In late July, PulseNet staff alerted Centers for Disease Control and Prevention epidemiologists of a cluster of E. coli O157 isolates from eight states with an indistinguishable pulsed field gel electrophoresis (PFGE) genetic pattern. Several of the case-patients revealed that they had consumed undercooked ground beef. Most patients had eaten ground beef prior to their illness onsets and had purchased the ground beef from one of two different grocery store chain outlets. Four consumer samples of ground beef - one sample from a Dorothy Lane Market and three samples from a Whole Foods Market were contaminated with the outbreak strain. The outbreak strain was also isolated in a sample of intact beef collected from a Dorothy Lane Market.

Traceback investigations indicated that the beef originated from Nebraska Beef, Ltd. Nebraska Beef, Ltd., was the sole source of the contaminated beef for Dorothy Lane Markets and was one of multiple suppliers for Whole Foods Market. On July 28, Dorothy Lane Markets announced a retail-level recall of ground beef products. Whole Foods Market announced a recall on August 8, and the slaughter facility initiated a nationwide recall of beef products linked to outbreak 2. This recall was expanded on August 14 to include approximately 1.36 million pounds of additional intact beef cuts.

In May, 2008, beef processed by Nebraska Beef, and available in Kroger Grocery Stores in Ohio and Michigan, was linked to a multistate outbreak of a different strain of E. coli O157:H7.