Whole Genome Sequencing of foodborne pathogens

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.