NBC Today Show
Chipotle CEO Steve Ells.
"This was a very unfortunate incident and I'm deeply sorry that this happened," Ells said on NBC's Today Show. "But the procedures we're putting in place today are so above industry norms that we are going to be the safest place to eat."
The outbreak linked to Chipotle has expanded to nine states, with 47 of the 52 people sickened having reported eating at the chain.
Ells said it's a "really tough time" for Chipotle.
Chipotle's stock price has plunged more than 20% since the outbreak was first reported.
Sales have also declined. Chipotle has warned that its same-store sales could fall for the first time in company history this quarter. The company is expecting a decline of between 8% and 11%.
After weeks of investigation, health officials still haven't found the source of the outbreak.
"We have closed our restaurants out of an abundance of caution and tested all the ingredients, surfaces -thousands and thousands of tests - and they call came back negative for E. coli," Ells said.
He said there's a silver lining to the outbreak, however, because it has forced Chipotle to reassess and improve its food safety regulations.
A team of epidemiologists and food safety experts has investigated the delivery, handling, cooking, and serving of all 64 of Chipotle's ingredients, and developed better food safety standards for the chain going forward.
"It has caused us to put in practices... that will put us 10 to 15 years ahead of industry norms and I believe this will be the safest restaurants to eat at," Ells said.
When asked whether Chipotle would be able to recover financially from the outbreak, Ells said, "Well certainly but that's not what we're thinking about now we're thinking about the safety and quality of our ingredients."
Analysts expect same-store sales to continue declining through at least June 2016. The slide could extend even longer, if history is any indication.
A similar outbreak of E. coli illnesses linked to Taco Bell restaurants in 2006 sent same-store sales into negative territory for five straight quarters, Quartz reports.