In 1993, 25 years ago, we had what the Center for Disease Control and Prevention (CDC) still calls the “Western States E. coli outbreak.”  Most of us call it the Jack in the Box outbreak, the one that sickened 723 victims, most of them under 10 years of age. Four kids died and 178 persons were left with permanent kidney and/or brain damage.

This was a significant food safety change in that it shocked the world into realizing that what was felt to be safe food could, in fact, be very dangerous.

It also taught us that undercooking hamburger could sicken your customers.

It also resulted in E. coli O157:H7 being determined to be a ground beef adulterant, to be followed later by six more strains of non-O157:H7 STECs being added to the adulterant list.

It brought about major sweeping changes in the beef industry, including the declaration that food safety practices were no longer proprietary information.

But in my mind, while outbreak was not, in itself, a food safety change, it did result, in addition to the above, one more new tool in the tool kit of food safety that has changed the land scape forever — Pulsed-field Gel Electrophoresis: PFGE for short.

The CDC, went to work perfecting this tool that would dramatically change the epidemiology of foodborne illness investigation.

The time line
In 1996 the CDC launched PulseNet, which included the PFGE labs, with four original state public health laboratories in Massachusetts, Minnesota, Texas and Washington State along with the Association of Public Health Laboratories and federal partners. Training for PFGE was held at the CDC and the four labs and the U.S. Department of Agriculture labs attended and received certification.

By 2001 all 50 states had their public health labs trained and certified along with all food regulatory laboratories including those at the Food & Drug Administration and USDA.

In 2006, the E. coli O157:H7 outbreak that sickened 225 in 27 states and included five deaths was quickly identified as coming from a farm in the Salinas Valley in California because of PFGE. Without that tool, maybe thousands more would have fallen ill before the finger pointing shifted from ground beef to green leafy vegetables.

PFGE has been called the fingerprint of the DNA of the germ. If two samples from two specimens are identical, they have the same source; just like two identical twins have the same DNA and it is different from all other specimens.

Specimens are taken from sickened patients, from food identified as possible sources and from routine testing in food processing facilities.

Samples taken from ill patients are cultured in the usual hospital laboratory settings and, if positive for bacteria commonly associated with a foodborne illness, like E. coli or salmonella, the specimens are transferred to the state’s public health laboratory for the PFGE testing.

The PFGE results are transferred to the CDC and downloaded into a PulseNet computer using a software program named BioNumerics.

When two or more specimens from separate sources are identified as being identical, they are no longer what once would have been isolated cases of foodborne illnesses.

Prior to PFGE, about the only times a common source was identified and recalls initiated were when several attendees of a community function, like a wedding reception for church luncheon, all fell ill in the same time frame and were exposed to the same food.

In the previously mentioned E. coli spinach related outbreak, the first case was reported on Aug. 23. Shortly thereafter separate outbreaks with identical PFGE test results were reported in Wisconsin and Oregon.

Without PFGE there is no way these early outbreaks would have been linked.

Because of the distance separating these two states, fresh ground beef was off the hook and the investigation broadened.

The New Mexico public health department, which had identified 554 cases, identified the exact same strain from a bag of precut lettuce in one victim’s refrigerator. The focus narrowed further. We had the culprit, but where did it originate and what to tell consumers and what to recall?

By the end of September, a relatively short five weeks, the specific farm and distributor were known and recalls initiated.

Eventually investigations incriminated, or at least sharply suggested in FDA-speak, a Black Angus ranch near the lettuce farm that had the same DNA strain of E. coli in its manure as did some feral pigs running wild between the ranch and farm.

To paraphrase Nancy Donley, then executive director of the organization now known as STOP Foodborne Illness, if you look long enough and hard enough when investigating an E. coli outbreak, you will eventually bump into a cow.

In conclusion, PFGE does not reduce contaminated food being delivered to our retailers and our door steps, but it can reduce the amount available for sale and consumption by much more quickly identifying a source and initiating a recall along with notifying consumers and public health leaders.

The downside is that large numbers of sickened consumers and industry names lead to headlines, while the previously isolated cases of foodborne illnesses with no link to the industry did not.

And I think this bad publicity is contributing to the increased demand from the public for a safer food supply, which led to the Food Safety Modernization Act. Whether that will actually be another major development in food safety remains to be seen, but Congress and FDA feel mighty good about it.