Add Pennsylvania to the list of Chipotle poisoning outbreak states.
Co-author: Andrew Porterfield
The number of recent food poisoning cases linked to the fast-food restaurant soared this week to more than 500 with the Centers for Disease Control and Prevention announcing 6 additional cases in four more states: Pennsylvania, North Dakota, Kansas and Oklahoma. 
"For more than 15 years, we've been working hard to change the way people think about and eat fast food," Chipotle Co-CEO and founder Steve Ells told Fortune earlier this year.
Well, Ells nailed that one.
Most of the Salmonella, norovirus and E. coli outbreaks have no known source (although the Minnesota outbreaks from Salmonella came from tomatoes). The agency has said it could not determine which food is responsible for the outbreak because of Chipotle's food handling policies--which has startled CDC officials.
"One of the challenges here has been that we have been able to identify the restaurants where people ate, but because of the way Chipotle does its record-keeping, we have been unable to figure out what food is in common across all those restaurants," Dr. Ian Williams, chief of the outbreak response and prevention branch of the CDC, told the New York Times.
Food poisoning with integrity
Chipotle's troubles have undermined its public claims that it uses safer and higher quality organic and local ingredients when available. Its chief financial officer John Hartung said during a recent call with analysts that the chain sources only about 10% of its ingredients within a few hundred miles of its restaurants. Those numbers are probably startling to most of its customers based on Chipotle's marketing assertions that it runs an ecological, sustainable business.
"When you go local, oftentimes these are very small farmers," Ron Cegnar, president of Lexington, Ky.-based supply chain company CEO Partners, told Nation's Restaurant News. "They may not have the treatment facilities on the water. Livestock may be getting into watering systems. They may not have the staff to do inspections. Plus you have a lot more points of supply. Instead of just three national suppliers, you have multiple local suppliers. So your risk probability goes up."
This poisoning crisis was not unexpected--at least according to Chipotle. In a February regulatory disclosure filed in February, the company acknowledged that safety and health related food problems were all but inevitable at its restaurants:
We have made a significant commitment to serving local or organic produce when seasonally available, and a small portion of our restaurants also serves produce purchased from farmers markets seasonally as well. These produce initiatives may make it more difficult to keep quality consistent, and present additional risk of food-borne illnesses given the greater number of suppliers involved in such a system and the difficulty of imposing our quality assurance programs on all such suppliers. Quality variations and food-borne illness concerns could adversely impact public perceptions of Food With Integrity or our brand generally.
So what has Chipotle done in the last two months to bring its marketing more in line with its stomach churning sourcing practices? It's doubled down on the braggadocio. In it's latest gambit to dig its way out of its public confidence hole, in what it calls a "day after" promise on its "food with integrity" page, Chipotle underscores its commitment to a 'local and sustainable sourcing' policy. 
"We're committed," Chipotle writes:
To sourcing the very best ingredients we can find and preparing them by hand... We're committed because we understand the connection between how food is raised and prepared, and how it tastes. We do it for farmers, animals, the environment ... We care deeply about where our ingredients come from. While industrial farming practices have evolved to maximize profits and production, we make an extra effort to partner with farmers, ranchers, and other suppliers whose practices emphasize quality and responsibility.
The microbial outbreaks have led some scientists, journalists wondering if the company's focus on where its food comes from is the wrong one. As a headline in Vox puts it: 
Chipotle and GMOs
In 2013, the restaurant chain announced that it would serve only food that did not come from genetically modified sources. The reason? According to the company's website:
While some studies have shown GMOs to be safe, most of this research was funded by companies that sell GMO seeds and did not evaluate long-term effects. More independent studies are needed. 
