Chipotle says cyclospora didn't directly impact its lettuce, but the parasitic outbreak has still taken a bite out of its sales.

The fast-casual chain said Wednesday that news of the outbreak tied to fresh produce hurt its July sales, dampening momentum coming into the month. The decline in sales was modest, Chief Executive Scott Boatwright said.

Chipotle gets romaine lettuce used for its bowls and burritos from California, not Mexico. Federal health officials have linked one outbreak of cyclospora-related illnesses to shredded iceberg lettuce that U.S. produce giant Taylor Farms sourced from Mexico.

"News like this, to be quite honest, hurts everyone. This isn't an isolated event for one brand," Boatwright said in an interview. "We hate to see it."

Still, shares surged 6% in extended trading. The gains came after Chipotle raised its full-year same-store sales outlook following swifter business in the second quarter. The company is bringing back customers across income and age groups, Boatwright said.

Operating margins fell for the quarter, as the company kept prices lower than the rate of inflation in food and labor costs. Boatwright said Chipotle needs to absorb those costs to keep customers buying its bowls, and the company is also stepping up marketing and its digital offers.