Mapping Genomes to Understand Contaminated Foods

The FDA can now pinpoint exactly which ingredient makes people sick in outbreaks.

Last week, two companies issued national recalls of their products due to listeriacontamination. For Sabra Dipping Company, which is recalling 30,000 cases of hummus, no illnesses or deaths have been reported to the Centers for Disease Control (CDC) thus far. But for Blue Bell Creameries, the CDC has confirmed a small number of cases in Kansas, resulting in three deaths. The company has since expanded its recall as well as suspended operations at its Oklahoma plant. (The products being recalled are listed here.)

Food-borne illness is nothing new, but in the past it looked quite different. In 1911, 48 people died and 2,000 were taken ill with septic sore throat, the result of a Boston dairy that did not pasteurize. In 1924, raw oysters caused an outbreak of typhoid fever that claimed 150 lives in 12 cities. These are "diseases that now rarely occur," wrote Robert Tauxe, the deputy director of the Division of Foodborne, Waterborne, and Environmental Diseases at the CDC, and Emilio Esteban, the head of the USDA's Food Safety and Inspection Service Laboratories.

Today, food-borne illness is a distinct, and in some ways scarier, problem from those sorts of earlier outbreaks. The industrialization of food, which has morphed the sector from small operations to multinational conglomerates, has given rise to new diseases—salmonella, E. coli, and listeria—and the scale of distribution means that outbreaks can affect hundreds of people across multiple states at a time. Tauxe and Esteban cite three significant outbreaks in the last 30 years: In 1986, 3,200 people were infected with salmonella from pasta that contained spoiled eggs; a West Coast E.coli outbreak from undercooked burgers sickened hundreds and killed four children in 1993; and in 1996 nearly 1,500 people in 20 states were sick from a parasite in contaminated raspberries. All told, the CDC says that 48 million Americans get sick every year from food-borne diseases, and about 3,000 people die.

In more than two-thirds of all cases, the cause of the illness is never identified. Several national databases, such as the CDC's FoodNet, have been created to track food illnesses and the pathogens that cause them. Additionally, high-tech advances in analyzing food samples work in tandem with traditional epidemiological approach of interviewing patients to solve the mystery of food-borne illnesses.

In recent years, the Food and Drug Administration (FDA) has started to usewhole genome sequencing for outbreak investigations. Eric Brown, the director of the FDA’s Division of Microbiology, explained that genome sequencing was initially brought to the organization for the purpose of discovering detailed genetic information for salmonella strains. In 2009, a salmonella outbreak involving salami resulted in the first pilot of using whole genome sequencing in identifying the harmful ingredient. Scientists analyzed pieces of nuts and vegetables in the salami to figure out what was tainted.

"As a pilot, we sequenced many of those strains from pistachios, peppers, and all the other [salmonella strains] that we had in the freezer and we compared those to the clinical strains that we sequenced also," explains Brown. "It was basically like going from using a backyard telescope that you bought at Costco to the Hubble telescope."

Errol Strain, a mathematical statistician at the FDA’s Center for Food Safety and Applied Nutrition, said that whole genome sequencing is now being used in real time for pathogens that cause food-borne illnesses. The information is stored on the FDA's publicly accessible database,Genome Trakr. Strain says that such precise information is making it easier for the FDA to do detective work for outbreaks before they become large scale. For example, a 2014 nut butter outbreakconnected several seemingly unrelated cases and traced its source using genome sequencing.

Strain suggests that genome sequencing could be the next step for the food industry to safeguard their products. Last year, the FDA started a sort of X Prize challenge for food safety—a way to encourage innovation to improve public safety. They will reward finalists $20,000 for breakthrough technologies to detect salmonella in fresh produce.

Once detected, a contaminant needs to be tracked across distribution centers so that it can be effectively recalled. Tracing technologies for food products have improved since bar codes were introduced in the 1973. RFID technology—which uses radio frequencies to track food—is pricey, but holds the potential of being able to find contaminated food faster. Other high-tech solutions in the recall realm include QR codes and spray-on DNA barcodes.

We've certainly come a long way since John Snow, the physician who solved the 1854 cholera outbreak in Britain, figured out that germs in the water supply killed more than a hundred people in just three days. Since germ theory wasn't widely accepted then, Snow also had the hard task of convincing other physicians and the public of what he had discovered. One of the benefits of genomic food-safety measures is that the evidence is convincing: A perfect match at the genetic level is hard to argue with.

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