Let’s begin with a little background on this subject... Molecular epidemiology is a science that combines the field of molecular biology with traditional epidemiologic research. Molecular biology refers to the study of the molecules that are building blocks associated with living organisms. The two types of molecules that molecular biology studies are proteins and nucleic acids. The two nucleic acids are known as deoxyribonucleic acid or DNA, and ribonucleic acid or RNA. The genetic information of each living organism is carried in either their DNA (for every living thing except for some viruses), or their RNA (for some viruses only).

Each human has a unique DNA sequence (with the exception of identical siblings) that is the result of a combination of their mother’s and father’s DNA sequences. While bacteria also carry their genetic information in DNA sequences, there is no combination of these sequences during normal reproduction. One bacterium simply divides into two bacteria. So, unless there is a mutation or another alteration in the genetic sequence, bacteria that descend from a single bacterium (known as a clone) will all have identical DNA sequences. Even after a few generations of growth, bacteria with a common single ‘ancestor’ will have similar, if not identical, DNA sequences.

Pulsed-field gel electrophoresis (PFGE) is a technique used to produce the DNA fingerprints from these DNA sequences. DNA fingerprinting by PFGE involves isolating a DNA sequence from an organism, cutting it into pieces, and then measuring the number and size of the pieces. The pieces are separated by running them through a gel, which functions as a sieve. Smaller pieces go through quickly, while larger pieces travel more slowly. The resulting pattern of bands, which looks like a bar code, is the DNA fingerprint.

Prior to the introduction of PFGE, we could identify bacteria by name (e.g., Salmonella or Shigella), and, in some instances, by other characteristics (e.g., antibiotic resistance patterns or serotypes) to help us determine if bacteria were related to one another. We are now able to determine much more precisely how closely related bacteria are to one another by comparing their DNA fingerprints. Identical or very similar DNA fingerprint patterns strongly suggest a close relationship, while bacteria with distinctly different patterns are not closely related.

What is PulseNet? PulseNet is a national computer network of public health laboratories. (Utah’s Public Health Laboratory is one of 22 state public health laboratories currently participating in the PulseNet.) These laboratories use PFGE to obtain DNA fingerprints of bacteria that are believed to be associated with foodborne illnesses. Once a DNA fingerprint is identified by a laboratory in the PulseNet, it is loaded into the computer network. This network allows laboratories to compare their DNA fingerprints with those that have been isolated from other PulseNet sites throughout the country. In a short time after submitting the DNA fingerprint to the network, the laboratory is notified whether or not there is a match for it in PulseNet. The pattern is also stored for three months in the network so that it may be compared to fingerprints that may be subsequently submitted. PulseNet contains DNA fingerprints of Escherichia coli O157:H7 isolates now. There are plans to add DNA fingerprints of Salmonella typhimurium soon.

This new system should permit public health experts to identify foodborne outbreaks associated with a common source rapidly and accurately. This computer network provides a nationwide database of DNA fingerprints that can be searched within hours. A mechanism to share such complex data at this speed has never existed before. An additional strength of this new system is that it requires participating laboratories to use the same procedures to identify DNA fingerprints. In the past, all laboratories did not use the same procedures, and this made the comparison of DNA fingerprints between laboratories difficult or impossible.

Why is PulseNet necessary? When people think of foodborne outbreaks, the classic ‘bad potato salad at the church supper’ scenario often comes to mind. Obviously, the advanced technology behind PulseNet may not be nearly as important as old-fashioned epidemiology in this kind of situation. With changing food distribution patterns, however, foods may be distributed to multiple states or even multiple countries before bacterial contamination is detected. For example, two recent recalls involved tons of ground beef possibly contaminated with E. coli O157:H7 that had been purchased by consumers throughout the United States. PulseNet allows public health experts to compare the DNA fingerprints of bacteria from widely dispersed locations so they can determine if the bacteria are related to each other (and may be from a common exposure). The DNA fingerprints from patient specimens can also be compared to the DNA fingerprints obtained directly from the implicated food itself.

In the past, selected physician offices have been contacted weekly to collect numbers of influenza-like illness seen during the previous week. This year the Centers for Disease Control and Prevention wanted to expand the physician-based surveillance of influenza-like illnesses. To do this, a toll-free number was provided, and each week the physicians, or someone in their office, would dial up and provide numbers for the previous week. Initially, Utah had nearly a dozen physicians who agreed to participate in the physician based surveillance. Unfortunately, the physician based surveillance did not work as expected and participation waned as the season progressed. Consequently, we may be going back to weekly calls to selected offices.

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The Bureau of Epidemiology
Box 142104
Salt Lake City, UT 84114-2104
or call (801) 538-6191

Approval 8000008: Appropriation 3705