Abstract
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.
Highlights
1.1 Inception of GenomeTrakr Within the FDA MissionIn 2012 FDA began a pilot project called GenomeTrakr to build a public genomic reference database of historical food and environmental isolates of Salmonella
Foodborne pathogen isolates collected by FDA field laboratories were a major contributor of the food and environmental isolates in the PulseNet PFGE database
Food and environmental isolates contributed from state public labs varies from state to state depending on sampling efforts and levels of collaboration with respective state agriculture lab(s)
Summary
The goal of this project was to improve the accuracy and response time for identifying the causes of foodborne outbreaks, to identify harborage in facilities, and to aid in establishing preventative controls [1]. In this pilot WGS data were collected by a distributed set of public health laboratories, transferred to the FDA for quality screening, uploaded under an umbrella BioProject at NCBI’s SRA database (Fig. 1).
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