By Julie Steenhuysen

CHICAGO (Reuters) – U.S. regulators want food companies to be more proactive in preventing food-borne diseases, citing new data showing that multistate outbreaks – which involve widely distributed products – cause more than half of all food poisoning deaths, even though they account for just 3 percent of all outbreaks.

The call to action comes amid multistate E. coli outbreaks involving 167,427 pounds (76,000 kg) of ground beef made by All American Meats of Omaha, Nebraska, and the closing of 43 Chipotle Mexican Grill Inc restaurants in Washington and Oregon. The outbreak is Chipotle’s third this year.

Just three germs – Salmonella, E. coli, and Listeria – cause 91 percent of outbreaks, contaminate widely distributed foods such as vegetables, beef, chicken and fresh fruits, and end up sickening people in many states, according to a new report by the U.S. Centers for Disease Control and Prevention.

Top officials from the CDC were joined by the U.S. Food and Drug Administration and the U.S. Department of Agriculture in issuing the warning on Tuesday.

“Reacting to problems isn’t sufficient in today’s food system, nor is it the best way to practice public health,” Dr. Kathleen¬†Gensheimer, director of FDA’s Coordinated Outbreak Response & Evaluation Network, said in a teleconference.

Gensheimer stressed that in the past, food safety has been focused on reacting to outbreaks, but new regulations set to take effect in 2016 will require companies to take a science-based approach to building safety controls into food production.

“Industry is a very critical partner,” she said.

For example, although it is still not clear what caused the E. Coli outbreak at Chipotle, Gensheimer said on the call that the company has shared “all of their records and is working with us in any way possible to give us information about their suppliers.”

Gensheimer also said after the current investigation ends, the company expressed interest in meeting with FDA and the CDC to work out ways to prevent future outbreaks.

CDC Director Dr. Tom Frieden said state-of-the-art disease tracking tools, and the introduction of gene tools, are helping to quickly track down the source of food-borne outbreaks in collaboration with state and national partners.

Frieden said disease detectives are “cracking the cases much more frequently than in past years because we have this new DNA fingerprinting tool being used increasingly,” but many cases still go unsolved.

He said companies are also stepping up to help, noting new requirements at Wal-Mart Stores Inc for food suppliers that set new control for suppliers to reduce contamination and the wholesaler’s Costco’s use of membership card lists to notify customers about recalled foods.

In recent months, the CDC, FDA and USDA have been trying to persuade U.S. food companies to voluntarily submit the genetic sequences of the pathogens they find in their food production plants to a nationwide database that could be used to track down the source of outbreaks earlier.

In the report, scientists analyzed CDC data on outbreaks from 2010 to 2014, comparing outbreaks that occurred in two or more states to those that occurred in a single state.

They found that the 120 multistate outbreaks accounted for 11 percent of illnesses, 34 percent of hospitalizations and 56 percent of deaths. An average of 24 multistate outbreaks occurred each year.

The report stressed the need for food industries to play a bigger role in improving food safety by keeping detailed records to allow for faster tracing of foods, using store loyalty cards to identify which foods made people sick, and notifying customers of recalls.

(Reporting by Julie Steenhuysen; editing by Bill Rigby and Andrew Hay)