By the time the C.D.C. ended its investigation into the outbreak, 55 people had been infected with the outbreak strain from 11 states in the initial outbreak, and 22 individuals were hospitalized. 

ATLANTA — An official with the Centers for Disease Control and Prevention defended the agency’s handling of E. coli O26 outbreaks that were linked to Chipotle Mexican Grill restaurants.

Executives with Chipotle have complained that C.D.C. web updates confused and misinformed consumers as to the status of the outbreak. And in a letter to the agency, Bryant “Corky” Messner of Messner Reeves L.L.P., which represents Chipotle, detailed the company’s concerns.

Specifically, the C.D.C. did not follow its own guidelines for disseminating information to the public, and the web updates misinformed consumers.

“We understand the importance of notifying the public of a significant health risk and also understand the importance of proving relevant and meaningful updates when there is an ongoing public health risk,” Mr. Messner wrote. “However, each update must stand on its own as to whether there is a significant health risk that necessitates an update to the public.

“We are not claiming that the C.D.C. intentionally misrepresented certain information. However, certain web updates actually misinformed the public because they were confusing and unclear. A review of media coverage, citing the C.D.C. updates, reflects the confusion and inaccuracies. Despite no ongoing threat, with four weeks passing between the last exposure date and the most recent web update, the web updates did not serve to protect the public and, in fact, led to inaccurate conclusions.”

By the time the C.D.C. ended its investigation into the outbreak, 55 people had been infected with the outbreak strain from 11 states in the initial outbreak, and 22 individuals were hospitalized.

C.D.C. also investigated a second outbreak of E. coli O26 linked to Chipotle, but the agency didn’t include those illnesses in the case count for the initial outbreak. However, all five people infected in the second outbreak reported eating at a Chipotle Mexican Grill before getting sick.

In response, Jeremy Sobel, associate director for Epidemiological Sciences at the C.D.C., explained that reported illness onset dates for the two outbreaks ranged from Oct. 19, 2015, to Dec. 1, 2015.

“Given that two to three weeks typically pass between when a person becomes ill to when the illness is reported to PulseNet and the most recent illness onset date of December 1, 2015, we disagree that there was “no ongoing threat” at the time of the web postings, particularly since the investigation of these two outbreaks linked to Chipotle Mexican Grill Restaurants has not identified a specific cause,” Dr. Sobel wrote. “A public health professional would not conclude that transmission had ceased until at least several weeks after the last reported case.”

Chipotle also complained that the C.D.C. used inappropriate methods to define case patients. Sobel said case patients are defined as those that “appear on reports of ill people to the PulseNet system infected with the molecularly-defined outbreak strain of the pathogen; they are not based on whether a person consumed food at Chipotle Mexican Grill before becoming ill.”

Chipotle’s business suffered in the wake of its food safety problems. In the most recent quarter, the company reported a net loss of $26.4 million, or 88c per share, compared with net income of $122.6 million, or $3.88 per share, in the year-ago quarter. Revenues dropped 23.4%

The fast-casual chain launched food safety initiatives and free food offers via mobile and direct mail in an effort to win back customers.