17957
Vibrio population structure - Genetic and population structure analysis of clinical and environmental Vibrio parahaemolyticus strains
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
2725 Montlake Boulevard East
Seattle
WA
98112
USA
206-860-3200
http://www.nwfsc.noaa.gov
NWFSC Home
Online Resource
Metadata Contact
2015-10-01
Organization
Northwest Fisheries Science Center
NWFSC
nmfs.nwfsc.metadata@noaa.gov
2725 Montlake Boulevard East
Seattle
WA
98112
USA
206-860-3200
http://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
2019-06-05
https://www.webapps.nwfsc.noaa.gov/parr/Vibrio_Population_Structure_Supplementary_material_4425.pdf
2015-10-01
Organization
Northwest Fisheries Science Center
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
2022-08-09T17:11:07
2019-06-05
Northwest Fisheries Science Center
NWFSC
2725 Montlake Boulevard East
Seattle
WA
98112
USA
206-860-3200
http://www.nwfsc.noaa.gov
1001
Public
No
2019-06-05
1 Year
2020-06-05