Food Forensics: Using Genetic Fingerprinting to Trace Food Borne Illness

April 2009
By Emily Terrell

Tags: basics, techniques, forensics

Imagine that you roll out of bed one morning only to double over with severe stomach pains and nausea. At first you think it must be the flu, especially considering that your friends are sick too. Later, you hear about a few cases of salmonella in your region. The only correlation between the cases seems to be the recent consumption of Mexican food…which reminds you that you and your friends had a chips and salsa party last week. You begin to wonder: is it the flu or is it salmonella?  

Approximately 11-13 million Canadians face this question each year. It is estimated that 1.1 million of these cases represent acute bacterial disease (like severe salmonella poisoning) and cost around $1.1 billion annually in lost revenue and associated expenses. Thus, it is important to quickly identify the cause of outbreaks and the source of contaminations. Health agencies such as the Centers for Disease Control and Prevention (CDC) rely on a number of techniques including genetic fingerprinting to trace food borne illness to its source.   

What Causes Food Borne Illness?
Food borne illness is primarily caused by eating food contaminated with bacteria, viruses, or parasites. In North America, 79% of outbreaks of food borne illness have been caused by contaminating pathogenic (disease-causing) bacteria, including the Maple Leaf Foods outbreak (Listeria monocytogenes), the Peanut Corporation of America outbreak (Salmonella typhimurium), and the tomato/pepper outbreak of 2008 (Salmonella enterica, Saintpaul serotype).   

In order to trace food borne illness, it is necessary to identify what type of organism is causing the illness as well as the species and strain of the organism. A bacterial species is generally defined as a group of organisms that share approximately 70% of their genetic sequence and have similar traits (E. coli). Within each species, organisms are further characterized into strains, which are based on slight differences in genetic makeup and traits (e.g. E. coli 0157:H7). Many outbreaks are identified when scientists are able to genetically match a bacterial strain from infected individuals to a food product that was consumed prior to becoming ill. Genetic fingerprinting is one way to identify and match illness-causing bacterial strains.  

What is Genetic Fingerprinting?
Genetic fingerprinting is a way of using an organism’s DNA sequence to create a visible molecular “fingerprint” which can be compared and potentially matched to fingerprints of known strains (Fig. 1). There are many different ways of creating genetic fingerprints; the technique discussed here, Pulsed Field Gel Electrophoresis (PFGE), is one approach used by the CDC, which maintains databases of PFGE fingerprints from strains of E. coli, Salmonella, Shigella, Listeria, and Campylobacter.  

Figure 1: An example of the genetic fingerprints of various yeast strains.

Pulsed Field Gel Electrophoresis (PFGE)
Scientists often separate DNA fragments based on size. One way to do this is to load samples onto a gel and run a uniform electrical current through the gel. Because DNA is negatively charged, the current causes it to run toward the positive terminal. Because the DNA is forced through the gel, smaller fragments travel faster than larger fragments, making it possible to separate and visualize the DNA by size, as compared to a known ladder (Fig. 2).

Figure 2: Agarose Gel Electrophoresis. The arrows represent the direction of DNA migration (toward the positive charge).

PFGE uses this basic principle to separate much larger fragments of DNA; however, because large fragments don’t separate well with conventional gel electrophoresis, PFGE uses equal pulses of diagonal electrical current to move the DNA in a zigzag trajectory that results in a net forward motion and successfully separates large fragments by size (Fig 3).   

Figure 3: Pulsed Field Gel Electrophoresis. Small arrows represent the actual path of DNA migration while the larger arrow shows the net migration. Electrical current is pulsed alternately with electrode A and electrode B.

Application of PFGE to Food Borne Illness
Once a suspected pathogenic organism has been cultured, PFGE can be used in conjunction with other methods to identify the strain. To do this, the organism is chemically treated to disrupt its cell membrane and then digested with a specific enzyme that breaks DNA strand at particular sites. This results in many large fragments of DNA that can be separated by size on an agarose gel using PFGE. The resulting genetic fingerprint pattern can then be compared to known fingerprints in the CDC’s database, which can provide strain identification or outbreak pattern recognition from PFGE fingerprints originating from a large geographical area.     

What about the your illness?
After hearing about the Salmonella outbreak, you and your friends go to hospital, where you are admitted and treated for Salmonella poisoning. A week later, you notice that one of your favourite salsas has been recalled, based on a PFGE-based CDC recommendation. Six months later, you hear that the same Salmonella strain has been isolated in a Mexican field of Jalapeño peppers, and the Salmonella outbreak is considered contained. Although you’re not quite ready to host another chips and salsa party, you feel confident that your next bite of Mexican food will not be your last!

How PFGE Fits into a Real Investigation – Conduct your own investigation