Collaboration Details

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Title of Collaborative Activity:

Pathogen Detection Project and Interagency Collaboration on Genomics for Food and Feed Safety (Gen-FS)

Description of Collaborative Activity:

The Pathogen Detection Project is a multi-agency collaboration that is combining data from pathogen outbreaks with other information to determine the major source of contamination. The project is conducted via a centralized system that integrates sequence data for bacterial pathogens obtained from food, the environment, and human patients. A number of public health agencies in the US and internationally are collecting samples from these sources to facilitate active, real-time surveillance of pathogens and foodborne disease. The agencies sequence the samples and submit the data to the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM) at the National Institutes of Health (NIH), which analyzes the sequences against others in its database to identify closely related sequences. The aim is to uncover potential sources of contamination by linking isolates from food or the environment to human illness and to quickly report the sequence relationships to public health scientists in order to aid traceback investigations and outbreak response. Collaborating agencies include the Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), United States Department of Agriculture (USDA) Food Safety and Inspection Service, and Public Health England. The US agencies formalized their collaboration in a charter document (Interagency Collaboration on Genomics for Food and Feed Safety (Gen-FS)) that includes coordinating activities on antimicrobial resistance.

Type of Collaborative Activity:

Resource Development

Year the Collaborative Activity Originated:


NIH Participating Institutes/Centers/Office of the Director:


HHS Agency Collaborators on this Activity: