In April 2015, a hospital patient in London, U.K., tested positive for a potentially deadly fungus — Candida auris.
Within a week, the patient one bed over had it too. A month later, two more people caught it. When hospital workers tested the intensive care unit, they found C. auris growing on the floor, radiators, windowsills, equipment monitors and keypads, according to a journal article about the outbreak.
Despite thorough cleaning and infection control measures, within 16 months, 50 people were colonized by the fungus, though luckily, none died.
In other hospitals, C. auris was transmitted from patient to patient by contaminated temperature probes, blood pressure cuffs and computer keyboards. Worryingly, not only did it stick around in the environment, in many cases, it was hard to treat — C. auris is often resistant to antifungal medication.
Of 140 patients infected during the first 10 months of a recent outbreak in Spain, 41 developed invasive blood infections. Even with treatment, 17 people died, according to a journal article.
C. auris has appeared in Canada too, said Amrita Bharat, a research scientist at the National Microbiology Lab, which is run by the Public Health Agency of Canada. Since 2012, there have been 19 cases — much less than the 617 cases seen in the U.S. as of March 29, 2019, according to a recent update from the Centers for Disease Control and Prevention.
“So far, we’ve been successful in keeping our cases contained and we haven’t seen any of the large hospital outbreaks that other countries have seen,” Bharat said. She attributes that to strong detection and infection-control measures implemented at Canadian hospitals and awareness of the fungus.
But not all fungi are so scary.
The microbiome
We’re all covered in fungus. “There’s likely hundreds of species on us at any one time,” said Julianne Kus, a clinical microbiologist and clinical lead of Public Health Ontario’s Mycology Reference Laboratory.
Some of those are “transient,” she said, simply passing through as we inhale them in our environment or get them on our skin.
Some of them make us their home.
“They are part of our natural microbiome. They co-exist with other organisms like bacteria. They’re on our skins, they’re on our mucosal membranes, they’re in our digestive tract.”
According to one study published in Nature, different fungi colonize different body parts. Aspergillus seems to like our forearms. Saccharomyces likes our nostrils. And everything seems to like our feet — our heels, toenails and the space between our toes are home to a teeming garden of fungi. One family of fungus, Malassezia, seems to live on most of our skin.
Although they comprise a much smaller proportion of the organisms that live on and inside us than bacteria, scientists think they might matter and are working to figure out just what the fungi are up to.
“We’re realizing now that they’re actually very important for health as well as disease,” said Natalie Knox, head of computational biology in the bioinformatics section of the Public Health Agency of Canada.
“So, similar to bacteria, there’s good fungi and then bad fungi. And then there’s some that actually are seemingly not harmful for humans, but given the opportunity they can cause disease or infection.”
Taking antibiotics, for example, kills both the bacteria that’s hurting us, and the other more benign bacteria that lives inside us, Kus said. “And when those bacteria are gone, there’s kind of a gap, and fungi or yeast can fill that void when there’s no bacteria there.”
In some women, that can lead to an overgrowth of Candida fungus in the vagina — otherwise known as a yeast infection. “And that often happens after a course of antibiotics because all of your healthy bacteria that are normally inhabiting you there are no longer there and that balance has been totally disrupted,” Kus said.
Patients with weakened immune systems are also prone to fungal infections, she said. “We have an increasing number of immune-compromised people in our population.”
Partly, this is due to medical advances. “Cancer treatment, organ transplants, helping people who live with chronic inflammatory diseases like rheumatoid arthritis — the treatments for all of these weakens their immune systems.”
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That means that these people aren’t able to fight off the fungi like they used to, she said.
That’s one of the reasons why researchers are so worried about drug-resistant fungi.
Drug resistance
Another is that we just don’t have that many drugs. There are just three major families of antifungal medication, and according to a review article published in Science in 2018, some samples of Candida auris have been found to be resistant to all three.
While all the Canadian cases, so far, were still susceptible to one family of drugs, Bharat said, “I think that with only three classes of antifungal drugs, any resistance we see is concerning.”
“We don’t have as many drugs to play around with as we do against bacteria,” Kus said.
“So even a little bit of antifungal drug resistance is a big problem for people who have fungal illness.”
“We are now witnessing an unprecedented worldwide increase in antifungal resistance,” wrote the authors of the 2018 Science article. They suggested that antifungal resistance was coming from two major sources: all the antifungal medication increasingly used in hospitals, especially in immunocompromised patients to prevent fungal infections, and the increased use of antifungals in agriculture.
“Agriculturally, there is a group of antifungal agents called the azoles. The chemical structure of those antifungals that are used on crops is very, very, very similar to what we use medically,” Kus said.
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Aspergillis fumigatis, another fungus that can infect humans, is developing azole resistance — more than one-quarter of Aspergillis infections in the Netherlands are resistant to azoles, according to the journal, and the drugs are increasingly failing as frontline therapies.
Until we have new antifungal drugs, for now, Kus said, it’s important to advocate for the judicious use of antifungals in health care — maybe also in agriculture, she thinks.
“They’re opportunistic pathogens. They take advantage of the situation when it presents itself.”