Last Updated Nov 4, 2015 6:02 PM EST
As of Wednesday, 41 cases of the illness have been reported -- 12 in the Portland, Oregon, area and 29 in Washington state. The outbreak has sent a dozen people to the hospital and closed 43 Chipotle restaurants in the two states.
Scientists said Tuesday that they had identified the specific microorganism responsible, believed to be found on fresh produce such as lettuce, tomatoes, cilantro or onions, or possibly even spices. The Mexican-style fast food chain has fostered a reputation for fresh, locally-sourced ingredients.
The chain voluntarily closed the locations in the two states affected after health officials alerted the company to a growing number of E. coli cases involving people who shared one common experience: a meal at Chipotle during the last two weeks.
E. coli is the name of a type of bacteria that lives in human intestines and in the intestines of animals. Most types of E. coli are harmless, but some can make you sick, according to the U.S. Department of Health and Human Services.
Dr. Scott Lindquist, Washington's state epidemiologist, said the specific microorganism responsible for the current outbreak is Shiga toxin-producing E. coli O26.
Now officials are doing more tests on samples of human waste and on any E. coli found in food samples, looking for exact DNA matches. That, in turn, should indicate which ingredient carried it into the meals of diners, Lindquist said.
Lindquist said they may know by Wednesday which produce, if any, tests positive for the same bacteria.
Authorities have already asked Chipotle to turn over information about its food suppliers.
"We're really relying on working closely with Chipotle," said Dr. Katrina Hedberg, Oregon's state epidemiologist.
Chipotle Mexican Grill Chairman Steve Ells said in a statement Tuesday that the company immediately closed numerous locations "out of an abundance of caution, even though only eight restaurants have drawn concern."
The company also said it is doing its own tests in restaurants and distribution centers. It is fully sanitizing the restaurants, replacing all of the food, and testing batches of ingredients in its supply chain, the statement said.
The outbreak is not the first that Chipotle has had to contend with in recent months. Last July, five people became sick with another strain of E. coli after eating at a Seattle area Chipotle. Then in August, 64 cases of salmonella illness were linked to tainted tomatoes served up at two Chipotle locations in Minnesota. That same month, 80 customers and 18 employees of a Chipotle in southern California became ill, and some tested positive for norovirus.
Multi-state outbreaks of foodborne illness have increased sharply in recent years, the U.S. Centers for Disease Control and Prevention reported Tuesday. On average, two dozen occurred from 2010 to 2014, up from six a year from 1973 to 2010. That's partly due to better detection, but food industry consolidation has meant companies ship to wider networks of grocery stores and restaurants now, so tainted products can spread more widely as well.
In this case, identifying the supplier of any contaminated produce should be easier because Chipotle uses traceability software, made by the Durham, North Carolina-based company FoodLogiQ, and has promised its consumers that it can trace every box of fresh ingredients from farm to table, in real time.
"Ideally, any of these trace-back systems should help," said Jaydee Hanson, a senior policy analyst at the Center for Food Safety, a Washington, D.C.-based nonprofit that promotes food safety and sustainable agriculture.
Health officials believe knowing the distribution of food along Chipotle's supply chain will give them useful information, said Dr. Jeff Duchin, health officer for Seattle and King County Public Health.
"We're really hoping that the trace-back will give us some good clues about what the cause could be," Duchin said. He acknowledged, however, that this will be a difficult investigation because so many of the same ingredients go into multiple dishes at Chipotle.
In 2008, health officials initially suspected raw tomatoes to be the source of a salmonella outbreak that sickened people around the country, Hanson said. Without adequate ways of tracing tomatoes or other contaminated produce to their origins, everybody stopped buying tomatoes, everywhere.
"Being able to quickly find where the problem is, is why our organization and others have been arguing for good traceability, from farm to fork," Hanson said. "Chipotle is to be commended for trying to put in place a system to trace its supply, and hopefully it works this time."
According to a CDC statement, Oregon health officials asked their residents who have eaten at Chipotle between October 14 and 23 to seek medical help if they become ill with vomiting and bloody diarrhea, and to mention the Oregon outbreak.
In the meantime, Washington State Department of Health Food Safety Specialist Janet Anderberg said a broader investigation needs to be conducted at the federal level.
"In a broader scope, perhaps CDC would be a better agency to take a look at those kinds of things, and determine if there is a pattern associated with that," Anderberg said.
The company also said in the Tuesday statement that it is retaining two food safety consulting firms to help the food chain assess and improve its "already high standards for food safety."
"The safety of our customers and integrity of our food supply has always been our highest priority," said Chipotle's Ells.
To fight the spread of E. coli illness, health officials recommend washing hands thoroughly before cooking and after diapering a baby or after visiting a farm and petting animals. Cook meat thoroughly and avoid high-risk foods, especially undercooked ground beef, unpasteurized milk or juice, soft cheeses made from unpasteurized milk, or alfalfa sprouts.