CHICAGO — The federal government is rolling out a powerful new, and increasingly affordable food safety weapon to about 30 states next year and to all 50 within two years.

Dr. Robert Tauxe, who runs the foodborne, waterborne and environmental disease division of the federal Centers for Disease Control and Prevention in Atlanta, told attendees at the Food Safety Summit that the federal government is going to put the cutting edge technology known as whole genome sequencing into the field with Listeria being its first target. The use of the technology to provide the DNA fingerprint that is left behind by disease-causing bacteria is already being used by the CDC’s own laboratories to identify the source of foodborne disease outbreaks with more detail and clarity. Academic researchers, also participating in the three-day Food Safety Summit, said the reason state and university labs are going to WGS is the dramatic reduction in the cost of obtaining DNA fingerprints in the lab. Cornell University’s Martin Wiedmann said the cost of the “changing picture” for whole genome sequencing is the test that cost $100 million when the technology first arrived on the scene is now down to about $1,000. It means that for $25 or $50 DNA fingerprints can be isolated from smaller samples. Wiedmann, Cornell’s Gellert Family Professor of Food Safety, said whole genome sequencing has been used as a detection tool by CDC in several recent Listeria outbreaks, including those associated with Blue Bell ice cream, Haroun Dairies soft cheese, Dole packaged salads and others. Foodborne illness investigators have been relying on DNA fingerprinting for about 20 years, but traditionally those have been obtained through pulsed-field gel electrophoresis, also known as PFGE. Whole genome sequencing, or WGS, produces DNA fingerprinting that is more detailed and more likely to identify sources of outbreaks of enteric illnesses.

The practical implication of more WGS testing will be more detection of more outbreaks, according to Wiedmann. Tauxe said the roll out of the technology to the state labs will require the launch of PulseNet 2.0 for handling the WGS data. PulseNet is the 20-year old system connecting laboratories working with CDC for sharing and sub-typing DNA “fingerprints.” Wiedmann said that while Listeria is often referred to as being ubiquitous in the environment, food plant managers must stop thinking that the pathogen cannot be eliminated from their facilities. “It cannot have a niche, it cannot have places in your plant where it can survive,” he said. Cornell University researchers have found Listeria is ubiquitous in the environment, ranging from 1.3 percent to 8 percent in samples from New York state parks to 20 percent to 30 percent of samples taken from farm land. Next to that, Listeria’s long incubation period that can extend from a week to 60 days or more is a problem for food safety investigators, the Cornell professor said. “It’s very hard to remember all that you’ve eaten going back for two months,” he said. In response to a question about the future, Tauxe predicted whole genome sequencing might eventually be used to determine what an ill person has eaten as well. Wiedmann predicts the shift to whole genome sequencing will mean 30-times more detections of Listeria outbreaks. “We need to up our game,” he said in reference to the food industry. “Our ability to detect an outbreak has increased (from) 50 to 100 times in 20 years.” He said what is needed in food plants to combat Listeria is persistence. Too many, he said, have “house bugs and pet Listeria.” Steven Tsuyuki, senior director for corporate sanitation and sanitary design for Canada’s Maple Foods, said the 2008 Listeria outbreak associated with his company almost put them out of business. It was one of the most deadly outbreaks in Canadian history, resulting in at least 23 deaths. In the years since, he said Maple Leaf has cut the number of facilities in half as it worked to design production lines and equipment to control Liseria. (To sign up for a free subscription to Food Safety News, click here.)