Protecting families from contaminated food and water
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Protecting families from contaminated food and water
Posted in Our Blog on June 19, 2026
What is Whole Genome Sequencing?
With all of the foodborne illness outbreaks in the news lately, the term whole genome sequencing has been tossed around. But what is whole genome sequencing anyway?
For the answer to this question, we must start with a little science lesson.
To answer the question, “What is whole genome sequencing,” you must first take a step back to understand what whole genome sequencing is looking at.
DNA.
If you have watched any number of popular Crime Scene shows or remember a bit about this topic in your high school biology class, you may remember this acronym.
DNA is short for deoxyribonucleic acid.
Virtually every cell in a living organism has DNA. It is the code that tells each cell what to do. It says, “you are here, so you are a liver cell.” Or “you are here, so you are a skin cell.” It contains codes for your eye color, hair color, and tells each cell just about everything it needs to know to function.
It is replicated and then passed onto the next cell when it is time to make another one.
All of that information is packed onto tightly wrapped coiled helixes paired together with chemical bonds.
How much information?
In humans, a single strand of DNA measures only 6 microns across. But if you stretched out the DNA from one cell it would be 2 meters long! There are 3 million bases in a single strand of DNA. It is one of the tiniest but largest molecules!
But humans are not the only organisms that contain DNA. Plants, animals, and single-celled bacteria have it too!
All of that biological information is coded by a sequence of base pairs.
In DNA, base pairs are made up of four basic molecules. They are adenine (A), cytosine (C), guanine (G), and thymine (T).
The sequences that these bases appear on the DNA strand matter.
But more importantly for foodborne illness investigation purposes, they are fairly stable. So much so, that minor differences in bacterial strands stay the same when they replicate. This is the basis for using whole genome sequencing in different applications.
So, what is whole genome sequencing anyway?
Whole genome sequencing is a scientific process of gathering information about the order of those bases.
It starts with extracting DNA from organic cells. There are many different ways to do this.
Some laboratories chemically open these microscopic cells with materials that break down cell walls. Others shred the cells through mechanical DNA extraction methods.
DNA can be gathered by running the cell pieces through specialized filters designed to let everything but molecules the size of DNA through. Or other similar methods.
Once the DNA is acquired, the real magic happens.
Each piece of DNA is analyzed for the bases (A, C, G, and T) that it contains. Then the order of each base on the DNA section is determined.
This information provides the sequence of that sample’s DNA.
It could look something like: A-T-G-G-C-C-T-A-G-T-A-A-C-G-T-A-A-A-G-C-T-……
Once obtained, this unique sequence can be compared to other samples of DNA.
Whole genome sequencing can match sick patient DNA back to a source? How does this happen?
Let’s explore a hypothetical case example.
A patient reports to their healthcare provider that they are very sick.
They have been experiencing bloody diarrhea, vomiting, and stomach pain. But those symptoms have seemed to resolve. But they are still feeling very sick. They aren’t producing much urine and they are very pale.
The doctor suspects a type of bacterial infection and obtains a sample. Due to the seriousness of the symptoms, the doctor admits the patient to the hospital, because they are experiencing symptoms associated with an E. coli complication known as hemolytic uremic syndrome, or HUS.
The patient’s sample is tested for the more common foodborne, intestinal illnesses. Bacteria like Salmonella, Campylobacter, E. coli, and others like it.
In this case, the patient’s sample tests positive for E. coli.
As part of a foodborne illness reporting requirement, the sample is sent off for whole genome sequencing. If you have been following along, you will know how that is done. The results are uploaded to a foodborne illness surveillance network database where it can be compared to other patient samples.
If a cluster of illnesses with the same intestinal bacterial illness is observed or the whole genome sequencing is connected to a larger outbreak, the patient will be interviewed.
They will be asked about the foods and drinks that they consumed prior to becoming sick. Where they ate them. Where they got them from.
Investigators will compare those answers to other sick people in the outbreak. If there is an overlap, a traceback investigation can begin.
During the traceback investigation, outbreak investigators will try to determine the brands of foods that the interview answers had in common.
They can do this through shopper rewards cards or receipts if available.
Once a common source is identified, outbreak investigators will perform manufacturer site investigations and collect samples. If available, samples of open packages in the patient’s possession will also be tested.
These samples will be screened, and if positive, whole genome sequencing will be performed.
Fortunately, whole genome sequencing can distinguish between minor differences, even in the same strain of bacteria.
If the patient samples are a genetic match to food samples, a source has been identified!
Once a food source has been identified, a recall can be announced.
Recalls remove potentially harmful or hazardous foods from the food supply.
This entire process hopefully leads to fewer people becoming sick once a problem is discovered. Investigators can feel confident that the source was responsible for the original patient’s illness and others connected to the outbreak.
If you’d like to know more about food safety topics in the news, like “What is Whole Genome Sequencing and Why is This Test Used in Foodborne Illness Investigations?,” check out the Make Food Safe Blog. We regularly update trending topics, foodborne infections in the news, recalls, and more! Stay tuned for quality information to help keep your family safe, while The Lange Law Firm, PLLC strives to Make Food Safe!
By: Heather Van Tassell (contributing writer, non-lawyer)