Second Chipotle E. Coli Outbreak Highlights Struggle to Find Source of Bacteria

Experts say fresh produce, meat and employee behavior will be scrutinized.

— -- A second E. coli incident linked to Chipotle restaurants has highlighted the difficulty in discovering the source of the outbreak as its fresh produce and food supply chains come under scrutiny.

This strain of E. coli has a different DNA profile from the previous outbreak of E. coli related to the restaurant chain where 53 people were sickened from Oct. 19, 2015, to Nov. 14, 2015, the CDC says. Officials are still investigating the source of both outbreaks and whether they are at all related.

Chris Arnold, a spokesman for the Denver-based fast-casual restaurant chain, said new safety measures were already being implemented and new food safety programs were being used to ensure customer's safety.

"We have indicated before that we expected that we may see additional cases stemming from this, and CDC is now reporting some additional cases," Arnold told ABC News today via email. "Since this issue began, we have completed a comprehensive reassessment of our food safety programs with an eye to finding best practices for each of the ingredients we use."

The restaurant is now implementing "high-resolution testing of ingredients, end of shelf-life testing of ingredients, continuous improvement in the supply system based on testing data, and enhanced food safety training," Arnold said.

"With all of these programs in place, we are confident that we can achieve a level of food safety risk that is near zero.”

The company uses just 68 ingredients total, founder and Chairman Steve Ells has said, including tomatoes and corn in the salsa and lettuce that are used raw. Experts say various parts of the Chipotle food supply will be under scrutiny, including where its fresh produce originates and how employees prepare food, as officials attempt to find the source of the outbreak.

Dr. Frank Esper, a pediatric infectious disease physician at University Hospitals Case Medical Center in Cleveland, said the first E. coli outbreak that sickened 53 people across nine states and over at least four weeks could indicate that the fresh food was already contaminated before it left the supplier.

He pointed out that some suppliers can use produce from multiple farms and if something is contaminated, the result can be wide-reaching problems for consumers.

"[It can] create a large bottleneck from lots of farms and goes to one distribution and sends it out to entire regions of U.S.," Esper explained, of how large suppliers can mix together produce from multiple farms.

Dr. William Schaffner, an infectious disease expert at Vanderbilt University in Tennessee, said health officials will be looking at food records to try to see which food went to which locations in the hopes of identifying a source for the recent E. coli outbreaks.

"We don’t know if it’s the same food item or related food item or completely different in each [outbreak]," Schaffner told ABC News today. "At the moment, we’re all kind of scratching our heads."

Schaffner said the genetic differences between the bacteria in these two E. coli outbreaks were slight, but that it remains unclear whether they were related. He said Chipotle will have to rethink its entire supply chain to keep customers safe and not have to cook virtually all food to ensure its safety.

"If you cook food thoroughly, you’ll kill all pathogens before it arrived at the restaurant. However, virtually every restaurant chain provides some food that’s not cooked," Schaffner explained. "If that food is fresh produce, then you’re dependent on the whole chain going from the farm to the distributor to maintain the integrity of the food."