​​​​Harnessing​ WGS Data to Stop Foodborne Outbreaks​

​Geno​​meTrakr is a laboratory network that utilizes whole genome sequencing (WGS) for pathogen identification. ​​Led by FDA's Center for Food Safety and Applied Nutrition (CFSAN)​, the GenomeT​rakr network​ is comprised of public health and university laboratories that collect and share genomic and geographic data from foodborne pathogens. The data, which are housed in public databases at the National Center for Biotechnology Information​, can be accessed by researchers and public health officials for real-time comparison and analysis that can speed foodborne illness outbreak investigations and reduce foodborne illnesses and death. 

The images to the right show the various domestic and international laboratories that participate in the Genome​​​Trakr network. ​

APHL Activities

GenomeTrakr Meeting

APHL supports GenomeTrakr activities through training, technical meetings, and information dissemination. APHL assists with the planning of the annual GenomeTrakr Meeting, an invitation-only meeting that will bring together laboratories, industry, academia and federal partners to discuss best practices, common challenges, and how collected data is utilized in various foodborne outbreak investigations. 

View presentations from previous conferences.​

Resources

​Many laboratories are looking to outside entities to source isolates for sequencing. FDA has provided a contract template for the transferring materials from outside sources to the laboratory. This template can be customized to fit your laboratory's needs.

APHL/FDA Bioinformatics Training

APHL and FDA have partnered to create a one-hour bioinformatics webinar​ focused on the basics of phylogeny and how it can be applied to whole genome sequencing data during outbreak investigations. 

WGS Software and Platform Training​​​

FDA CFSAN has developed short training modules to help laboratories utilize various tools and platforms when analyzing WGS data. These videos can also be found on the Galaxy Trakr's YouTube channel.

Galaxy Trakr Overview ​
This video provides an overview of Galaxy Trakr, an open source, web-based platform for accessible, reproducible and transparent computational biomedical research. It allows users without programming experience to easily specify parameters and run individual tools as well as larger workflows.

Galaxy Trakr Interface
This tutorial walks the viewer through the four parts of the Galaxy Trakr interface: the tool list on the left, the viewing panel in the middle and the analysis and data history on the right.

Seqsero Training
This training video demonstrates how users can utilize Seqsero software to determine serotypes, or groups within a single species of microorganisms, such as bacteria or viruses, which share distinctive surface structures.​