'Needle in a haystack': Expert says finding daycare E. coli outbreak source complex

CALGARY — Health investigators and scientists are diving deep into food and fecal samples to zero in on the cause of an ongoing E. coli outbreak affecting Calgary daycares, but experts say definitive answers may be hard to come by.

“You are trying to find the same organism with the same fingerprint,” said Timothy Sly, an epidemiologist and professor emeritus at Toronto Metropolitan University.

There have been 264 lab-confirmed cases of the bacterial infection since the outbreak at 11 daycares was declared on Sept. 4.

As of Tuesday, 25 patients were in hospital, 22 of whom have hemolytic uremic syndrome, a complication affecting the blood and kidneys. Six patients were on dialysis at Alberta Children's Hospital.

Dr. Mark Joffe, Alberta's chief medical officer of health, has said a central kitchen serving the daycares is almost certainly the source of the infections.

Investigations into what ultimately cause E. coli outbreaks can be complex, involve a lot of lab work and don’t always nail it down, said Sly.

But he said there’s always one source at the headwaters of such outbreaks: cattle.

For waterborne E. coli outbreaks, the water source has been contaminated by runoff from cattle feedlots. Romaine lettuce outbreaks happen because the leafy green is grown next to where cattle eat. Apple juice outbreaks are from cattle wandering through orchards.

But, as Sly suspects may be the cause in Calgary, often it's directly from the source: undercooked beef.

Piecing together the puzzle isn’t straightforward, he said. Investigators will look to food handlers, those infected and the food itself.

"You can say it's E. coli, but you have to go further to find out which strain,” he said.

Sly said samples will have been collected from people who work in the kitchen and those infected with E. coli.

People in the lab will be looking to connect the genome markers to find the same strain. Then food samples from the kitchen will be tested for a match.

“To identify the actual source of the E. coli, you would need to isolate the outbreak strain from one of the foods that was served,” said Michael Gaenzle, professor and Canada Research Chair in the University of Alberta's department of Agricultural, Life and Environmental Sciences.

The bacteria related to this outbreak is Shiga toxin-producing E. coli. Less than 10 cells can make a person sick, Gaenzle said. It also makes it difficult to identify in food because there are a trillion bacterial cells in a gram. On top of that, the food served may have already been thrown out.

"You are looking for the needle in the haystack,” he said.

If there are no good samples from food, Gaenzle said experts will go back to conventional wisdom about E. coli outbreaks.

The size and scale of this outbreak means it's unlikely that cross-contamination or cockroaches in the kitchen were the main cause, he said. That leaves experts looking to food.

Leafy greens like lettuce and spinach are also less likely to be the cause, Gaenzle said. If it was greens, other people who purchased produce would be getting sick.

Gaenzle said he suspects investigators will find a link to undercooked beef. It would explain the sickness being contained within the daycares, and parents have said their children were served meat loaf in the days before the sickness spread.

"That's reasoning based on a pattern of past outbreaks,” Gaenzle said.

Alberta Health Services has not confirmed what food children were served.

Gaenzle said investigations can take weeks. He’s spoken to people in Alberta Health Services who say the labs are completely swamped and a definitive answer matching food samples to those infected may never come.

But Gaenzle said this outbreak shows there needs to be improved oversight for food service companies, especially those who cater to daycares. A report detailing health violations at the kitchen earlier this month found improper sanitation, live cockroaches and issues around food handling.

Ultimately, he said, the lesson may be “humans make mistakes.”

Gaenzle has a daughter in daycare and said when he learned of the outbreak, he thought, “This is really, really bad."

This report by The Canadian Press was first published Sept. 13, 2023.

— By Kelly Geraldine Malone in Saskatoon

The Canadian Press