A Chipotle Mexican Grill in San Francisco on July 21, 2015. (REUTERS/Robert Galbraith)

The Centers for Disease Control and Prevention announced Monday that it is looking into five more cases of  food-borne illness linked to Chipotle Mexican Grill outlets, but that the bacteria that caused these illnesses appears to have a different DNA fingerprint than the E. coli strain involved in the larger outbreak.

Three of the new cases are in Oklahoma, one in Kansas and one in North Dakota and sequencing of the E. coli strain identified it as a rare variant of O26 . The customers reported eating at Chipotle outlets between Nov. 18 to Nov. 26 and which corresponds to about a week before they became ill.

The CDC said that since it does not know whether this new outbreak is related to the larger one it is not including it in its count of the total number of cases. One more person has fallen ill in Pennsylvania in the first cluster bringing the total impacted to 53 in nine states. Twenty of those patients had symptoms serious enough that they had to be hospitalized.

"The epidemiologic evidence available at this time suggests that a common meal item or ingredient served at Chipotle Mexican Grill restaurants in several states is a likely source of this outbreak," the CDC said.

Separately, a group of at least 80 students at Boston College fell ill after eating at a Chipotle in what is believed to be a third group of food poisonings. In this case, local health officials blamed norovirus from a sick employee.

Chipotle stock has taken a beating over the past few months as the number of cases has mounted. Earlier this month Chipotle CEO and founder Steve Ells went on national TV to apologize for the recent spate of illnesses and vowed to make the company's restaurants the safest places to eat by going above and beyond the industry's best practices for food safety.

Chipotle restaurant workers fill orders for customers on the day that the company announced it will only use non-GMO ingredients in its food on April 27, 2015 in Miami, Florida. (Photo by Joe Raedle/Getty Images)

Foodborne outbreaks in the United States have become bigger and deadlier in recent years and have included all sorts of food from fresh fruits to meats. In a briefing with reporters in November, CDC Director Thomas Frieden said that the number of major food outbreaks has tripled over the past 20 years.

"On average, there are about two per month, and they can be big and they can be lethal," Frieden said.

The CDC has been using new gene-sequencing tools to try to pinpoint down and stop outbreaks faster. It involves trying to match pieces of DNA in contaminated food to pathogens in people who are sick. The technique has helped government investigators solve numerous cases -- including some "cold cases" that from years past -- but in the case of the Chipotle outbreak it has so far failed to get to the bottom of the mystery of what food specifically caused the illnesses.

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