WHOLE GENOME SEQUENCING: THE BASICS

PUBLISHED ARTICLE

Sept 28, 2016 | EcoSure Food Safety Monitor

By Miriam Eisenberg, MS, RD, CP-FS

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With some recent outbreaks, there seemed to be illnesses popping up around the country that were identified as being the same outbreak. How do we determine how these illnesses are connected? A process called whole genome sequencing (WGS) is used. Without turning this into a genetics lesson, a genome is the genetic material of an organism including its DNA, genes and other genetic components. Genomes of organisms are unique rather like fingerprints. The Food and Drug Administration (FDA) and the Centers for Disease Control are using this technology to more precisely identify foodborne pathogens and their sources during foodborne illness outbreaks. By applying it in novel ways, there is the potential to help reduce foodborne illnesses and deaths over the long term both in the U.S. and abroad by more accurately defining the scope of outbreaks and providing actionable information so the most effective preventive controls can be implemented.

When people are sick across the country with the same illness (e.g., Salmonella or E. coli), genetic information from food or environmental isolates along with those from sick individuals are sent to a database that can link pathogens with the same genomes. This allows for determination of which illnesses may be part of the same outbreak, identify geographic regions that may be the source of the contaminated product, and further link illnesses. You can imagine how helpful this is with an outbreak—whether locally contained or when a single supplier sends a tainted product all over the country.

The Centers for Disease Control and Prevention (CDC) has over 80 geographically-spread PulseNet laboratories, within seven regions, using WGS as they scan their respective territories for outbreaks. Results among the 80 labs are linked. This advance gives public health officials the capability to connect outbreaks with more accuracy, likely identifying outbreaks sooner before large numbers of people may be affected. It is already helping find and define more outbreaks as it reveals the pathways of the stealthier foodborne pathogens.

The genome sequences are archived in a genomic reference database called GenomeTrakr which is also used by several other countries. GenomeTrakr can be used to find the contamination sources of current and future outbreaks, better understand the environmental conditions associated with the contamination of agricultural products, identify sources and help develop new rapid methods and culture independent tests.

For more information on the Whole Genome Sequencing Program (WGS), visit the FDA’s WGS webpage.

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