The monumental Food Safety Modernization Act, signed into law by US President Barack Obama in January, promises to add much-needed improvements to the security of the US food supply. Yet a technological advance, rather than a major legislative overhaul, could have the largest impact on the government's ability to identify contaminated foods and rid them from store shelves.

In a proof-of-principle study published last month, scientists from the US Food and Drug Administration (FDA) reported that, compared with traditional DNA fingerprinting, next-generation sequencing more precisely identified the bacterial strain and the food product responsible for a 2009–2010 outbreak of Salmonella that sickened more than 250 people across the US.

In response to that outbreak, a Rhode Island food manufacturer recalled nearly 1.5 million pounds of salami, prosciutto and other spiced deli meats. At the time, food safety officials couldn't tease apart which particular ingredient had made people sick, as standard genetic fingerprinting techniques alone proved inconclusive. But, in a retrospective analysis, FDA researchers used so-called shotgun sequencing to identify the cause of the outbreak: a particular strain of Salmonella contaminating pepper spices used to coat the deli meats (New Engl. J. Med. 364, 981–982, 2011).

Using new sequencing technologies to decipher food-related illness “may help pinpoint the source faster and implement recall procedures for all affected products—things that could definitely mitigate the severity of an outbreak,” says Byron Brehm-Stecher, a food scientist at Iowa State University in Ames who was not involved in the study. Eric Brown, acting director of the FDA's microbiology division, acknowledges that next-generation sequencing techniques will be useful in the future, but he cautions that the current pace of data analysis precludes using these methods in the midst of rapid-response food safety emergencies.

Sequencing alone will also never fix all of the government's food tracking woes. As exemplified by another paper published last month, spotty record keeping in the food supply chain continues to hinder investigations of foodborne illness. In that study, scientists from the US Centers for Disease Control and Prevention argued that better product traceability could have prevented the mistaken identification of tomatoes in a major 2008 Salmonella outbreak. The contamination was later found to be linked to jalapeño and serrano peppers (New Engl. J. Med. 364, 918–927, 2011).

To fill in the gaps, the FDA, backed by funding from the country's new legislation, is establishing a full-time, multidisciplinary team of about 40 people to handle outbreaks as they happen. And, to lead the group, the agency is currently recruiting a new medical director to serve as the 'point person' on decisions over food product recalls and facility inspections.

Such measures strengthen the FDA's ability to do science-based prevention of food-borne disease, argues Jeff Farrar, the agency's associate commissioner for food protection. “Obviously, if you are an entirely reactive agency it is very difficult to get ahead of the curve,” he says.