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    Infectious Disease Control Unit
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Whole Genome Sequencing

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                                                                                          Resources- WGS


Whole genome sequencing (also known as WGS, full genome sequencing, complete genome sequencing, or entire genome sequencing) is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.


 

Introduction to Whole Genome Sequencing (WGS)  

Whole genome sequencing (WGS) reveals the complete DNA make-up of an organism, enabling laboratory scientists and epidemiologists to better understand variations both within and between species. Understanding these variations allows differentiation between organisms with a precision that other technologies do not allow.  Government agencies at all levels are in the process of integrating WGS to take advantage of the improved precision.  Examples include:  

  • Food and Drug Administration (FDA) has been using WGS since 2008.  The FDA is using WGS to perform basic foodborne pathogen identification during foodborne illness outbreaks, and applying it in novel ways that have the potential to help reduce foodborne illnesses and deaths over the long term both in the U.S and abroad

 

o   Compare pathogens isolated from food or environmental samples with clinical isolates from patients. If the pathogens found in the food or food production environment match the pathogens from the sick patients, a reliable link between the two can be made, which helps define the scope of a foodborne illness outbreak. WGS performs the same function as Pulse Field Gel Electrophoresis (PFGE) but has the power to differentiate virtually all strains of foodborne pathogens, no matter what the species. Its ability to differentiate between even closely related organisms allows outbreaks to be detected with fewer clinical cases and provides the opportunity to stop outbreaks sooner and avoid additional illnesses.

 

o   Pair genomic information of foodborne pathogens with their geographic location and apply the principles of evolutionary biology to determine the relatedness of the pathogens. Knowing the geographic areas that pathogens are typically associated with can be a powerful tool in tracking down the root source of contamination for a food product, especially multi-ingredient food products whose ingredients come from different states or countries. The faster public health officials can identify the source of contamination, the faster the harmful ingredient can be removed from the food supply and the more illnesses and deaths that can be averted.

 

FDA is spearheading an international effort to build a network of laboratories that can sequence the genomes of foodborne pathogens and then upload the genomic sequence of the pathogen and the geographic location from which the pathogen was gathered into a publicly accessible database. As the size of the database grows, so will its strength as a tool to help focus and speed investigations into the root cause of illnesses.  GenomeTrakr is a growing distributed network of labs with the capability to utilize WGS for pathogen identification.










 

Last updated May 22, 2017