Usually cooking foods to the right temperature and for the correct amount of time will kill bacteria. However, if you have the recalled cookie dough, Nestle and the FDA have said not to eat the Toll House cookie dough even if it is baked. So far the people getting sick said they ate the dough raw.
I think they are concerned with people getting ill from the E coli on their hands and work surfaces when handling the raw dough. The E coli bacteria can spread easily.
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