17957 Vibrio population structure (Genetic and population structure analysis of clinical and environmental Vibrio parahaemolyticus strains) Data Set Published / External 17938 Migrated from Resource Enhancement and Utilization Technologies Division Project Completed 2008-05-31 2019-06-05 Vibrio parahaemolyticus (Vp) is a marine bacterium capable of causing severe gastroenteritis in humans, usually through the consumption of raw shellfish. Before 1995, Vp-vibriosis was sporadic world-wide and caused by a relatively heterogeneous population of the bacterium. Since then, outbreaks have become more epidemic, with foci of infections traced to seafood harvested from single or geographically-linked sites. While initial outbreaks in Asia (and later in South America and the U.S. Gulf Coast region) have been attributed to a single serotypically-related pandemic clonal complex, other serotypes have been implicated in distinct geographical areas, including the Pacific Northwest and Alaska in the U.S. Current risk assessment models are based on the presence of the virulence-associated genes tdh and trh, yet illnesses have been attributed to tdh- and/or trh- isolates. Previous phylogenetic studies have shown that Vp, like most Vibrio spp., is a genetically diverse species, and as yet there has been no definitive conclusion as to what genes are essential for virulence. Using phenotypic, genetic, and genomic comparison methods such as Multi-Locus Sequence Typing (MLST), we are examining the hypothesis that a set of highly-virulent clones of Vp with increased pathogenic potential have recently emerged in the PNW, and determining whether the emergence can be correlated with specific environmental parameters. MLST and other genotyping analyses of clinical and environmental Vp isolates from PNW sources demonstrate the extensive patterns of diversity as seen elsewhere. However, the majority of PNW strains obtained from human infections form a distinct clonal complex separate from most environmental isolates. Interestingly, many environmental isolates obtained from PNW sources are phylogenetically related to the pandemic clonal complex, but this group has not been associated with clinical infections in the region. Genome sequences. Laboratory data Loaded by batch 4246, 01-29-2013 18:48 Subject to Public Access to Research Results (PARR): Yes Peer Reviewed Publication: Vibrio population structure. publication Theme Vibrio Theme abundance Theme climate change Spatial NWFSC Montlake Instrument DNA Sequencer Northwest Fisheries Science Center Seattle WA USA Data Set Other Other DNA Sequencer Platform Not Applicable Not Applicable Data Steward 2015-10-01 Person Strom, Mark S Mark.Strom@noaa.gov 2725 Montlake Blvd East Seattle WA 98112 206-860-3377 Distributor 2015-10-01 Organization Northwest Fisheries Science Center NWFSC nmfs.nwfsc.metadata@noaa.gov https://ror.org/05r7z1k40 2725 Montlake Boulevard East Seattle WA 98112 USA 206-860-3200 https://www.nwfsc.noaa.gov NWFSC Home Online Resource Metadata Contact 2015-10-01 Organization Northwest Fisheries Science Center NWFSC nmfs.nwfsc.metadata@noaa.gov https://ror.org/05r7z1k40 2725 Montlake Boulevard East Seattle WA 98112 USA 206-860-3200 https://www.nwfsc.noaa.gov NWFSC Home Online Resource Originator 2015-10-01 Person Strom, Mark S Mark.Strom@noaa.gov 2725 Montlake Blvd East Seattle WA 98112 206-860-3377 Point of Contact 2015-10-01 Person Strom, Mark S Mark.Strom@noaa.gov 2725 Montlake Blvd East Seattle WA 98112 206-860-3377 -122.3062 -122.3062 47.6449 47.6449 NWFSC Montlake: NWFSC Montlake lab, Seattle Range 2008-10-01 2012-10-05 Unclassified Genbank, http://www.ncbi.nlm.nih.gov/genbank/, Accession numbers: AONA00000000 AOOV00000000 AOOW00000000 AOOX00000000 AOOY00000000 AOOZ00000000 AOPA00000000 AOPB00000000 AOPC00000000 AOPD00000000 AOPE00000000 AOPF00000000 AOPG00000000 AOOU00000000 AOPH00000000 AOPI00000000 AOPJ00000000 AOPK00000000 AOPL00000000 NA https://www.webapps.nwfsc.noaa.gov/parr/Vibrio_Population_Structure_Supplementary_material_4425.pdf 2015-10-01 Organization Northwest Fisheries Science Center https://ror.org/05r7z1k40 Vibrio population structure Genetic and population structure analysis of clinical and environmental Vibrio parahaemolyticus strains https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/4425 Vibrio population structure Online Resource Web site NWFSC Dataset Information page. genome sequences Other - Genbank formatted genomes High Sequence reads were filtered through SOLiD Accuracy Enhancement Tool (SAET) and PCR duplicated reads were removed using the fastq_nodup tool from the SEAStAR pipeline . Genomes were assembled in color-space using the CLC Assembly Cell version 4.1. No 25 Yes No No 0 days No Delay Other 365 Data is maintained in a US Government data repository for genetic sequence information (Genbank) variety of bioinformatics-based analyses gov.noaa.nmfs.inport:17957 Jeffrey Cowen 2013-01-29T18:48:52 SysAdmin InPortAdmin 2026-03-04T19:17:17 2019-06-05 Northwest Fisheries Science Center NWFSC 2725 Montlake Boulevard East Seattle WA 98112 USA 206-860-3200 https://www.nwfsc.noaa.gov 1001 Public No No 2019-06-05 1 Year 2020-06-05