Investigators have linked at least three different kinds of E. coli to Nestle's cookie dough but remain stumped about how the bacteria got into the product, ABC News has learned.
The U.S. Food and Drug Administration has completed DNA testing of E. coli recently found in an unopened package of cookie dough at Nestle's plant in Danville, Va.
Those tests, according to sources familiar with the investigation and confirmed by the FDA, determined the genetic fingerprint of the E. coli found at the plant is different than E. coli that has been linked to a 30-state outbreak that has sickened at least six dozen people.
Sources also say an altogether different strain of E. coli was found in dough recovered from the home of a victim, meaning at least three different types of E. coli have been associated with cookie dough made by Nestle.
Today Nestle USA spokeswoman Laurie MacDonald told ABC News the Danville plant is slowly returning to production -- in phases -- after it was turned upside down in the wake of the E. coli outbreak.
MacDonald said the company dismantled its entire production line, inspected and cleaned all the parts and then put it back together. She said Nestle also has conducted extensive testing of ingredients. The company has discarded all ingredients that had been stockpiled and replaced them with all new flour, eggs, margarine and other items.
Before any ingredient goes into cookie dough in the future, MacDonald says, it will undergo "very extensive pretesting."
While the FDA has wrapped up its investigation of the Danville plant, inspectors are still searching for a plausible scenario for how any E. coli got into the dough.
"The investigation is winding up. It is not exactly over yet," said Dr. David Acheson, the assistant commissioner for food safety. "But we have not figured out the likely ingredient."
FDA inspectors who combed through Nestle's plant found only minor discrepancies and nothing that explains the E. coli mystery. In fact, Acheson said, investigators may have exhausted all of their leads.
"We've followed everything that we think is most likely and haven't come up with anything," Acheson said. "It is unlikely that we will ever make a final determination of how this contamination occurred."
The FDA does not, however, believe this was a case of product tampering.
"There's no indication that this was deliberate," Acheson said.
Investigators discovered the first hard evidence of a link on June 29 when they found E. coli at the Danville, Va., plant where Nestle makes Toll House cookie dough.
The "smoking gun" was found in an unopened package of raw chocolate chip cookie dough that had been manufactured Feb. 10, 2009, but had not yet been shipped.
Nestle issued a press release June 29 confirming that the FDA had informed the company "that it has found and confirmed evidence of E. coli 0157:H7 in a retained production sample of 16.5 oz. Nestle Toll House refrigerated chocolate chip cookie dough bar."
Nestle had already issued a nationwide recall June 19 for its Toll House cookie dough products, acting on the strong suspicions of epidemiologists.
The food maker warned consumers not to eat raw Toll House cookie dough as fears about possible E. coli contamination spread to more than two dozen states.