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Short Citation:
Northwest Fisheries Science Center, 2022: Vibrio population structure - Genetic and population structure analysis of clinical and environmental Vibrio parahaemolyticus strains, https://www.fisheries.noaa.gov/inport/item/17957.

Item Identification

Title: Vibrio population structure - Genetic and population structure analysis of clinical and environmental Vibrio parahaemolyticus strains
Short Name: Vibrio population structure (Genetic and population structure analysis of clinical and environmental Vibrio parahaemolyticus strains)
Status: Completed
Creation Date: 2008-05-31
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

Supplemental Information:

Subject to Public Access to Research Results (PARR): Yes

Peer Reviewed Publication: Vibrio population structure. publication

Keywords

Theme Keywords

Thesaurus Keyword
UNCONTROLLED
None abundance
None climate change
None Vibrio

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
None NWFSC Montlake

Instrument Keywords

Thesaurus Keyword
UNCONTROLLED
None DNA Sequencer

Physical Location

Organization: Northwest Fisheries Science Center
City: Seattle
State/Province: WA
Country: USA

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: Other
Data Presentation Form: Other

Support Roles

Data Steward

CC ID: 853178
Date Effective From: 2015-10-01
Date Effective To:
Contact (Person): Strom, Mark S
Address: 2725 Montlake Blvd East
Seattle, WA 98112
Email Address: Mark.Strom@noaa.gov
Phone: 206-860-3377

Distributor

CC ID: 853179
Date Effective From: 2015-10-01
Date Effective To:
Contact (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
URL: NWFSC Home

Metadata Contact

CC ID: 853177
Date Effective From: 2015-10-01
Date Effective To:
Contact (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
URL: NWFSC Home

Originator

CC ID: 853181
Date Effective From: 2015-10-01
Date Effective To:
Contact (Person): Strom, Mark S
Address: 2725 Montlake Blvd East
Seattle, WA 98112
Email Address: Mark.Strom@noaa.gov
Phone: 206-860-3377

Point of Contact

CC ID: 853180
Date Effective From: 2015-10-01
Date Effective To:
Contact (Person): Strom, Mark S
Address: 2725 Montlake Blvd East
Seattle, WA 98112
Email Address: Mark.Strom@noaa.gov
Phone: 206-860-3377

Extents

Extent Group 1

Extent Group 1 / Geographic Area 1

CC ID: 853186
W° Bound: -122.3062
E° Bound: -122.3062
N° Bound: 47.6449
S° Bound: 47.6449
Description

NWFSC Montlake: NWFSC Montlake lab, Seattle

Extent Group 1 / Time Frame 1

CC ID: 853185
Time Frame Type: Range
Start: 2008-10-01
End: 2012-10-05

Access Information

Security Class: Unclassified
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

Distribution Information

Distribution 1

CC ID: 853182
Start Date: 2019-06-05
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

URLs

URL 1

CC ID: 853183
URL: https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/4425
Name: Vibrio population structure
URL Type:
Online Resource
File Resource Format: Web site
Description:

NWFSC Dataset Information page. genome sequences

Technical Environment

Description:

Other - Genbank formatted genomes

Data Quality

Accuracy:

High

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
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

Lineage Statement:

variety of bioinformatics-based analyses

Catalog Details

Catalog Item ID: 17957
GUID: gov.noaa.nmfs.inport:17957
Metadata Record Created By: Jeffrey W Cowen
Metadata Record Created: 2013-01-29 18:48+0000
Metadata Record Last Modified By: Jeffrey W Cowen
Metadata Record Last Modified: 2019-06-05 16:05+0000
Metadata Record Published: 2019-06-05
Owner Org: NWFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Review Frequency: 1 Year