(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Bacteria: NE > Proteobacteria: NE > Gammaproteobacteria: NE > Vibrionales: NE > Vibrionaceae: NE > Vibrio: NE > Vibrio harveyi group: NE > Vibrio parahaemolyticus: NE
Warning: This entry is a compilation of different species or line or strain with more than 90% amino acid identity. You can retrieve all strain data
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) Vibrio parahaemolyticus 50: N, E.
Vibrio parahaemolyticus 901128: N, E.
Vibrio parahaemolyticus AQ3810: N, E.
Vibrio parahaemolyticus Peru-466: N, E.
Vibrio parahaemolyticus AQ4037: N, E.
Vibrio parahaemolyticus AN-5034: N, E.
Vibrio parahaemolyticus K5030: N, E.
Vibrio parahaemolyticus 10329: N, E.
Vibrio parahaemolyticus RIMD 2210633: N, E.
Vibrio parahaemolyticus 3259: N, E.
Vibrio parahaemolyticus VP-NY4: N, E.
Vibrio parahaemolyticus O1:Kuk str. FDA_R31: N, E.
Vibrio parahaemolyticus NIHCB0757: N, E.
Vibrio parahaemolyticus 10290: N, E.
Vibrio parahaemolyticus O1:K33 str. CDC_K4557: N, E.
Vibrio parahaemolyticus VP250: N, E.
Vibrio parahaemolyticus BB22OP: N, E.
Vibrio parahaemolyticus VP232: N, E.
Vibrio parahaemolyticus 949: N, E.
Vibrio parahaemolyticus NIHCB0603: N, E.
Vibrio parahaemolyticus VPCR-2010: N, E.
Vibrio parahaemolyticus VP2007-095: N, E.
Vibrio parahaemolyticus VPTS-2010_2: N, E.
Vibrio parahaemolyticus V-223/04: N, E.
Vibrio parahaemolyticus 49: N, E.
Vibrio parahaemolyticus 863: N, E.
Vibrionales bacterium SWAT-3: N, E.
Vibrio alginolyticus 40B: N, E.
Vibrio sp. Ex25: N, E.
Vibrio alginolyticus 12G01: N, E.
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MAFTTRLMKLDSFCRYIVEFRCIAQKDNRKIKRNFMKKNTLAFATALALG SVLSVAHANEAAQSSVEQVTPKAITYPTTQKVDVVDDYFGTKMSDPYRWL EDDLSPETAEWVKAQNAVTFDYLSKIPYREQIEERITKLMDYEKQSQPFK EGRFTYFYKNDGLQNQDVLYRQLGDGDAEIFLDPNTFSEDGTTSLAGVSF SRDGSLVAYSISEGGSDWRKVIVLDTETKKPVGETLVDIKFSGISWLGNQ GFYYSSYDKPKGSELSAKTDQHKLYFHKLGTKQSEDQLIFGGFEEEKYRY VGGYTSDDERYLFISASVSTSGNKLFFKDLSKPNSPLKTILDNTSSDTWV IDNQGTKLYLVTNLNAPNKRVVTVDASQPQPKNWKDLIPETKNVLRVSTA GGNLFASYIVDAISMVKQYDMNGKLIREIKLPDIGSAYGFSGKKDETEVY YSFTNYKMPSTTYRLNIKDGDSEVYYKSKAPFDPALYDSRQVFYTSKDGT KVPMIITYKKGTPMDGCAPTILYGYGGFNISLTPSFNPTRAAWLELGGVY AVANIRGGGEYGKEWHNAGIQMQKQNVFDDFIAAAEYLIDEKVTSSNKLA INGGSNGGLLVGAVMTQRPELFKVALPAVGVLDMLRYHTFTAGAGWAYDY GTAEQSKEMFQYLKGYSPVHNVKAGVEYPATLITTGDHDDRVVPAHSYKF AAELQSKQAGSNPTLIRIETNAGHGAGTPTRKIIETNADIYSFALFNMGI EKLQ
BACKGROUND: Vibrio parahaemolyticus is a common cause of foodborne disease. Beginning in 1996, a more virulent strain having serotype O3:K6 caused major outbreaks in India and other parts of the world, resulting in the emergence of a pandemic. Other serovariants of this strain emerged during its dissemination and together with the original O3:K6 were termed strains of the pandemic clone. Two genomes, one of this virulent strain and one pre-pandemic strain have been sequenced. We sequenced four additional genomes of V. parahaemolyticus in this study that were isolated from different geographical regions and time points. Comparative genomic analyses of six strains of V. parahaemolyticus isolated from Asia and Peru were performed in order to advance knowledge concerning the evolution of V. parahaemolyticus; specifically, the genetic changes contributing to serotype conversion and virulence. Two pre-pandemic strains and three pandemic strains, isolated from different geographical regions, were serotype O3:K6 and either toxin profiles (tdh+, trh-) or (tdh-, trh+). The sixth