Vermont health inspectors found the DNA of Shiga toxin in unopened packaged beef at a South Royalton restaurant and believe that undercooked hamburgers at Worthy Burger were the source of an E. coli contamination that sickened several people in late summer, a Vermont health official said Tuesday.

Bradley Tompkins, a health surveillance epidemiologist with the Department of Health, also said two more cases of E. coli have been linked to people who dined at the restaurant, and that there now are six confirmed and three probable cases of E. coli in the Vermont outbreak. All have recovered, although to varying degrees, he said.

Tompkins said eight of the nine diners ate ground beef at Worthy Burger between the end of August and the middle of September, when investigators with the Vermont Department of Health inspected the restaurant, recommended some changes, and took some beef and lettuce, which is served on the hamburgers, to test.

The lettuce tested negative — “we do not believe lettuce played a role in this outbreak,” Tompkins said — but the health department found the DNA for Shiga toxin in the ground beef.

When they tried to grow the E. coli in the lab, however, it came out to be a slightly different strain than the one found in the patients from Vermont. Still, Tompkins said, the department believes the beef is to blame.

“It’s certainly not conclusive that it did come from the ground beef, (but) based on the interviews that were done with the patients and that we found the E. coli and the Shiga toxins … we do believe the outbreak was caused by the ground beef that was being undercooked from the restaurant,” Tompkins said.

Asked which farm the beef came from and where it was slaughtered and packaged — Worthy Burger relies on local suppliers for its grass-fed beef and other food — Tompkins referred a reporter to the U.S. Department of Agriculture’s Food Safety and Inspection Service, which oversees slaughterhouses.

USDA spokeswoman Gabrielle Johnston said “there’s still debate whether it’s actually been linked to the beef” and said the matter is “still under investigation.”

Aaron Lavallee, another USDA spokesman who was on the same phone line with Johnston, said the agency was not at a point where it would name which slaughterhouses are being investigated, but said officials are “trying to trace this back all the way to the slaughter facility.”

Worthy Burger’s Executive Chef Jason Merrill said on Tuesday the beef that was tested was taken from the restaurant’s walk-in cold storage in its original packaging from a Vermont slaughterhouse, leading him to suggest the contamination could have occurred at what he called a “USDA-inspected plant.”

“The samples they took from us were in a receiving walk-in, and we hadn’t even touched it,” he said.

“I believe the beef was OK (at the farm), and when it got to the slaughterhouse, that’s when the infection happened,” Merrill said.