In an intensive care unit at Boston Children's Hospital, Dr. Greg Priebe was treating a teenager whose lungs had failed. To make matters worse, the patient spiked a fever from an infection brewing in his bloodstream: a type of bacteria called lactobacillus, commonly found in probiotic capsules and foods like yogurt.

"I knew that he was taking a probiotic containing lactobacillus at the time," Priebe recalls, "and I wondered whether they could be the same."

This case back in 2014 reminded Priebe of a patient who had developed a lactobacillus infection after back surgery a couple of years earlier. Patients on probiotics tend to take them at home and then just keep taking them in the hospital, he says.

"Those two cases kind of made me start thinking that maybe there is a problem there, because that patient was also taking a probiotic containing lactobacillus," Priebe says.

Probiotics are generally seen as safe — a benign way to bolster the "good" bacteria in the body, particularly when they're depleted by antibiotics. The question was: Had "friendly" probiotic bacteria somehow run amok and turned into enemies?

Enter the microbial detectives from the hospital's team that fights infections. They searched the records they keep of all the microbes that show up on blood cultures, says their medical director, Dr. Tom Sandora.

"And over about a five-and-a-half year period, we noticed that there were six patients who had been receiving probiotics in the ICU who had a positive blood culture — a blood stream infection — with this particular bacteria called lactobacillus," he says. "And so that seemed like it was something that was worth looking into a little bit further."

To prove that the bacteria in the probiotics capsules had actually morphed into the patient infections, they needed to analyze the DNA sequences of both.

"The sequencing is like a way to fingerprint the bacteria, and that fingerprinting can implicate the probiotic in the crime," Sandora says.

They used state-of-the-art technology called whole genome sequencing that can compare all the "bases" — the As, Cs, Ts and Gs that are like the letters in the book of your DNA.

"And you can actually say, 'OK! These bacteria are 99.999% identical,' " says Idan Yelin from the Technion - Israel Institute of Technology, who worked on that DNA analysis.

"This allowed us to say, 'These bacteria are actually direct ancestors of the bacteria found in the blood,' " he says.

It was ground-breaking work to nail down the DNA match so definitively using the latest tools, says Christina Merakou, a post-doctoral fellow at Children's.

Her analysis helped show that one strain of the lactobacillus became resistant to an antibiotic. So the friendly bacteria didn't just turn into an enemy, it turned into a kind of a superbug.

But the researchers emphasize that the risk of infection they found in no way means that probiotics are dangerous for everyone.

Gregory Priebe, Christina Merakou and Thomas Sandora in one of the intensive care rooms at Boston Children’s Hospital (Jesse Costa/WBUR)

Merakou, who is Greek and "grew up eating yogurt," says the study looked only at seriously ill patients at Children's.

"So I wouldn't stop eating yogurt because of our study," she says, "but we do need to be more careful in the hospital about what's going on, and maybe give some guidelines even to the parents."

The hospital tightened its protocols for using probiotics in 2016, Priebe says, and a year later essentially banned probiotics for ICU patients who have a central line — a tube placed in a large vein for easy access.

He says it's not clear exactly how ICU patients get bloodstream infections from probiotics, but it's likely that the bacteria leak out of the gut because it loses its normal barriers.

Overall, in the researchers' study in the journal Nature Medicine, ICU patients on probiotics were about 120 times more likely to develop a lactobacillus infection than those not on probiotics, Priebe says. None of the patients died from the infections, he says.

Other research has found benefits from probiotics, particularly for diarrhea linked to antibiotics.

A major international study of the risks versus the benefits of probiotics in the ICU is now underway. Because it is a "gold-standard" trial — randomized, placebo controlled — "it will tell us whether the risk of blood infection is outweighed by other potential benefits of the probiotic, like preventing other types of infections," Priebe says.

The Children's study is not the first to show risks of infection from probiotics but it really nails them down, says Dr. Patricia Hibberd, chair of the department of Global Health at the Boston University School of Public Health. She researches probiotics but wasn't involved with this new study.

"The message has to go out to the general public that if they have a condition that could put them at risk, they shouldn't take probiotics," she says. "And those conditions are weakened immune system, gut problems, and being in an ICU."

She encourages anyone with concerns to speak with their doctor.

"But we've also got to get the doctors better educated about the risks as well," she says, "because there is so much positive press for probiotics. I think that is the public health priority."

And, she says, our understanding of probiotics — pro and con — is still in its infancy — so more research is critical.