Whole Genome Sequencing
The laboratory process that determines the complete DNA sequence of an organism's genome at a single time is called:
- Whole Genome Sequencing (WGS)
- Full Genome Sequencing
- Complete Genome Sequencing
- Entire Genome Sequencing
This process involves arranging 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)
WGS reveals the complete DNA makeup of an organism. This enables laboratory scientists and epidemiologists to better understand differences both within and between groups. Understanding these differences allows differentiation between organisms with a precision that other technologies do not allow. Government agencies are in the process of integrating WGS to take advantage of the improved precision.
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. Then apply it in ways that have the potential to reduce foodborne illnesses and deaths over the long term both in the U.S. and abroad.
Compare pathogens isolated from food or environmental samples with clinical isolates from patients. If the pathogens found in food or food production environment match the pathogens from the sick patients, a link between the two can be made. This helps define the scope of a foodborne illness outbreak. WGS performs the same function as Pulse Field Gel Electrophoresis (PFGE) but can differentiate all strains of foodborne pathogens, no matter what the species. Its ability to differentiate between even related organisms allows outbreaks to be detected with fewer clinical cases and allows stopping outbreaks sooner and avoiding more illnesses.
Pairing genomic information of foodborne pathogens with their geographic location and applying rules of evolutionary biology to find the relation of the pathogens. Knowing the geographic areas that pathogens are associated with, can be a great tool in tracking the root source of contamination for a food product. Especially for 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 distribution network of labs with the capability to use WGS for pathogen identification.