors that induce AHPND. In this study, Pacific white shrimp (Litopenaeus vannamei) were challenged with recombinant PirA and PirB by a reverse gavage method and then at 30 m, 1, 2, 4, and 6 h time points, the hepatopancreas of five individual shrimp were removed and placed into RNA later. We conducted RNA sequencing of the hepatopancreas samples from a no PirA/B control (n = 5) and PirA/B-treated shrimp at the different time intervals (n=5). We evaluated the different gene expression patterns between the time groups to the control with a focus on identifying differences in innate immune function.
2023-05-05 | GSE200137 | GEO
Project description:Bacteria in nature are widely exposed to differential fluid shears which are often a trigger for phenotypic switches. The latter mediates transcriptional and translation remodeling of cellular metabolism impacting among others virulence, antimicrobial resistance and stress resistance. In this study, we evaluated the role of fluid shear on phenotypic switch in an acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio parahaemolyticus M0904 strain under both in vitro and in vivo conditions. The results showed that V. parahaemolyticus M0904 grown at lower shaking speed (110 min-1 constant agitation, M0904/110), causing low fluid shear, develop cellular aggregates or floccules. These cells increased levan production (as verified by concanavalin binding) and developed differentially stained colonies on Congo Red agar plates and resistance to antibiotics. In addition, the phenotypic switch causes a major shift in the protein secretome. At 120 min-1 (M0904/120), PirA/B toxins are mainly produced, while at 110 min-1 PirA/B toxin production is stopped and an alkaline phosphatase PhoX becomes the dominant protein in the protein secretome. These observations are matched with a very strong reduction in virulence of M0904/110 towards two crustacean larvae, namely Artemia and Macrobrachium. Taken together, our study provides substantial evidence for the existence of two phenotypic forms in AHPND Vibrio parahaemolyticus strains displaying differential phenotypes that could be of interest in understanding the epidemiology of AHPND under aquaculture conditions. It might provide the basis for AHPND control by steering phenotypes.
2020-02-05 | PXD015617 | Pride
Project description:Vibrio parahaemolyticus AHPND+ strain
| PRJNA604195 | ENA
Project description:In order to gain a better understanding of the impact of Vibrio parahaemolyticus infection on genetic regulation of Litopenaeus vannamei,we performed a transcriptome analysis in the hepatopancreas of Litopenaeus vannamei challenged with Vibrio parahaemolyticus, using the Illumina HiSeq 2500 platform.
2020-06-18 | GSE107697 | GEO
Project description:In order to gain a better understanding of the impact of Vibrio parahaemolyticus infection on genetic regulation of Litopenaeus vannamei,we performed a miRNA-seq analysis in the hepatopancreas of Litopenaeus vannamei challenged with Vibrio parahaemolyticus, using the Illumina HiSeq 2500 platform.
2020-06-18 | GSE107696 | GEO
Project description:BackgroundDue to its rapid lethal effect in the early development stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) has been causing great economic losses, since its first outbreak in southeast China in 2009. Vibrio parahaemolyticus, carrying the pirA and pirB toxin genes is known to cause AHPND in shrimp. The overall objective of this study was to sequence the whole genome of AHPND positive V. parahaemolyticus strains isolated from shrimp (Peneaus monodon) of the south-west region of Bangladesh in 2016 and 2017 and characterize the genomic features and emergence pattern of this marine pathogen.ResultsTwo targeted AHPND positive V. parahaemolyticus strains were confirmed using PCR with 16S rRNA, ldh, AP3 and AP4 primers. The assembled genomes of strain MSR16 and MSR17 were comprised of a total of 5,393,740 bp and 5,241,592 bp, respectively. From annotation, several virulence genes involved in chemotaxis and motility, EPS type II secretion system, Type III secretion system-1 (T3SS-1) and its secreted effectors, thermolabile hemolysin were found in both strains. Importantly, the ~ 69 kb plasmid was identified in both MSR16 and MSR17 strains containing the two toxin genes pirA and pirB. Antibiotic resistance genes were predicted against β-lactam, fluoroquinolone, tetracycline and macrolide groups in both MSR16 and MSR17 strains.ConclusionsThe findings of this research may facilitate the tracking of pathogenic and/or antibiotic-resistant V. parahaemolyticus isolates between production sites, and the identification of candidate strains for the production of vaccines as an aid to control of this devastating disease. Also, the emergence pattern of this pathogen can be highlighted to determine the characteristic differences of other strains found all over the world.
| S-EPMC6889531 | biostudies-literature
Project description:Vibrio parahaemolyticus strain:AHPND Genome sequencing
| PRJNA1110797 | ENA
Project description:Naturally bacteria are commonly forced to remain in stationary phase. There is no increase in cell mass, however, cell division keep on. Vibrio (V.) parahaemolyticus is an aquatic bacterium capable of causing foodborne gastroenteritis outbreaks all over the world. So far, little is known about whole genomic expression of V. parahaemolyticus in the early stationary phase compared with the phase of exponential growth. Since under starvation cell sizes decrease and endogenous metabolism reduces, genes are considered to be highly repressed in the stationary phase. However, our data shows in total 172 induced genes, while 61 genes were repressed in the early stationary phase compared with exponential phase. In fatty acid and phospholipid metabolism functional category only induced genes were found, whereas in three other metabolic functional groups appeared no significant up-regulated genes (adjusted P-value<0.05). Genes in two metabolic functional categories remained stable in the early stationary phase. DAVID analyses were carried out exploring the gene regulation. In total, ten functional categories showed a total up-regulation in early stationary phase, while only three metabolic functional categories showed a down-regulation and four categories showed stably in early stationary phase. Early stationary phase gene expression was detected in total bacterial RNA of V. parahaemolyticus. Two phases (exponential phase and early stationary phase) were used in 8 biological replicates. Gene expression in exponential phase was used for normalization.
2015-01-31 | E-GEOD-65448 | biostudies-arrayexpress
Project description:Vibrio parahaemolyticus is a Gram-negative marine bacterium. Strain RIMD 2210633, the wild type strain of the organism, causes acute gastroenteritis in humans. Human intestinal factor bile often affects the global gene regulation in some species of enteropathogenic bacteria. To determine the genes in V. parahaemolyticus that respond to bile, we investigated the differences in the transcriptomes of the wild type strain and the vtrA-null strain grown in Luria-Bertani medium cultivated with or without 0.04% crude bile. The vtrA gene encodes the previously identified T3SS2 regulator. Our goal is to demonstrate bile regulon controlled by VtrA in V. parahaemolyticus.
2010-10-10 | GSE21666 | GEO