Whole Genome Sequencing of foodborne pathogens

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The FDA’s Center for Food Safety and Applied Nutrition (CFSAN) has created the first integrated network of state and federal laboratories (GenomeTrakr) to use whole genome sequencing to track foodborne pathogens to improve outbreak response and effective monitoring of preventative controls. The GenomeTrakr network has created a publically available, global database containing the genetic makeup of thousands of foodborne disease causing organisms. This project is intended to develop a stronger international rapid surveillance system for pathogen trace-back by further enhancing the GenomeTrakr network and the growing database. The accurate and timely subtyping and subsequent clustering of isolates of a bacterium associated with a foodborne outbreak event is essential for successful investigation and eventual trackback to a specific food or environmental source. The genomic information provided by the GenomeTrakr network points investigators to specific food products potentially related to an outbreak, and provides insight into the origin of the contaminated food. This project will promote public health and state agricultural laboratories sequence pathogenic foodborne bacterium to be added to the on-line database. The local laboratories will be required to sequence a minimum of 250 food, environmental or animal isolates to be added to the database to identify future outbreaks. The local laboratories will also be required to participate in GenomeTrakr in a standard process requiring consistency of the sequencing and analysis while also participating in meetings, conferences and proficiency tests to ensure standardization between laboratories.