Vibrio population structure - Genetic and population structure analysis of clinical and environmental Vibrio parahaemolyticus strains
Northwest Fisheries Science Center
Data Set
(DS)
| ID: 17957
| Published / External
Created: 2013-01-29
|
Last Modified: 2022-08-09
Project (PRJ) | ID: 17938
ID: 17957
Data Set (DS)
* Discovery• First Pass
» Metadata Rubric
Item Identification
* » Title | Vibrio population structure - Genetic and population structure analysis of clinical and environmental Vibrio parahaemolyticus strains |
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Short Name | Vibrio population structure (Genetic and population structure analysis of clinical and environmental Vibrio parahaemolyticus strains) |
* Status | Completed |
Creation Date | 2008-05-31 |
Revision Date | |
• Publication Date | 2019-06-05 |
* » Abstract |
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. |
* Purpose |
Laboratory data |
Notes |
Loaded by batch 4246, 01-29-2013 18:48 |
Other Citation Details | |
• Supplemental Information |
Subject to Public Access to Research Results (PARR): Yes Peer Reviewed Publication: Vibrio population structure. publication |
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Keywords
Theme Keywords
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None | abundance |
None | climate change |
None | Vibrio |
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* Spatial Keywords
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None | NWFSC Montlake |
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None | DNA Sequencer |
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Physical Location
• » Organization | Northwest Fisheries Science Center |
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• » City | Seattle |
• » State/Province | WA |
• Country | USA |
• » Location Description |
Data Set Information
* Data Set Scope Code | Data Set |
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• Data Set Type | Other |
• Maintenance Frequency | |
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» Data Presentation Form | Other |
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Support Roles
* » Support Role | Data Steward |
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* » Date Effective From | 2015-10-01 |
Date Effective To | |
Person | Strom, Mark S |
Address |
2725 Montlake Blvd East Seattle, WA 98112 |
Email Address | Mark.Strom@noaa.gov |
Phone | 206-860-3377 |
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* » Support Role | Distributor |
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* » Date Effective From | 2015-10-01 |
Date Effective To | |
Organization | Northwest Fisheries Science Center (NWFSC) |
Address |
2725 Montlake Boulevard East Seattle, WA 98112 USA |
Email Address | nmfs.nwfsc.metadata@noaa.gov |
Phone | 206-860-3200 |
Fax | |
Mobile | |
URL | http://www.nwfsc.noaa.gov |
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* » Support Role | Metadata Contact |
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* » Date Effective From | 2015-10-01 |
Date Effective To | |
Organization | Northwest Fisheries Science Center (NWFSC) |
Address |
2725 Montlake Boulevard East Seattle, WA 98112 USA |
Email Address | nmfs.nwfsc.metadata@noaa.gov |
Phone | 206-860-3200 |
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Mobile | |
URL | http://www.nwfsc.noaa.gov |
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* » Support Role | Originator |
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* » Date Effective From | 2015-10-01 |
Date Effective To | |
Person | Strom, Mark S |
Address |
2725 Montlake Blvd East Seattle, WA 98112 |
Email Address | Mark.Strom@noaa.gov |
Phone | 206-860-3377 |
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* » Support Role | Point of Contact |
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* » Date Effective From | 2015-10-01 |
Date Effective To | |
Person | Strom, Mark S |
Address |
2725 Montlake Blvd East Seattle, WA 98112 |
Email Address | Mark.Strom@noaa.gov |
Phone | 206-860-3377 |
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Extents
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Extent Group 1 / Geographic Area 1
* » W° Bound | -122.3062 |
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* » E° Bound | -122.3062 |
* » N° Bound | 47.6449 |
* » S° Bound | 47.6449 |
* » Description |
NWFSC Montlake: NWFSC Montlake lab, Seattle |
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* » Time Frame Type | Range |
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* » Start | 2008-10-01 |
End | 2012-10-05 |
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* » Security Class | Unclassified |
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» Data Access Procedure |
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 |
• » Data Access Constraints |
NA |
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Distribution Information
Start Date | 2019-06-05 |
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End Date | Present |
» Download URL | https://www.webapps.nwfsc.noaa.gov/parr/Vibrio_Population_Structure_Supplementary_material_4425.pdf |
Distributor | Northwest Fisheries Science Center (NWFSC) (2015-10-01 - Present) |
File Name | Vibrio population structure |
Description |
Genetic and population structure analysis of clinical and environmental Vibrio parahaemolyticus strains |
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URLs
URL | https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/4425 |
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Name | Vibrio population structure |
URL Type | Online Resource |
File Resource Format | Web site |
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NWFSC Dataset Information page. genome sequences |
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Other - Genbank formatted genomes |
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» Quality Control Procedures Employed |
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. |
Data Management
» Have Resources for Management of these Data Been Identified? | No |
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» Approximate Percentage of Budget for these Data Devoted to Data Management | 25 |
» Do these Data Comply with the Data Access Directive? | Yes |
» Is Access to the Data Limited Based on an Approved Waiver? | No |
» If Distributor (Data Hosting Service) is Needed, Please Indicate | No |
» Approximate Delay Between Data Collection and Dissemination | 0 days |
» If Delay is Longer than Latency of Automated Processing, Indicate Under What Authority Data Access is Delayed |
No Delay |
» Actual or Planned Long-Term Data Archive Location | Other |
» If World Data Center or Other, Specify | Genbank/NCBI |
» Approximate Delay Between Data Collection and Archiving | 365 |
» How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive? |
Data is maintained in a US Government data repository for genetic sequence information (Genbank) |
Lineage
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variety of bioinformatics-based analyses |
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Catalog Details
Catalog Item ID | 17957 |
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Metadata Record Created By | Jeffrey W Cowen |
Metadata Record Created | 2013-01-29 18:48+0000 |
Metadata Record Last Modified By | SysAdmin InPortAdmin |
» Metadata Record Last Modified | 2022-08-09 17:11+0000 |
Metadata Record Published | 2019-06-05 |
Owner Org | NWFSC |
Metadata Publication Status | Published Externally |
Do Not Publish? | N |
Metadata Workflow State | Published / External |
Metadata Last Review Date | 2019-06-05 |
Metadata Review Frequency | 1 Year |
Metadata Next Review Date | 2020-06-05 |
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