(AP Photo/Larry Crowe, File)

Always cook your cookies.

The Food and Drug Administration warned this week that Americans shouldn't eat cookie dough or other raw batters, even if it's egg-free, due to the risk of contracting E. coli .

Many may think it's the risk of salmonella and raw eggs that the FDA wants Americans to avoid. But this warning is about tainted flour after E. coli outbreaks in recent months were linked to cookie dough made with flour manufactured by General Mills.

And the reason is sort of disgusting: animal poop. When  birds and other animals do their business above wheat fields, they can spread  bacteria from their infected feces onto the grain. That wheat is later processed into flour. While the process is intended to kill pathogens, it's not as intense as, for example, pasteurizing milk.

"There's no treatment to effectively make sure there's no bacteria in the flour," said Martin Wiedmann, food safety professor at Cornell University.

So if you eat cookie dough, you might be eating, in a sense, the diseased remnants of bird poop.

Although General Mills has recalled 10 million pounds of flour under three brands -- Gold Medal, Signature Kitchen’s, and Gold Medal Wondra -- Wiedmann said it's unlikely the FDA will ever cancel the warning about cookie dough.  Flour is not designed to be an "eat-ready" product, like crackers or strawberries.

Risk of becoming infected is nearly nullified when you boil, bake, roast, microwave or otherwise heat and cook with flour. None of that happens when you eat dough, and you're exposed to much of what happened to the wheat before it came into your kitchen.

It's affected dozens already. As of June 8, 42 cases had been reported in 21 states, with 11 hospitalizations. A General Mills processing facility in Kansas City, Mo., was cited as the source of the outbreak.

General Mills announced on May 31 that it was researching illnesses that had been reported between Dec. 21, 2015, to May 3 with health officials. On Friday, the investigation was expanded to illnesses reported in the fall of 2015.  The company emphasized that E. coli could be eliminated through cooking and advised washing hands after contact with flour or dough.

This particular strain is called Shiga toxin-Escherichia coli producing O121. A similar type of E. coli caused 35 deaths in a 1993 outbreak centered around Jack in the Box, which infected 732 people who ate under-cooked beef patties.

Wiedmann said very few die from O121. But it could cause kidney failure in severe cases if left untreated. The elderly, children under 5 and those with weakened immune systems are most at risk. More common symptoms are abdominal cramps and diarrhea, which the FDA notes is often bloody. It typically lasts a week.

For that reason, the FDA says no more cookie dough -- or anything else raw that you might eat that has flour, like cake, pizza or bread.

It's a new warning, but Wiedmann underscored that flour isn't becoming more unsafe. It's just that researchers are more aware of the risks. New forms of genetic testing allow food safety investigators to "fingerprint" and identify the DNA of the bacteria that's found in patients. A national database of that bacteria then allows the Centers for Disease Control and Prevention to group strains and identify possible outbreaks.

"Our food is getting safer, but also our ability to detect problems is getting better," Wiedmann said.

Correction: An earlier version of this story identified E. coli as a virus. It's a bacteria.