Nice to see my microbiological friends Linda Harris and Trevor Suslow, both of the University of California, Davis, mentioned in this National Geographic piece.

Rachel Becker writes that Chipotle Mexican Grill has had a rough couple of months.

First, a series of foodborne outbreaks radiating from Chipotle restaurants across the country sickened hundreds. Then, the U.S. Attorney’s Office served the fast-casual restaurant chain with subpoenas in an investigation into an August outbreak of norovirus—the virus infamous for causing explosive diarrhea—at a California Chipotle location.

In early December, Chipotle declared that it would revamp its food handling practices to become an industry leader in food safety. It even took the unprecedented step of announcing it would close more than 2,000 locations for four hours on February 8 so employees could attend a company-wide meeting broadcast from Denver to discuss the company’s new food safety procedures.

But the bad press just keeps coming. In a country where foodborne illnesses sicken 48 million people, hospitalize 128,000, and kill 3,000 each year, does Chipotle deserve the scrutiny it’s been getting? Or is the company that makes its money selling “Food with Integrity,” shunning the standard fast food supply chain in favor of “responsible” food, just getting picked on for trying to stand out?

Linda Harris, a food safety microbiologist at the University of California, Davis (left, exactly as shown, and she was on my PhD advisory committee), thinks that the scrutiny is fair, adding that the number of outbreaks Chipotle has had this year is “verging on the ridiculous.”

“I think if other restaurants have had problems over that time frame and in those states, it would have been reported as much as it was for Chipotle,” she says.

In July, five people in Seattle came down with E. coli O157:H7 infections after eating at a local Chipotle. Then in August, norovirus struck a southern California Chipotle, sickening a final count of 234 people including 18 employees according to Ventura County environmental health spokesperson Doug Beach.

Around the same time, tomatoes contaminated with Salmonella Newport found their way into 22 Chipotle locations in Minnesota, infecting 64 people. Between October and December two strains of another type of E. coli, E. coli O26, infected 60 people in total who had eaten at Chipotle. To cap off a series of unfortunate events, in December 136 people were infected with norovirus in Boston after eating at the fast-casual restaurant—the outbreak was traced back to a sick employee.

Fortunately, there have been no deaths. But there has been a lot of diarrhea.

Chipotle has taken steps to address the problems. It’s moved tomato, lettuce, and cheese preparation to a central kitchen, implemented more testing for dangerous microbes, added a blanching step for some of the produce, changed marinating procedures, and added financial incentives for restaurant managers that are contingent on high food safety audit scores.

But it wasn’t enough to stop the financial bleeding. The restaurant announced on February 2 that revenue went down the toilet in the fourth quarter of 2015 with a 44% decrease in profit.

Doug Powell, a former professor of food safety at Kansas State University and founder of the appropriately named food safety blog, barfblog.com, says that he anticipated these outbreaks at Chipotle years ago.

“I’ve pointed this out since 2007,” he says. “They were more concerned about GMO-free, sustainable, natural, antibiotic-free—and in my experience when you do that, you tend to lose your focus on the things that actually make people sick.”

(Chipotle, to some extent, also anticipated these problems; their 2014 Annual Report listed food borne illness as a potential consequence of their emphasis on using fresh produce in their restaurants.)

Chris Arnold, a Chipotle spokesperson, disagrees that Chipotle’s priorities were misplaced. “I don’t think there is any validity at all to that,” he says. “We have always maintained food safety programs that are consistent with industry standards. These incidents have shown us that we need to do better, and that is what we are doing.”

Trevor Suslow, who specializes in food safety of produce at University of California, Davis, says that assessing whether Chipotle’s new food handling strategies will be effective requires that Chipotle make more details available. He expressed concerns that blanching—dipping foods into boiling water for a matter of seconds—might not kill certain kinds of bacteria embedded in produce or coating food items in a biofilm.

And Suslow, Harris, and Powell also note that there are limits to how much food testing can protect a food supply chain. “Product testing is a very last icing on the cake, if you will, of food safety management. It’s a verification activity only. It should not be the basis of your food safety management program,” Harris says.

Chipotle spokesperson Arnold responds that testing is an important part of their new plans, but not the only part. It’s “the layering of all of these program components that contribute to the strength of the whole food safety program,” he says in an email.

Instead, Harris and Powell say, the key to avoiding repeated outbreaks is a systemic culture of food safety.

“I think it really goes back to Chipotles’ attitude,” Powell says. “They want to put all of their money into sustainable, GMO-free, organic, whatever. That’s great. I don’t really care about how it’s grown. I care if it’s going to make people barf.”