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Chipotle Illnesses Have Food Safety Experts 'Scratching Their Heads'

Just when it looked like it might be safe once again to eat at Chipotle, a new spate of food poisoning related to the restaurant chain has sprung up.

More E.Coli Linked To Chipotle 1:23

Five people who ate at Chipotle restaurants in Kansas, North Dakota and Oklahoma have been sickened with a similar, though slightly different, strain of E.coli, the nasty bacteria blamed for the earlier outbreak.

While noting that it's possible that the new illnesses could be related to the previous incidents, the Centers for Disease Control and Prevention is currently treating them separately.

Chipotle had closed 43 restaurants in the western states after the first outbreak in October. Those restaurants were reopened in November.

Though diners might be tempted to choose another restaurant until the investigations are done, experts say that we're hearing more about Chipotle's troubles now because they've already been in the news once.

"Most food borne illnesses are not reported," said Dr. Jonathan Fielding, former director of public health for Los Angeles County and currently a professor of health policy and management at the Fielding School of Public Health at the University of California, Los Angeles, and a professor of pediatrics at the UCLA School of Medicine. "When there is a very public airing of an initial outbreak people are much more likely to report illness. It's not surprising to me that there is increased vigilance on the part of people who have eaten there."

How Do You Catch E. Coli? 0:42

That's certainly true for Sarah Mathews, who says she's a fan of the restaurants but is worried about safety.

"It's popular; it's quick; and it's good," Mathews told NBC News. "It's good food and so it's concerning. Obviously I don't want to eat somewhere that could potentially get me sick."

Raised awareness aside, experts are perplexed by the second outbreak.

"Everybody is scratching their heads," Fielding says.

Chris Arnold, communications director for Chipotle Mexican Grill, Inc., said the company is doing everything possible to identify the source of the contamination.

"The CDC has said that that it is not known if these cases are connected to the previous ones," Arnold said. "Our experts are assessing that, and we are continuing to work diligently with CDC and FDA on their investigation."

"Investigators have not been able to definitively identify a source for this outbreak, though we are continuing to work with them to try to do so," he added. "If there is a silver lining in not knowing for sure what the cause is, it is that it has prompted us to do a comprehensive reassessment of all of the ingredients we use with an eye to establishing best practices for the handling of each ingredient we use. The result of this reassessment is an enhanced food safety plan that should allow us to eliminate or mitigate risks in this area to a level near zero."

For his part, Fielding says he's surprised that a food culprit hasn't been found yet for the first outbreak. "It's uncommon not to have found the common offending food," he said.

Though initial testing indicated that the strain of E.coli in the latest outbreak is different from the earlier one, the CDC is running more tests to confirm that.

"The investigation is ongoing to determine if they are related," said Kate Fowlie, a CDC spokesperson. "It's too soon to say — we need more info. We won't have results until January as this advance laboratory process typically takes a couple weeks to complete."

It's unclear whether the two outbreaks are related to the same ingredient served at Chipotle, because "we still don't know what ingredient caused the larger outbreak," said Fowlie. "It could be a situation where two different DNA fingerprints contaminated the same ingredient."

A similar case of multiple DNA fingerprints occurred with last summer's Blue Bell ice cream outbreak, when listeria contamination of some of its products killed three people.