Salmonella enterica (ID 183844) - BioProject

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Accession: PRJNA183844 ID: 183844

Salmonella enterica

GenomeTrakr umbrella project for Salmonella enterica

See Genome Information for Salmonella enterica

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This project is a component of the GenomeTrakr umbrella project

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22 additional projects are components of the GenomeTrakr umbrella project.

This umbrella project holds a set of data bioprojects, each representing a laboratory sequencing Salmonella enterica in collaboration with GenomeTrakr's open genomic epidemiology surveillance effort for the real-time monitoring of foodborne pathogens.

Accession	PRJNA183844
Type	Umbrella project (Subtype:Disease)
Keyword	GMI
Organism	Salmonella enterica[Taxonomy ID: 28901] Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; Salmonella enterica
Publications	Timme RE et al., "Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.", One Health Outlook, 2020;2(1):20 Allard MW et al., "Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database.", J Clin Microbiol, 2016 Aug;54(8):1975-83
Submission	Registration date: 13-Dec-2012 Center for Food Safety and Applied Nutrition
NCBI Links	NCBI Pathogen Detection
Related Resources	FDA Whole Genome Sequencing Program (WGS) NCBI Pathogen FTP Salmonella Outbreaks Whole Genome Sequencing (WGS) Fast Facts FDA GenomeTrakr Video
Relevance	Agricultural, Medical, Industrial, Environmental

Project Data:

Resource Name	Number of Links
Sequence data
Nucleotide (total)	218416
WGS master	101309
Genomic DNA	694
SRA Experiments	110045
Protein Sequences	8768059
Publications
PubMed	10
PMC	9
Other datasets
BioSample	112408
Assembly	101748

SRA Data Details

Parameter	Value
Data volume, Gbases	49,756
Data volume, Tbytes	29.09

Salmonella enterica encompasses the following 76 sub-projects:

Project Type

Number of Projects

Genome sequencing

Highest level of assembly :

Complete genome
Chromosomes
Contigs
SRA or Trace
No data links
Total

9
1
54
5
6
75

BioProject accession	Assembly level	Name	Title
PRJNA810433	Contigs	Bacterial Foodborne Pathogens Whole Genome sequencing- Office of the Texas State Chemist, AgriLife Research, Texas A&M University System	Bacterial Foodborne Pathogens Whole Genome sequencing- Office of the Texas State Chemist, AgriLife Research, Texas A&M University System (Texas A&M University)
PRJNA684629	Contigs	GenomeTrakr - Arizona - 2020 proficiency testing	GenomeTrakr - Arizona - 2020 proficiency testing (AZ GenomeTrakr submission...)
PRJNA308180	Complete genome	GenomeTrakr Project: Environmental Salmonella isolates, Emory University - FDA-CFSAN	GenomeTrakr Project: Environmental Salmonella isolates, Emory University - FDA-CFSAN (FDA)
PRJNA659259	Contigs	GenomeTrakr Project: Kentucky Department for Public Health	GenomeTrakr Project: Kentucky Department for Public Health (KY Dept. for Public Health...)
PRJNA186035	Complete genome	Salmonella	GenomeTrakr Project: US Food and Drug Administration (Center for Food Safety and...)

List all 75 'Genome sequencing' projects...