To back up its claims, Chipotle cites a review that's been a favorite of anti-GMO, pro-organic industry activists. It ignored the statements by more than 270 independent organizations that have publicly stated that GM foods are as safe or safer, and are often grown more sustainably, than organic or conventional foods -- including the European Commission and the National Academy of Scientists -- and instead cited a paper by ENSSER, short for the European Network of Scientists for Social and Environmental Responsibility, which is a self-avowed ideological opponent of biotechnology with the discredited research of Gilles-Éric Séralini, a founder of ENSSER, as its scientific sentinel:
In October 2013 a group of about 300 scientists from around the world signed a statement rejecting the claim that there is a scientific consensus on the safety of GMOs for human consumption. These scientists would like to see more research conducted, and they'd like more of the research to be conducted by independent third parties, not the companies marketing GMO crops themselves.
The company also cites another study, this by economist Charles Benbrook, who recently was forced out of his position at Washington State University (an adjunct professorship funded by the organic food industry).
One recent study by researchers at Washington State University estimated that between 1996 and 2011, pesticide and herbicide use increased by more than 400 million pounds as a result of GMO cultivation. This and other evidence suggests that GMO crops are fueling an escalating arms race with weeds and insects.
The study helped reinforce the mistaken belief -- uncritically embraced by Chipotle for crass marketing purposes -- that the use of GMOs has resulted in an increase in the use of chemical inputs, when an independent meta-study indicates that GMO use has resulted in an average 37 percent reduction in the use of pesticides.
Finally, the company mis-characterizes the findings of the International Agency for Research on Cancer (IARC, and not directly the World Health Organization, as claimed by Chipotle and others) study on glyphosate, which is an herbicide used to grow corn, soy and other crops engineered to resist the chemical:
The World Health Organization recently designated Glyphosate as "probably carcinogenic to humans". The use of glyphosate is extremely widespread. More than 9 percent of the landmass of the continental United States is planted with crops genetically modified for glyphosate resistance. Given the concerns surrounding these types of GMOs and the chemicals associated with them, we felt it was particularly important to seek out non-GMO ingredients when possible.
Resisting soy for resistant sunflower
What about Chiptole's claim that "We partner with farms that prioritize the long-term health of their land"? Well, sort of.
The company came under fire when it had to admit that animals that it sourced probably came from cows that consumed GMO feed, and the beverages it served "in our restaurants contain genetically modified ingredients, including those containing corn syrup, which is almost always made from GMO corn."
But its most transparently cynical move was its decision to change what oil it used in its food preparations. As part of its "commitment" to "prioritize" the environment and eschew GMO ingredients, Chipotle announced it would stop using soy oil, which in this country is mostly made using GM soy, and instead switch to sunflower oil, which is not genetically modified. As NPR has noted:
As an example of the ways that GMOs can damage the environment, Chipotle points to the problems caused by herbicide-tolerant GMO crops and how they encourage farmers to use a single herbicide, usually glyphosate, or Roundup. This, in turn, has led to the emergence of herbicide-resistant weeds, which Chipotle calls "superweeds."
What Chipotle did not tell credulous consumers is that the sunflower oil that replaced soy oil has shown to be more resistant to herbicides, not less -- resulting in the use of even more chemical inputs than GMO soy. Sunflower oil has been bred using conventional breeding techniques to resist an herbicide called an ALS inhibitor. Anti-GMO campaigners--and that now includes Chipotle -- somehow fashion that genetic modification breeding process to be more "natural" than precision genetic modification.
Here's the rub. As NPR and other commentators and scientists have noted, the weeds that plague sunflower plants, like GMO soy plants, have also become weed resistant; it's a very real fact of modern farming: weeds eventually develop resistance to herbicides. The problem is actually worse with plants resistant to ALS inhibitors than to those developed to be resistant to glyphosate. There are about 30 weeds that resist glyphosate; ALS inhibitors, used on sunflowers, are plagued by more than 150 types of resistant weeds, according to an analysis by Andrew Kniss, plant scientist at the University of Wyoming. In other words, if Chipotle was truly trying to protect the environment by moving away from herbicide resistant crops as it claims, it made a cynical an unsustainable choice in turning to sunflower oil.
