This project comprises a set of umbrella bioprojects, each established for a pathogen being sequenced by the GenomeTrakr network. These genomes, along with those collected by other networks, like PulseNet, are analyzed in real-time by public health officials who are detecting and responding to foodborne outbreaks and contamination events. Automated clustering and genotyping screens for these data can be found at NCBI Pathogen Detection (linked below).
| Accession | PRJNA593772 |
| Type | Umbrella project |
| 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
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| Submission | Registration date: 5-Dec-2019
NCBI |
| NCBI Links | |
| Related Resources | |
| Relevance | Medical |
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| Nucleotide (total) | 1049369 |
| WGS master | 154348 |
| Genomic DNA | 1099 |
| Transcript | 5822 |
| SRA Experiments | 171653 |
| Protein Sequences | 17521245 |
| Publications |
| PubMed | 50 |
| PMC | 47 |
| Other datasets |
| BioSample | 177264 |
| PopSet | 2 |
| Assembly | 154861 |
Multispecies encompasses the following 22 sub-projects:
| Project Type | Number of Projects |
Genome sequencingHighest level of assembly : SRA or Trace |
5
|
BioProject
accession | Assembly
level | Organism | Title |
|---|
| PRJNA954325 | SRA or Trace | Aeromonas sp. | Genomic Characterization of Environmental Aeromonas sp. from the Shenandoah Valley of Virginia (Virginia Division of Consolidated...) | | PRJNA741099 | SRA or Trace | Listeria monocytogenes | Listeria monocytogenes Genome sequencing and assembly (Institute of Environmental...) | | PRJNA720150 | SRA or Trace | Salmonella enterica | Salmonella enterica genome sequencing and assembly (Institute of Environmental...) | | PRJNA1086499 | SRA or Trace | Salmonella enterica | Salmonella enterica Genome sequencing and assembly (University of Kentucky) | | PRJNA741100 | SRA or Trace | Shigella | New Zealand Shigella Genome sequencing and assembly (Institute of Environmental...) |
|
| Umbrella project | 17 |
BioProject
accession | Name | Title |
|---|
| PRJNA692474 | Bacillus cereus | GenomeTrakr umbrella project for Bacillus cereus (FDA) | | PRJNA258021 | Campylobacter sp. | GenomeTrakr umbrella project for Campylobacter jejuni and Campylobacter coli (FDA/CFSAN) | | PRJNA290488 | Clostridium botulinum | GenomeTrakr umbrella project for Clostridium botulinum (US Food and Drug Administration) | | PRJNA258402 | Cronobacter sp. | Cronobacter sp. (FDA/CFSAN) | | PRJNA357477 | Cyclospora cayetanensis | CycloTrakr (Cyclospora cayetanensis GenomeTrakr) (CFSAN) | | PRJNA826518 | Enterococcus | GenomeTrakr umbrella project for Enterococcus (FDA Center for Food Safety...) | | PRJNA230919 | Escherichia coli | GenomeTrakr umbrella project for Escherichia coli and Shigella sp. (FDA/CFSAN) | | PRJNA706695 | Klebsiella oxytoca | Umbrella for Klebsiella oxytoca (FDA Center for Food Safety...) | | PRJNA706693 | Klebsiella pneumoniae | Umbrella for Klebsiella pneumoniae (FDA Center for Food Safety...) | | PRJNA856239 | Legionella sp. | Legionella GenomeTrakr Project: FDA-CFSAN (FDA Center for Food Safety...) | | PRJNA514048 | Listeria sp. | GenomeTrakr umbrella project for Listeria sp (FDA Center for Food Safety...) | | PRJNA706684 | Multispecies | GenomeTrakr umbrella for diverse pathogen species (FDA Center for Food Safety...) | | PRJNA183844 | Salmonella enterica | GenomeTrakr umbrella project for Salmonella enterica (Center for Food Safety and...) | | PRJNA494553 | Staphylococcus | GenomeTrakr Umbrella Project for Staphylococcus sp. (FDA Center for Food Safety...) | | PRJNA245885 | Vibrio sp. | GenomeTrakr umbrella project for Vibrio parahaemolyticus (FDA/CFSAN) | | PRJNA374341 | Vibrio vulnificus | GenomeTrakr Umbrella Project for Vibrio vulnificus (US Food and Drug Administration) | | PRJNA774554 | Yersinia enterocolitica | GenomeTrakr umbrella project for Yersinia enterocolitica (FDA Center for Food Safety...) |
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