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Whole Genome Sequencing Update

Previous blogs have addressed Whole Genome Sequencing (WGS), what it is and its regulatory and public health uses.  With use of WGS expanding at an amazing rate, an update is both appropriate and necessary.  We recommend that everyone in the food industry keep an eye on this technology as it is now the method being used by the regulatory agencies in outbreaks.

We had previously mentioned that the regulatory and public health agencies were developing a library of results.  The library, known as the Genome Trakr Network, is now made up of “14 federal labs, 14 state health and university labs, 1 U.S. hospital lab, 5 labs located outside of the U.S., and collaborations with independent academic researchers.”

As of October 2015, there are 35,000 isolates in the Network, with over 1,000 added each month.  This is a 10-fold increase in the number of isolates added per month compared to 2013.

It is expected that the Network will continue to grow exponentially in 2016.  In addition to the Food and Drug Administration (FDA) and Food Safety and Inspection Service (FSIS) entering regulatory samples and the Centers for Disease Control (CDC) entering clinical samples, growth will come from many additional sources including:

  • The CDC and FDA are working to sequence every clinical, food, and environmental isolate of Listeria monocytogenes previously collected in the U.S.
  • Minnesota, Washington, and New York have paired with FDA to sequence Salmonella enteritidis isolates from clinical, food, and environmental samples. 
  • FDA is encouraging all state public health laboratories to sequence any pathogen involved in an outbreak and upload the genomic information to the Genome Trakr database.

It is also important to note that when an isolate is entered into the database, the geographic location of where the sample was taken is also entered.  Adding the information regarding where the sample is taken enables tracing of movement of the organism and can assist in identifying the likely geographic source of an outbreak.  Some may think of this as comparable to the National Crime Information Center used by the Federal Bureau of Investigation (FBI).  Just as the NCIC helps criminal justice professionals “apprehend fugitives, locate missing persons, recover stolen property, and identify terrorists,” the goal of the Genome Trakr is to link ill consumers with the specific food that caused them to become sick.

Significant progress is being made by the regulatory agencies with the increased amount of data that is now contained in the Genome Trakr.  Scientists have begun to compare similarities and differences at certain points in the DNA chain of pathogens from patients and products that have been entered in the database to determine the relationship between similar, but not identical, genome sequences (GS).  This current comparison method shows whether the GS are related and if they are likely derived from a common ancestor.

The use of these relationships among GS is being used to determine the source of products leading to outbreaks.  If the sample from ill consumers and a food product are closely related genetically, then the presumption is that there is food borne outbreak and the food caused the illnesses.  Several outbreaks where a close GS relationship was used to link case patients and food products have been identified, including peanut butter (2014), cheese (2014), stuffed raw chicken (2015) and ice cream (2015).

We anticipate these relationships and links to grow as the database continues its rapid growth rate.

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