BioProject accession	Assembly level	Name	Title
PRJNA810433	Contigs	Bacterial Foodborne Pathogens Whole Genome sequencing- Office of the Texas State Chemist, AgriLife Research, Texas A&M University System	Bacterial Foodborne Pathogens Whole Genome sequencing- Office of the Texas State Chemist, AgriLife Research, Texas A&M University System (Texas A&M University)
PRJNA684629	Contigs	GenomeTrakr - Arizona - 2020 proficiency testing	GenomeTrakr - Arizona - 2020 proficiency testing (AZ GenomeTrakr submission...)
PRJNA308180	Complete genome	GenomeTrakr Project: Environmental Salmonella isolates, Emory University - FDA-CFSAN	GenomeTrakr Project: Environmental Salmonella isolates, Emory University - FDA-CFSAN (FDA)
PRJNA659259	Contigs	GenomeTrakr Project: Kentucky Department for Public Health	GenomeTrakr Project: Kentucky Department for Public Health (KY Dept. for Public Health...)
PRJNA186035	Complete genome	Salmonella	GenomeTrakr Project: US Food and Drug Administration (Center for Food Safety and...)
PRJNA338674	Contigs	Salmonella	GenomeTrakr Project: Ohio Department of Agriculture Animal Disease Diagnostic Laboratory (FDA)
PRJNA183851	Contigs	Salmonella enterica	GenomeTrakr Project: Washington State Department of Health Public Health Laboratory (Washington State Department...)
PRJNA183850	Complete genome	Salmonella enterica	GenomeTrakr Project: NY State Dept. of Health, Wadsworth Center (New York State Dept. of Health...)
PRJNA183848	Contigs	Salmonella enterica	GenomeTrakr Project: Florida Department of Health, University of Florida (Florida Department of Health)
PRJNA183847	Contigs	Salmonella enterica	GenomeTrakr Project: Arizona State Public Health Laboratory (Arizona State Public Health...)
PRJNA215333	Complete genome	Salmonella enterica	GenomeTrakr Project: Minnesota Department of Health (FDA/CFSAN)
PRJNA217342	Contigs	Salmonella enterica	GenomeTrakr Project: Technology and Food Safety Services, Mexico (FDA/CFSAN)
PRJNA219491	Contigs	Salmonella enterica	GenomeTrakr Project: Virginia - Division of Consolidated Laboratory Services (FDA/CFSAN)
PRJNA227458	Contigs	Salmonella enterica	GenomeTrakr real-time SE: NY State Dept. of Health, Wadsworth Center (Wadsworth Center / NYSDOH)
PRJNA242847	Complete genome	Salmonella enterica	GenomeTrakr Project: USDA - Food Safety and Inspection Service (FDA)
PRJNA252015	Contigs	Salmonella enterica	Salmonella enterica Genome sequencing and assembly (Washington State Department...)
PRJNA259341	Contigs	Salmonella enterica	GenomeTrakr Project: Belgium (FDA/CFSAN)
PRJNA259925	Contigs	Salmonella enterica	GenomeTrakr Project: United Kingdom, Food and Environment Research Agency (Fera)
PRJNA260089	Contigs	Salmonella enterica	GenomeTrakr Project: Western Carolina University (FDA/CFSAN)
PRJNA266622	Contigs	Salmonella enterica	GenomeTrakr Project: Turkey (FDA Center for Food Safety...)
PRJNA271470	Contigs	Salmonella enterica	GenomeTrakr Project: Maryland Department of Health and Mental Hygiene (FDA Center for Food Safety...)
PRJNA271293	Contigs	Salmonella enterica	GenomeTrakr Project: Argentina (FDA Center for Food Safety...)
PRJNA243636	Contigs	Salmonella enterica	GenomeTrakr Project: UCD Centre for Food Safety (FDA/CFSAN)
PRJNA274995	Contigs	Salmonella enterica	GenomeTrakr Project: Hawaii State Department of Health - HSLD (US Food and Drug Administration)
PRJNA277983	Contigs	Salmonella enterica	GenomeTrakr Project: California Department of Public Health - FDLB Micro (US Food and Drug Administration)
PRJNA280335	Contigs	Salmonella enterica	GenomeTrakr Project: SDSU Veterinary & Biomedical Sciences/ DOH South Dakota (US Food and Drug Administration)
PRJNA284276	Contigs	Salmonella enterica	GenomeTrakr Project: Texas Department of State Health Services (FDA)
PRJNA293224	Contigs	Salmonella enterica	GenomeTrakr Project: Thakur Molecular Epidemiology Laboratory, NC State University (US Food and Drug Administration)
PRJNA298359	Contigs	Salmonella enterica	GenomeTrakr Project: Florida Department of Agriculture (US Food and Drug Administration)
PRJNA306262	Contigs	Salmonella enterica	GenomeTrakr project: Alaska State Public Health Laboratory-Anchorage (FDA)
PRJNA275961	Contigs	Salmonella enterica	GenomeTrakr: OSU-ICOPHAI project (US Food and Drug Administration)
PRJNA311905	No data links	Salmonella enterica	GenomeTrakr project: FDA-CFSAN, Moffett Center (FDA)
PRJNA312217	Contigs	Salmonella enterica	GenomeTrakr Project: New Mexico State University, Food Safety Laboratory (FDA)
PRJNA313928	Complete genome	Salmonella enterica	FDA-CFSAN Salmonella isolated from environmental sources in Northwest Mexico (FDA)
PRJNA322206	Contigs	Salmonella enterica	GenomeTrakr project: FDA-CFSAN, IFSH (FDA)
PRJNA338682	Contigs	Salmonella enterica	GenomeTrakr Project: State Hygienic Laboratory at the University of Iowa (FDA)
PRJNA342434	No data links	Salmonella enterica	GenomeTrakr Project: Joint Institute for Food Safety and Applied Nutrition (FDA)
PRJNA342956	Contigs	Salmonella enterica	GenomeTrakr Project: NSU- Halmos College of Natural Sciences and Oceanography_Microbiology & Genetics Laboratory (FDA)
PRJNA357723	Contigs	Salmonella enterica	GenomeTrakr Project: Penn State University \| Department of Food Science \| Dudley Lab (FDA)
