Dr. David McKeown said officials have talked to over 100 of those who reported getting sick and the only common food exposure that they had was the cronut burger served by Epic Burger and Waffles.
"Early laboratory tests indicated that samples of the cronut burger were contaminated by staphylococcus aureas toxin," he said.
The bacteria produces a toxin which can cause nausea, vomiting and diarrhea in two to four hours, and McKeown said the majority of healthy people will recover, but it can be serious for young children and the elderly.
Symptoms of food-borne illness were first reported Tuesday night when paramedics treated 12 people at the CNE, sending five of them to hospital.
By Wednesday night, the number of reported illnesses had reached almost 100.
McKeown said there is no way for consumers to tell if a burger is contaminated before eating it.
"There were no indications from that investigation of any other CNE food associated with this outbreak," he said.
Further tests are being conducted to determine which of the components of the burger was contaminated.
McKeown said Epic Burger and Waffles will remain closed until the results of those tests come back. He said officials are trying to reconstruct the sequence of events so they can better understand how the outbreak unfolded.
"In this case, no one has died," he said, adding that "it can be much worse."
CNE general manager David Bednar said his priority is to ensure the health and safety of fair patrons.
"We've stopped this now, we're confident it's over," he said.
Epic Burger and Waffles issued a statement Thursday saying it has never had issues in the past and it takes health and safety "very seriously."