The Centers for Disease Control and Prevention reports that 64 people have been hospitalized as a result of bacterial infection arising from contamination at Taco Bell restaurants in New York, Pennsylvania, New Jersey, and Delaware. Of these patients, 38 have been confirmed as E. coli strain O157:H7 infections. All of these patients have been infected with the same substrain as determined by DNA fingerprinting.
What this means is that all infections arose from a single source. There must be something in common among the restaurants in all four states. A preliminary analysis detected E. coli O157:H7 contamination of green onions in one of the restaurants but DNA fingerprinting showed that it was a different substrain, proving that this was not the soure of infection.
DNA fingerprinting is a powerful tool in tracing outbreaks of toxic bacteria. It also proves evolution. How is it done?
The figure below is an example of DNA fingerprinting from the following paper.
Hahma, B-K., Maldonadob, Y., Schreiberc, E., Bhuniab, A.K. and Nakatsua, C.H. (2003) Subtyping of foodborne and environmental isolates of Escherichia coli by multiplex-PCR, rep-PCR, PFGE, ribotyping and AFLP. Journal of Microbiological Methods 53; 387-399.
There are several different ways of making DNA fingerprints. In the one shown here, DNA is extracted from each substrain of bacteria and digested with a restriction enzyme called Xba I. This enzyme chops the DNA at specific sites in the genome corresponding to the DNA sequence TCTAGA. The result is that the genomic DNA is cut into large pieces of different sizes, ranging from about 100,000 base pairs (bp) to 500,000 base pairs (or 500kb). Since the whole genome of E. coli is about 4,600,000 bp in size, this means the there will be something like 20 DNA fragments produced by cutting with the enzyme.
The DNA fragments from different strains will show differences in sizes whenever the genome has been altered by the insertion of new DNA or the deletion of some existing DNA. These insertion/deletion events occur quite frequently in evolving populations as we saw recently in work done on human populations.
A solution containing the collection of fragments from a single strain is put on the top of an agarose gel and a strong pulsed field electric current is applied. Since DNA is negatively charged, the fragments will move into the gel and separate according to size—smaller fragments will move faster. In the example shown, the top of the gel is on the right and the bottom is on the left.
The large open bracket at the top right of the image covers various O157:H7 strains. The evolutionary tree on the left shows how this strain is related to other E. coli strains at the bottom of the image. Within the O157:H7 strains there are many serotypes that have descended recently from a common ancestor. Each serotype has a unique combination of restriction fragments of different lengths. That's the DNA fingerprint.
Note the cluster that's fourth from the top. It's labelled "Odwalla Juice" after an outbreak that occurred several years ago. (You may not be able to read it in the figure.) There are five lanes with identical DNA fingerprints indicating that these five different isolates (from five different patients) all came from the same source. The same technique is being used to trace the current outbreak.
The Centers for Disease Control and Prevention have already eliminated a number of cases by DNA fingerprinting. These patients are not part of the current outbreak. It's important to concentrate only on those patients that are part of the cluster having a common source and not be confused by other infections. That way, the source can be identified and eliminated.
Not to belabor a point, but none of this would be possible if it weren't for evolution and our understanding of how evolution works.