PRJNA357818	No data links	Salmonella enterica	GenomeTrakr Project: NSF International \| Applied Research Center (FDA)
PRJNA368989	Contigs	Salmonella enterica	GenomeTrakr Project: Michigan Department of Agriculture and Rural Development (FDA)
PRJNA369523	SRA or Trace	Salmonella enterica	GenomeTrakr Project: Massachusetts Department of Public Health (FDA)
PRJNA377900	Contigs	Salmonella enterica	GenomeTrakr Project: New York State Department of Agriculture and Markets (NYAG) (FDA)
PRJNA378379	Chromosomes	Salmonella enterica	GenomeTrakr Project: DVA, OARSA (CFSAN)
PRJNA419416	Contigs	Salmonella enterica	GenomeTrakr project: KSU - Food Science Institute - Food Microbiology and Food Safety (FDA)
PRJNA480281	Contigs	Salmonella enterica	Salmonella enterica SENASICA MX (SENASICA)
PRJNA336192	Contigs	Salmonella enterica	GenomeTrakr Project: Washington State University (FDA)
PRJNA319593	Complete genome	Salmonella enterica	GenomeTrakr project: Salmonella enterica, MDU PHL, Australia (Microbiological Diagnostics...)
PRJNA541970	Complete genome	Salmonella enterica	GenomeTrakr Project: U.S. Food and Drug Administration - CFSAN (FDA Center for Food Safety...)
PRJNA560080	Contigs	Salmonella enterica	Joint Institute For Food Safety And Applied Nutrition: Whole Genome Sequencing of Salmonella enterica isolated from water samples (FDA Center for Food Safety...)
PRJNA578395	Contigs	Salmonella enterica	GenomeTrakr Project: Kentucky Department for Public Health (FDA Center for Food Safety...)
PRJNA489746	SRA or Trace	Salmonella enterica	Salmonella enterica subsp. enterica (Institute of Clinical Pathology...)
PRJNA605356	SRA or Trace	Salmonella enterica	Genomic Characterization of Environmental Salmonella from the Shenandoah Valley of Virginia (Virginia Division of Consolidated...)
PRJNA613829	Contigs	Salmonella enterica	GenomeTrakr Project: Washington State Department of Agriculture (Washington State Department...)
PRJNA628951	Contigs	Salmonella enterica	Kansas State University Food Science Institute - Salmonella enterica (FDA Center for Food Safety...)
PRJNA669829	Contigs	Salmonella enterica	South Carolina Department of Health Salmonella enterica Genome sequencing and assembly (South Carolina Dept. of Health...)
PRJNA675595	Contigs	Salmonella enterica	GenomeTrakr Project: VT Dept. of Health, Salmonella enterica (Vermont Department of Health...)
PRJNA675624	Contigs	Salmonella enterica	GenomeTrakr Project: Michigan Department of Health and Human Services (Michigan Department of Health...)
PRJNA729420	Contigs	Salmonella enterica	Genome Trakr Project: Indiana State Health Department Laboratory (Indiana State Department...)
PRJNA758970	No data links	Salmonella enterica	Genome Trakr Project: Rhode Island Department of Health (Rhode Island State Health...)
PRJNA774258	Contigs	Salmonella enterica	GenomeTrakr Project: NJ Department of Agriculture, Animal Health Diagnostics Laboratory (New Jersey Department of...)
PRJNA795996	No data links	Salmonella enterica	Salmonella enterica Genome sequencing and assembly (GenomeTrakr Project: New...)
PRJNA800417	SRA or Trace	Salmonella enterica	GenomeTrakr Project: Salmonella, Missouri State Public Health Laboratory (Missouri State Public Health...)
PRJNA817286	Contigs	Salmonella enterica	GenomeTrakr Project: Georgia Department of Agriculture (Virginia Division of Consolidated...)
PRJNA822386	Contigs	Salmonella enterica	GenomeTrakr Project: Louisiana Department of Agriculture and Forestry (Virginia Division of Consolidated...)
PRJNA826447	Contigs	Salmonella enterica	GenomeTrakr Project: West Virginia Department of Agriculture (Megan Young)
PRJNA832232	SRA or Trace	Salmonella enterica	GenomeTrakr Project: Kansas State University (GenomeTrakr Project: Massachusetts...)
PRJNA861691	Contigs	Salmonella enterica	GenomeTrakr Project: State of New Hampshire Public Health laboratories (State of NH Public Health...)
PRJNA889815	Contigs	Salmonella enterica	Salmonella enterica Raw sequence reads for GenomeTrakr (CDPHE SARS-CoV-2 submissions)
PRJNA912184	Complete genome	Salmonella enterica	Salmonella enterica Genome sequencing and assembly GenomeTrakr project: INCIENSA (INCIENSA)
PRJNA939705	Contigs	Salmonella enterica	Salmonella enterica Genome sequencing and assembly (NOAA/NSIL)
PRJNA1073910	Contigs	Salmonella enterica	Salmonella enterica Genome sequencing and assembly (COFEPRIS-CCAYAC)
PRJNA237212	Contigs	Salmonella enterica subsp. enterica	GenomeTrakr real-time SE: Minnesota Department of Health (Minnesota Department of Health)
PRJNA656565	No data links	Salmonella enterica subsp. enterica	GenomeTrakr Project: Kentucky Department for Public Health (KY Dept. for Public Health...)
PRJNA818719	Contigs	WGS sequencing of S. Typhimurium involved in an outbreak in NSW	WGS sequencing of S. Typhimurium involved in an outbreak in NSW (Institute of Clinical Pathology...)

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Umbrella project

BioProject accession	Name	Title
PRJNA321162	MDU PHL, Australia: GenomeTrakr Whole Genome Sequencing (WGS) Program	MDU PHL, Australia: GenomeTrakr Whole Genome Sequencing (WGS) Program (Microbiological Diagnostics...)

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GenomeTrakr umbrella project for Salmonella enterica

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