Whole Genome Sequencing


Things to know about Whole Genome Sequencing if you are in the food industry





Things to know about Whole Genome Sequencing:


·         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.


·         Whole genome sequencing should not be confused with DNA profiling, which only determines the likelihood that genetic material came from a particular individual or group


·         Whole genome sequencing (WGS) is an advanced technique that determines the DNA sequence of microorganisms, and helps to differentiate them with greater detail than other contemporary technologies


·         FSIS intends to implement the use of this technology for characterization of all FSIS isolates


·         FSIS performs WGS on all Listeria monocytogenes isolates 


·         WGS as a tool to understand potential Listeria monocytogenes harborage or reoccurrence of contamination in establishments


·         On dual-jurisdiction establishments that produce both FDA and FSIS-regulated products


·         FDA is using this technology 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.


·         Whole genome sequencing reveals the complete DNA make-up of an organism, enabling us to better understand variations both within and between species. This in turn allows us to differentiate between organisms with a precision that other technologies do not allow.


·         The most basic application of this technology to food safety is using it to identify pathogens isolated from food or environmental samples. These can then be compared to 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. This type of testing has traditionally been done using methods such as PFGE, but there are some strains of Salmonella spp. that PFGE is unable to differentiate. Whole genome sequencing performs the same function as 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.


·         It can be used: to determine which illnesses are part of an outbreak and which are not; to determine which ingredient in a multi-ingredient food is responsible for an outbreak; to identify geographic regions from which a contaminated ingredient may have originated; to differentiate sources of contamination, even within the same outbreak; to link illnesses to a processing facility even before the food product vector has been identified; to link small numbers of illnesses that otherwise might not have been identified as common outbreak; and to identify unlikely routes of contamination.


·         It can be used as an industry tool for monitoring ingredient supplies, the effectiveness of preventive and sanitary controls, and to develop new rapid method and culture independent tests; to determine the persistence of pathogens in the environment; to monitor emerging pathogens; and as a possible indicator of antimicrobial resistance.


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