(Bloomberg) — Chipotle Mexican Grill Inc. is facing new questions about its food-safety procedures in Seattle, a sign the restaurant chain may have a hard time bouncing back from recent E. coli and norovirus outbreaks.

The city shut down a Chipotle in the South Lake Union neighborhood on Thursday after multiple inspections found it failed to keep food hot enough. The health department also gave unsatisfactory scores to nine of the 17 Chipotle restaurants in the Seattle area—even though the company previously closed the locations to revamp their food-handling standards.

The findings raise broader concerns about Chipotle's procedures for keeping food safe, a critical challenge as the company tries to restore its reputation. Seattle may provide the best window into its practices because all the restaurants in the area were closed and reopened in the wake of an E. coli outbreak. Despite the company deep-cleaning the restaurants and hiring a food-safety consultant, most of them are still getting subpar marks from local officials.

"It's not ideally what we want to see," said James Apa, a spokesman for the public-health department for Seattle and King County. While an unsatisfactory rating doesn't lead to a shutdown, it means at least one critical violation was found.

Undercooked chicken

The restaurants got unsatisfactory ratings for offenses such as not keeping meat hot enough and undercooking chicken. At multiple locations, employees weren't washing their hands after handling raw meat.

"Those are important violations," said Benjamin Chapman, an associate professor and food-safety specialist at North Carolina State University. "Those are risk factors for food-borne illness that have been identified in previous outbreaks."

The restaurant that was closed on Thursday was cited repeatedly because items such as chicken, beef and vegetables were kept below 130 degrees—a level deemed hazardous. Local officials raised similar concerns about a Chipotle in Boston, where more than 140 college students were sickened with norovirus.

The issue in Seattle was related to a food-preparation line used for takeout orders, said Chris Arnold, a Chipotle spokesman.

"We are looking into the cause of that and will certainly address it," he said.

The health department also got a preliminary report of someone suffering gastrointestinal problems after eating at the location on Dec. 7, though it hasn't determined the cause of that illness.

Boston College

Chipotle's reputation has been battered in recent weeks by the E. coli outbreak, which afflicted at least 52 people in nine states. That was followed in the past week by the norovirus incident at a location near Boston College. The restaurant was closed after scores of students got sick.

In addition to not keeping food hot enough, the Boston restaurant was cited for having a sick employee working on Dec. 3, right before the weekend when the norovirus cases were reported.

Norovirus causes vomiting and diarrhea and can spread anywhere people gather or food is served. It's the leading cause of outbreaks from contaminated food in the U.S., making about 20 million people sick a year, according to the Centers for Disease Control and Prevention. In cases where investigators disclosed the source of contamination, infected food workers were the cause 70% of the time, the agency says. 

'Near zero'

After Chipotle was linked to the E. coli outbreak in October, it temporarily shut down locations in Washington state and Oregon. The restaurant chain hired IEH Laboratories & Consulting Group to help refine its procedures. The company has revamped its supply chain and is conducting DNA testing of produce in an effort to keep food safe. The cause of the E. coli contagion still hasn't been found.

Mansour Samadpour, head of IEH Laboratories, said after the restaurants reopened that the new procedures made Chipotle an industry leader.

"While it is never possible to completely eliminate all risk, this program eliminates or mitigates risk to a level near zero," he said earlier this month.

That was followed by the norovirus contagion and the additional violations in Seattle, signaling that there may still be gaps in Chipotle's safety net.

Earlier outbreak

In July, a smaller E. coli outbreak occurred in Washington, sickening five people. Local authorities didn't alert the public because "by the time we were able to make a link with that Chipotle, at least 10 days had passed from the last meal date and no further cases had occurred," Apa said. The state health department and CDC were notified, he said.

After forcing the Chipotle to close this week, Seattle officials acknowledged that the location didn't have as many violations as the typical restaurant it shuts down. But the repeated infractions gave them cause for concern, the agency said on its blog.

"Staff are working with Chipotle to correct these problems, and the restaurant will be allowed to reopen pending an inspection," the health department said.

–With assistance from Craig Giammona.

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