How risky is it to eat raw flour, as in uncooked dough? Does eating raw flour or doughs containing raw flour pose a significant food safety risk (i.e., greater than other dry goods or ingredients in your kitchen)?  If so, are there particular cooking or baking processes where we should be most concerned about this risk?



Background:

There has been a flurry of news headlines in the past few days over the FDA's latest food hazard warning, claiming that raw flour is a significant concern and consumers should be warned not to consume any raw dough made with flour.  For some reason, almost every mainstream news source has chosen to focus on raw cookie dough (even though the FDA's warning applies equally to any raw dough or batter, whether for cookies, pies, bread, pizza, cakes, waffles, etc.), with the New York Times for example claiming that the "F.D.A. Ruins Raw Cookie Dough for Everybody" and Smithsonian Magazine noting "The FDA Just Declared War on Cookie Dough".

I've been aware for several years that flour bags in the U.S. now come with the warning "Do not eat raw flour, dough, or batter," I assume in response to the 2009 outbreak of E. coli from prepackaged cookie dough, whose source was ultimately traced to the flour.  The new FDA warning is in response to the present E. coli outbreak, which has apparently been confirmed as originating in flour and has resulted in the recall of 10 million pounds of flour.

I obviously don't wish to downplay the seriousness of this outbreak.  But I am interested in the rationale behind the FDA's warning.  In particular, is flour (and raw dough) actually a higher-risk food hazard than any other uncooked ingredient in a kitchen?  For example, we all know that raw vegetables and fruits have been responsible for hundreds of outbreaks, but the FDA has not issued a general warning against consumption of raw vegetables and fruit.  (Instead, the warnings tend to be against the specific batches of contaminated food, as well as a few specific high-risk raw vegetables like sprouts.)

And outbreaks of Salmonella and E. coli in the U.S. have been linked to almost every conceivable type of uncooked food.  For example, a whitepaper from a flour mill that produces heat-treated flour for safety notes that just among low-moisture foods, "Salmonella has been implicated in several foodborne outbreaks in low-moisture foods, including chocolate, powdered infant formula, raw almonds, toasted oat breakfast cereals, dry seasonings, paprika-seasoned potato chips, infant cereals, and ... peanut butter," and that was only up to 2004.  That list has grown significantly in the past decade.

Raw flour, like most of the dry foods listed above, has generally been considered extremely low-risk as a cause of foodborne illness.  (See for example this thread from a couple years back, where two different people reported asking state food safety experts about this issue and were told there's absolutely no reason for concern over raw flour.)

So, to sum up, is raw flour actually a higher risk?  99% of foods that you bring into your house with intent to eat raw and don't heat to 160F could conceivably be contaminated with bacteria, as numerous outbreaks have shown.  In most instances, the problem is traced to a specific source.  So why has raw flour been singled out for a general prohibition (as opposed to a warning about a specific contaminated batch, which applies to most fruit and vegetable outbreaks, as well as most of the dry goods outbreaks mentioned above)?

Is there some new information that justifies this broad and sweeping FDA prohibition on the basis of a couple outbreaks?  (And if contaminated flour is such a big deal now to justify the recall of millions of pounds of flour, what makes this new situation different from most wheat flour, which has been known for decades to have high rates of E. coli and Salmonella contamination, occurring in something like 13% of samples of flour?)
Does eating raw flour or doughs containing raw flour pose a significant food safety risk (i.e., greater than other dry goods or ingredients in your kitchen)?

Yes, as the level of bacteria has not been reduced/killed especially if the dough has been sitting/fermenting and/or contains harmful bacteria.  
Nb: Most flour isn't washed or treated (irradiated) before use.  
Although it is cosidered 'dry' it always contains a level of moisture and it's storage usually allows moisture transfer from the local environment that it is stored/used in.

If so, are there particular cooking or baking processes where we should be most concerned about this risk?

Not really, unless the cooking/baking process does not reach a high enough temperature or a long enough period to reduce/neutralise the bacteria that may be present.

I obviously don't wish to downplay the seriousness of this outbreak. But I am interested in the rationale behind the FDA's warning. In particular, is flour (and raw dough) actually a higher-risk food hazard than any other uncooked ingredient in a kitchen? For example, we all know that raw vegetables and fruits have been responsible for hundreds of outbreaks, but the FDA has not issued a general warning against consumption of raw vegetables and fruit. (Instead, the warnings tend to be against the specific batches of contaminated food, as well as a few specific high-risk raw vegetables like sprouts.)

While it can be argued on the quantities being consumed of flour compared to raw vegetables and fruits, and therefore the level of bacteria that the person is exposed to.  Besides most raw Fruit &amp; Vegetables should be washed, the soil and bacteria can be removed this way, and that is before some of these are peeled/trimmed.  Dried fruit and vegetables after washing (and in some cases peeling), can have a number of processes (such as pre-treated - soaking in an acidic solution, or blanched) and are usually kept in a dry environment.
Minimally processed vegetables (high risk), such as watercress can be irradiated.  FDA article on produce (buying, storing, preparing raw fruit &amp; vegetables)
However, raw nuts still have risks of bacteria (e.g. salmonella).  Most nuts are  treated (pasteurised - steam, blanched, roasted, or fumigated - propylene oxide)

So why has raw flour been singled out for a general prohibition (as opposed to a warning about a specific contaminated batch, which applies to most fruit and vegetable outbreaks, as well as most of the dry goods outbreaks mentioned above)?
Is there some new information that justifies this broad and sweeping FDA prohibition on the basis of a couple outbreaks? (And if contaminated flour is such a big deal now to justify the recall of millions of pounds of flour, what makes this new situation different from most wheat flour, which has been known for decades to have high rates of E. coli and Salmonella contamination, occurring in something like 13% of samples of flour?)

FDA Raw Flour/Dough update
Article on the investigation and the lead to the ban
Any further questions maybe better answered by getting in contact with the FDA
and the academic community.