There are a lot of things I love about my job, but one is the science behind linking people in dozens of states to food that they consumed that poisoned them. Once that link is scientifically determined, and the outbreak stopped, then the time comes to learn from the mistakes so the next outbreak can be avoided. Frankly, we all need to appreciate (can you say increase funding) those public servants who toil in local, state and federal health agencies tracking food borne diseases. Without the work of dedicated people interviewing victims, testing stool and analyzing data, most outbreaks would never be determined, most victims would never be fairly treated, and most outbreaks would repeated without learning from past manufacturing mistakes. The science behind all the hard work is fascinating – especially, the "CSI" part.

The process of obtaining the DNA fingerprint is called PFGE (Pulse Field Gel Electrophoresis). This technique is used to separate the DNA of the bacterial isolate into its component parts. It operates by causing alternating electric fields to run the DNA through a flat gel matrix of agarose, a polysaccharide obtained from agar. The pattern of bands of the DNA fragments — or “fingerprints” — in the gel after exposure to the electrical current is unique for each strain and sub-type of bacteria. By performing this procedure, scientists can identify hundreds of strains of E. coli O157:H7 as well as strains of Listeria and campylobacter, and other pathogenic bacteria. The PFGE pattern of the bacteria can then be compared and matched up to the PFGE pattern of the strain of infected persons who consumed the contaminated product.

MLVA (Multiple Loci VNTR Analysis) is a method employed for the genetic analysis of particular microorganisms, such as pathogenic bacteria, that takes advantage of the polymorphism of tandemly repeated DNA sequences. "VNTR" means "Variable Number of Tandem Repeats". This method is well known in forensic science since it is the basis of DNA fingerprinting in humans. When applied to bacteria, it contributes to forensic microbiology through which the source of a particular strain might eventually be traced back. In a typical MLVA assay, a number of well-selected and characterized (in terms of mutation rate and diversity) loci are amplified by polymerase chain reaction (PCR) so that the size of each locus can be measured. From this size, the number of repeat units at each locus can be deduced. The resulting information is a code that can be easily compared to reference databases.

When PFGE and MLVA patterns match, they, along with solid epidemiological work (e.g., was the person exposed to the suspect food item), are proof that the contaminated product was the source of a person’s illness.

In the Nestle Toll House Cookie Dough E. coli O157:H7 outbreak the science and epidemiological work produces the below partial “line list.” This list (as of June 25, 2009) lists 76 persons (that number is now 80) who are linked together by a common PFGE of E. coli O157:H7. Most have MLVA patterns reported – some were still pending. The bottom line is that this list, along with solid epidemiological work, show the “CSI” link between these 76 people and the Cookie Dough they consumed.