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Whole Genome Sequencing – At the Frontiers of Food Safety

April 19, 2016

By: Melinda Hayman, Ph.D., Director, Microbiology and Ai Kataoka, Scientist, Science Operations

Whole Genome Sequencing (WGS), sometimes also referred to under the wider umbrella of next generation sequencing (NGS), has gathered a lot of steam in the food safety arena in a very short time.  This is largely due to the efforts of the US Food and Drug Administration (FDA) and the US Centers for Diseases Control and Prevention (CDC).  Dr Eric Brown and Dr Peter Gerner-Smidt of the FDA and CDC respectively have led the implementation of this technology in the US. At the GMA Science Forum they explained how this technology is used for food safety.  Mr. Joseph Levitt from Hogan Lovells shared an industry case study.

Every living thing contains the genetic material DNA.  DNA can be read, or “sequenced”, which gives a map, or fingerprint, of that organism.  Sequencing technology has been around for a while, and we have been able to replicate smaller sections of DNA for over 30 years.  However, sequencing a whole genome has been much harder.  This is because of the massive amounts of data involved.  The first human genome was sequenced in 2003, and microorganisms before that.  These first attempts were major undertakings that were incredibly expensive and time consuming.  However, over the last few years this technology has evolved, allowing for cheaper and faster sequencing that can be used in a more routine capacity.

So how is this technology used by regulatory agencies? DNA testing can tell us if two humans are related, and similarly WGS can tell us if two bacterial isolates are the same (i.e. come from the same source), or if they are different.  If a person becomes ill from eating a food contaminated with pathogenic bacteria and a bacterial culture is collected, the culture will go to the CDC or a State Health laboratory.  Pathogens such as Listeria monocytogenes, Salmonella or pathogenic E. coli can be sequenced using this technology; currently CDC sequences every L. monocytogenes isolate they receive.  In parallel, the FDA collects the same organisms from foods and processing facilities.  These sequences go into a database, as do the sequences obtained from patients with foodborne illness.  The fingerprints of each organism are compared and the database can show if other people are sick from the same bug, and if the bug has been isolated from a specific food or manufacturing facility.  In this way CDC and FDA can more rapidly identify and stop outbreaks of foodborne illness than in the past.

The speakers shared specific examples of how this technology is being used as well plans for its use in the future.  It’s clear that this is just the beginning and that this field will continue to quickly expand and improve public health.


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