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      Draft Genome Sequences of Six Strains of Vibrio parahaemolyticus Isolated from Early Mortality Syndrome/Acute Hepatopancreatic Necrosis Disease Shrimp in Thailand

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          Abstract

          Some strains of Vibrio parahaemolyticus cause acute hepatopancreatic necrosis disease (AHPND) in shrimp. We sequenced 3 AHPND and 3 non-AHPND strains and found that all of them lacked the pathogenicity island relevant to human infection. A unique sequence encoding a type IV pilus/type IV secretion system was found in 3 AHPND strains.

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          Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae.

          Kozo MAKINO, Kenshiro Oshima, Ken Kurokawa … (2003)
          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. 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. 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. 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.
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            Determination of the infectious nature of the agent of acute hepatopancreatic necrosis syndrome affecting penaeid shrimp.

            Loc Tran, Linda Nunan, Rita M Redman … (2013)
            A new emerging disease in shrimp, first reported in 2009, was initially named early mortality syndrome (EMS). In 2011, a more descriptive name for the acute phase of the disease was proposed as acute hepatopancreatic necrosis syndrome (AHPNS). Affecting both Pacific white shrimp Penaeus vannamei and black tiger shrimp P. monodon, the disease has caused significant losses in Southeast Asian shrimp farms. AHPNS was first classified as idiopathic because no specific causative agent had been identified. However, in early 2013, the Aquaculture Pathology Laboratory at the University of Arizona was able to isolate the causative agent of AHPNS in pure culture. Immersion challenge tests were employed for infectivity studies, which induced 100% mortality with typical AHPNS pathology to experimental shrimp exposed to the pathogenic agent. Subsequent histological analyses showed that AHPNS lesions were experimentally induced in the laboratory and were identical to those found in AHPNS-infected shrimp samples collected from the endemic areas. Bacterial isolation from the experimentally infected shrimp enabled recovery of the same bacterial colony type found in field samples. In 3 separate immersion tests, using the recovered isolate from the AHPNS-positive shrimp, the same AHPNS pathology was reproduced in experimental shrimp with consistent results. Hence, AHPNS has a bacterial etiology and Koch's Postulates have been satisfied in laboratory challenge studies with the isolate, which has been identified as a member of the Vibrio harveyi clade, most closely related to V. parahemolyticus.
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              CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

              Marco Galardini, Emanuele G. Biondi, Marco Bazzicalupo … (2011)
              Recent developments in sequencing technologies have given the opportunity to sequence many bacterial genomes with limited cost and labor, compared to previous techniques. However, a limiting step of genome sequencing is the finishing process, needed to infer the relative position of each contig and close sequencing gaps. An additional degree of complexity is given by bacterial species harboring more than one replicon, which are not contemplated by the currently available programs. The availability of a large number of bacterial genomes allows geneticists to use complete genomes (possibly from the same species) as templates for contigs mapping. Here we present CONTIGuator, a software tool for contigs mapping over a reference genome which allows the visualization of a map of contigs, underlining loss and/or gain of genetic elements and permitting to finish multipartite genomes. The functionality of CONTIGuator was tested using four genomes, demonstrating its improved performances compared to currently available programs. Our approach appears efficient, with a clear visualization, allowing the user to perform comparative structural genomics analysis on draft genomes. CONTIGuator is a Python script for Linux environments and can be used on normal desktop machines and can be downloaded from http://contiguator.sourceforge.net.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 10 April 2014
                Publication date Collection: Mar-Apr 2014
                Volume: 2
                Issue: 2
                Electronic Location Identifier: e00221-14
                Affiliations
                [a ]Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
                [b ]Marine Shrimp Culture Research and Development Institute, Coastal Fisheries Research and Development Bureau, Department of Fisheries, Kasetklang Chatuchak, Bangkok, Thailand
                [c ]Charoen Pokphand Foods Public Co., Ltd., Aquatic Animal Health Research Center, Samutsakorn, Thailand
                [d ]Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
                Author notes
                Address correspondence to Ikuo Hirono, hirono@ 123456kaiyodai.ac.jp .
                Article
                Publisher ID: genomeA00221-14
                DOI: 10.1128/genomeA.00221-14
                PMC ID: 3983294
                PubMed ID: 24723705
                SO-VID: 661cc537-3e8a-4166-a95f-ef229db96e77
                Copyright © Copyright © 2014 Kondo et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                Date received : 25 February 2014
                Date accepted : 26 March 2014
                Page count
                Pages: 2
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date March/April 2014
                access-type free

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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