CHICAGO — Nestle USA will begin using heat-treated flour in its Toll House refrigerated cookie dough, months after the company temporarily pulled the product off of store shelves after the Food and Drug Administration found evidence of E. coli contamination.

The unit of Nestle SA said it will halt production at its Danville, Virginia, plant from Wednesday until Jan. 25 in order convert the plant to use heat-treated flour.

In June, Nestle recalled the cookie dough after the FDA said it was investigating possible E.coli related illnesses that might have been related to the eating of raw cookie dough.

The company resumed production at the plant using standards that included testing ingredients before they enter the facility, rigorous environmental sampling throughout the facility and testing of finished product before it is shipped to customers.

On Monday, two samples of cookie dough tested positive for E. coli, Nestle said. The contaminated product was discovered before it was shipped and dough on store shelves is not affected, it added.