Further underscoring Chipotle's contradictory standards, the company is fine about using dextrose and corn syrup in sweetened beverages, which it acknowledges are "made from GMO corn." There are a large number of ingredients that are produced using genetically modified microorganisms, including Vitamins B and C, the artificial sweetener aspartame, xanthan gum and a number of preservatives -- some of which are found in various Chipotle products.
Running from rennet
Another ingredient that Chipotle uses, and claims is "natural," is rennet, an enzyme used to make cheese. Infuriating some animal welfare advocates, anti-GMO activists have not been upfront about the fact that organic, non-GM rennet is obtained from the intestines of slaughtered calves. As the Genetic Literacy Project has noted, the rennet extracted from the stomach linings is usually a mixture of chymosin, pepsin (another enzyme) and other proteins. Because of the worldwide shortage of "natural" rennet, scientists genetically engineered a version. They figured out how to transfer a single gene from bovine cells that codes for chymosin into microbes, giving microbes the ability to produce chymosin. Today, more than 90 percent of the hard cheeses made in the United States, and in much of the West, use the genetically engineered protein made from GE yeast and bacteria.
For that reason, the Non-GMO Project will not offer its seal to any cheese made with fermentation-produced chymosin (FPC): "If a cheese has our seal on it, the consumer can be assured that it does not have [bioengineered] chymosin," notes that certification agency. FPC rennet is also not allowed in organic cheese based on the certification rules in the United States, Europe and Canada. Ironically, the most vocal and science-compromised anti-GMO groups, like GMO Free-USA, aggressively demonize common cheese.
So of course Chipotle, committed to not using GMO ingredients because of its claims there are inherent dangers associated with genetic engineering, doesn't use FPC rennet?
Well, no; organic rennet would be too expensive, so Chipotle uses the cheaper, GMO version -- and then tries to spin its expedient choice. In a Twitter exchange, Chipotle told University of Florida scientist Kevin Folta that it uses FPC, which the company went through contortions on its website to claim,
...is a vegetarian rennet that is classified as non-GMO by the EU and all existing U.S.state GMO labeling laws. While this enzyme is non-GMO, it is produced by bacteria that have been genetically modified... During the production process, the enzyme used to make cheese is completely separated from these organisms and does not contain any GMO material. The bacteria are classified as "processing aids" because they are not used as ingredients to make cheese. For this reason, cheese made with FPC enzyme does not contain any GMO material.
So let's get Chipotle's GMO policy straight: It rejects soy oil, because it it is made from GMO soy, even though the oil does not contain any GMO material. Yet it uses corn syrup and cheese and artificial sweeteners and vitamins made from GMOs because they do not contain any GMO material, even though the ingredients made by those processes are not genetically modified any less than FPC rennet is.
Chiptotle has breathed new life into the word "hypocrisy" when it comes to the debate over food, safety and GMOs.
Local sourcing?
Chipotle has do a lot more than just institute a better food sourcing, distribution and health inspection system. It's ripe for a complete overhaul of both its practices and its marketing scheme. You can only fool the public for so long.
There are ongoing, science-based health concerns about the amount of salt, sugar and refined flour in our diets, and the fast-food industry is certainly one of the world's largest contributors of those ingredients to our diet. Chipotle's by no means unique among restaurants and other processed food retailers for that, and it is by no means the first to experience microbial outbreaks. But it would appear that their dream of being uniquely GMO-free has been usurped by a uniqueness of another kind.
Andrew Porterfield is a writer, editor and communications consultant for academic institutions, companies and non-profits in the life sciences. He is based in Camarillo, California. Follow @AMPorterfield on Twitter.
Jon Entine, executive director of the Genetic Literacy Project, is a Senior Fellow at the World Food Center's Institute for Food and Agricultural Literacy, University of California-Davis. Follow @JonEntine on Twitter