Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback
This protocol outlines the all the steps necessary to become a GenomeTrakr data contributor. GenomeTrakr is an international genomic reference database of mostly food and environmental isolates from foodborne pathogens. The data and analyses are housed at the National Center for Biotechnology Information (NCBI), which is a database freely available to anyone in the world. The Pathogen Detection browser at NCBI computes daily cluster results adding the newly submitted data to the existing phylogenetic clusters of closely related genomes. Contributors to this database can see how their new isolates are related to the real-time foodborne pathogen surveillance program established in the USA and a few other countries, and at the same time adding valuable new data to the reference database.
Key wordsGenomeTrakr WGS Surveillance Genomics Foodborne pathogens Trackback
- 2.NCBI Pathogen Detection Homepage. https://www.ncbi.nlm.nih.gov/pathogens. Accessed 16 Jun 2018
- 5.CDC (2015) Annual report to the secretary, Department of health and human services. Improving governmental coordination and integration, interagency collaboration on genomics and food safety (Gen-FS), Section 1, pp. 22–23Google Scholar
- 9.Global Microbial Identifier (2011) The global microbial identifier homepage. http://www.globalmicrobialidentifier.org. Accessed 25 Jun 2018
- 12.Laing C ECTyper (and easy typer). In: GitHub. https://github.com/phac-nml/ecoli_serotyping. Accessed 25 Jun 2018