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).

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Image: NIAID