pandemic strain sequenced in this study was serotype O4:K68. RESULTS: Genomic analyses revealed that the trh+ and tdh+ strains had different types of pathogenicity islands and mobile elements as well as major structural differences between the tdh pathogenicity islands of the pre-pandemic and pandemic strains. In addition, the results of single nucleotide polymorphism (SNP) analysis showed that 94% of the SNPs between O3:K6 and O4:K68 pandemic isolates were within a 141 kb region surrounding the O- and K-antigen-encoding gene clusters. The "core" genes of V. parahaemolyticus were also compared to those of V. cholerae and V. vulnificus, in order to delineate differences between these three pathogenic species. Approximately one-half (49-59%) of each species' core genes were conserved in all three species, and 14-24% of the core genes were species-specific and in different functional categories. CONCLUSIONS: Our data support the idea that the pandemic strains are closely related and that recent South American outbreaks of foodborne disease caused by V. parahaemolyticus are closely linked to outbreaks in India. Serotype conversion from O3:K6 to O4:K68 was likely due to a recombination event involving a region much larger than the O-antigen- and K-antigen-encoding gene clusters. Major differences between pathogenicity islands and mobile elements are also likely driving the evolution of V. parahaemolyticus. In addition, our analyses categorized genes that may be useful in differentiating pathogenic Vibrios at the species level.
BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. RESULTS: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, < or = 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. CONCLUSION: The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.
Background Vibrio parahaemolyticus, a gram-negative marine bacterium, is a worldwide cause of food-borne gastroenteritis. V parahaemolyticus strains of a few specific serotypes, probably derived from a common clonal ancestor, have lately caused a pandemic of gastroenteritis. The organism is phylogenetically close to V cholerae, the causative agent of cholera.
METHODS:
The whole genome sequence of a clinical V parahaemolyticus strain RIMD2210633 was established by shotgun sequencing. The coding sequences were identified by use of Gambler and Glimmer programs. Comparative analysis with the V cholerae genome was undertaken with MUMmer.
FINDINGS:
The genome consisted of two circular chromosomes of 3288558 bp and 1877212 bp; it contained 4832 genes. Comparison of the V parahaemolyticus genome with that of V cholerae showed many rearrangements within and between the two chromosomes. Genes for the type III secretion system (TTSS) were identified in the genome of V parahaemolyticus; V cholerae does not have these genes.
INTERPRETATION:
The TTSS is a central virulence factor of diarrhoea-causing bacteria such as shigella, salmonella, and enteropathogenic Escherichia coli, which cause gastroenteritis by invading or intimately interacting with intestinal epithelial cells. Our results suggest that V parahaemolyticus and V cholerae use distinct mechanisms to establish infection. This finding explains clinical features of V parahaemolyticus infections, which commonly include inflammatory diarrhoea and in some cases systemic manifestations such as septicaemia, distinct from those of V cholerae infections, which are generally associated with non-inflammatory diarrhoea.
