Chicago cheese lovers looking for some traditional French cheeses may be out of luck this year.

“There are certain cheeses we simply aren’t seeing at all at the moment, like Morbier,” says Greg O’Neil co-owner of Pastoral Cheese Bread & Wine in Lakeview and the Loop. “This is unfortunate, because it is a classic and a mover.”

Newly enforced federal guidelines have stopped many types of imported raw milk cheeses—including Morbier and Roquefort— at the border in the last six months due to levels of non-toxigenic E. coli.

So what’s wrong with non-toxigenic E. coli?

WBEZ asked the Food and Drug Administration and a representative sent this:

“While these bacteria don’t cause illness, their presence suggests that the cheese was produced in unsanitary conditions.”

This statement runs contrary to 2009 draft guidance by the FDA stating:

“Because of the close association of raw milk with the animal environment, low levels of Escherichia coli may be present in raw milk or products made from raw milk, even when properly produced using GMPs. However, the presence of Escherichia coli in a cheese and cheese product made from raw milk at a level greater than 100 MPN/g (Most Probable Number per gram) indicates insanitary conditions…”

And so if, according to this 2009 FDA draft,  non toxigenic E. coli numbers under 100 MPN can occur in raw milk cheeses under GMP (good manufacturing practices), why did the FDA move in 2010 to lower that number by 90 percent for all dairy?   

That’s a question the American Cheese Society posed to the FDA last week.

“We want to know if there is research data, linkages to foodborne illnesses or a public health risk,” said ACS executive director Nora Weiser. “Because it’s important for us to know if that exists and if that is why they have lowered this standard.”

But, as of press time, the agency said it was still working on an explanation for its 2010 guideline.

The American Cheese Society is not the only entity cheesed off by the recent enforcement of the guidelines. Chicagoist writer Erika Kubick detailed her concern here. And the Cheese Importers Association of America is gearing up to confront the FDA soon.

“The CIAA would like to reinforce our concern that the FDA is taking regulatory action without recognizing the historic safety of imported cheeses like Roquefort,” the organization said in a statement. “We completely agree that food safety is at the forefront of this decision. However, as was have done with the wood board aging issue, the FDA is promoting regulation without taking all factors into consideration. This action was discussed at the recent CIAA board meeting, and our concerns will be communicated to the FDA shortly.”

If the presence of non-toxigenic E. coli in raw milk cheese posed a threat to American health, certainly the Centers for Disease Control and Prevention would know about it, right? Well, not really.

The CDC had nothing on its website about the bacteria so WBEZ contacted CDC press officer Christine Pearson. She said she would try to get some information on non-toxigenic E. coli but didn’t have an easy time of it.

She wrote back saying: “I heard back from one of my experts that nontoxigenic is not a term that we use.” Follow up questions last Friday remained unanswered.

This lack of clarity and explanation isn’t just affecting cheese imports. It also prompted award-winning Uplands Wisconsin cheesemaker Andy Hatch to skip making his famous Rush Creek Reserve raw milk cheese this fall.

“I’m intimidated by the lack of consensus or clarity,” Hatch told WBEZ’s Chewing the Fat food podcast. “I think most cheesemakers are saying the same thing. We’re not exactly sure how they’re approaching these cheeses…And it’s also so perishable so that if anything should hold up shipment, the window for sale is really tight, and so one little hiccup and you’ve spoiled months of work.”

International cheesemakers whose products have been “Red Listed” by the non-toxigenic E. coli guidelines have already been hurt by this hiccup. The questions remains, why?

Consumers who want to comment on the FDA rules can still do so here.

WBEZ will stay on this story and update it when the FDA responds to the American Cheese Society on the problems posed by exceeding 10 MPN per gram of non-toxigenic E. coli in raw milk cheese.

Monica Eng is a WBEZ producer and co-host of the Chewing The Fat podcast. Follow her at @monicaeng or write to her at meng@wbez.org