Fifteen years ago, scientists discovered a new species of deadly, drug-resistant fungus: Candida auris. It is today considered one of the most dangerous fungal pathogens on Earth. In this excerpt from “What if the mushrooms won?” » (Johns Hopkins University Press, 2024), author Arturo Casadevall examines the rise of this deadly fungus, which may be the first to have emerged as a result of climate change.
In 2009, doctors at a Japanese hospital published a paper identifying a new species of fungus they had found in the external ear canal of a 70-year-old patient. They called him Candida auriswith auris being the Latin word for ear.
At first, it wasn’t clear how worried anyone should be about this new discovery, if at all. Many new fungal species are reported in patients each year, but the vast majority of these turn out to be isolated cases that are not worth panicking about.
And C. auris remained under the radar for some time, remaining an obscure and unknown yeast in most parts of the planet – until it was discovered in hospital patients around the world, around the same time. Surprisingly, between 2012 and 2015, doctors in South Africa, Venezuela and the Indian subcontinent simultaneously reported treating seriously ill patients with what turned out to be C. auris infections (remember no one had heard of this fungal species a few years earlier).
Without contact or common points between them, these C. auris cases appeared independently on three different continents, with each fungus genetically distinct from the others.
This meant that the usual suspect of fungal spread – our globalized world – was not at play here. Something new was brewing. It quickly became apparent that this fungus was remarkably resistant to treatment. More than one in three patients have invasive disease C. auris infections in their blood were dying. In hospitals where this invasive fungal disease was non-existent, it is now a significant cause of death.
Nowadays, C. auris remains largely resistant to the antifungal treatments available to us, so once patients (and hospitals) become infected, it’s almost impossible to get rid of. Usually, doctors diagnose fungal infections after ruling out other sources, such as when a hospitalized patient has a fever that does not go away after treatment with antibiotics. Blood tests will likely show a high white blood cell count, another sign of infection, but doctors often can’t tell what type of microbe is causing the damage — or necessarily know how to treat it.
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Symptoms vary depending on the fungal species. Cryptococcus neoformans usually involves the brain and causes terrible headaches. Aspergillus tend to attack the lungs, meaning patients cough, become short of breath and reveal something resembling pneumonia on a chest X-ray.
Pathogenic fungi can be inhaled or enter the bloodstream through cuts and wounds; Infections can spread in the hospital through poorly maintained IV lines and catheters. Most often, common symptoms are fever, malaise, or just plain unwell. In hospitals where C. auris was being identified, it was spreading primarily among immunocompromised patients – although person-to-person transmissibility is a rare quality for an invasive fungus.
It could do this because, as doctors would learn, it can colonize human skin, persist for weeks on surfaces, and tolerate strong hospital disinfectants. Some hospitals have reported discovering C. auris spores persist in hospital rooms long after a patient has been discharged or died, even after other fungal species have been eliminated by cleaning agents. C. auris I didn’t stay abroad.
In 2016, the U.S. Centers for Disease Control and Prevention (CDC) issued an alert to healthcare professionals and laboratories to be on the lookout for the new pathogen. By then, a total of seven cases of drug resistance C. auris had previously been reported in hospitalized patients in four states: New York, New Jersey, Maryland and Illinois. C. auris was difficult to identify by traditional laboratory tests, so doctors were asked to report any suspicious microbes to the CDC.
Ten years after his identification, C. auris killed people in 40 countries on six continents. We don’t have exact numbers because many cases go unreported or unrecognized, but the figure is certainly in the thousands. In the United States alone, more than 2,000 infections have been confirmed in 27 states and the District of Columbia in 2022, and Mississippi reported its first cases (and deaths) of C. auris early 2023.
Fifteen years after the discovery of the fungus, the World Health Organization now considers C. auris one of the most harmful fungi for humans. The percentage increase in clinical cases of C. auris in the United States has increased every year, from a 44% increase in 2019 to a “dramatic” 95% increase in 2021, according to a 2023 CDC study published in the Annals of Internal Medicine.
Another worrying trend: the number of C. auris infections found to be resistant to antifungals in 2021 were approximately three times as numerous as in each of the previous two years. As the authors note, “screening is not performed uniformly across the United States, so the true burden of C. auris cases may be underestimated.
The march of the drug resisters C. auris clearly not slowing down. On the contrary, it is accelerating rapidly. How did a fungus, so deadly to immunocompromised humans, suddenly appear? And why was he killing people when he had never made anyone sick before? Where is he from? It is both mysterious and alarming.
After the discovery of C. auris, teams of researchers returned to explore ancient mushroom samples. They determined that the fungus had likely been present in some form since the late 1990s, but found no signs of its presence. C. auris before that and no evidence that he ever killed anyone before.
C. auris, of course, did not appear on Earth in the last 30 years, out of nowhere. This ancient life form certainly lived in the environment long before that, as shown by the fact that it had evolved into several different strains by the time it was identified. However, he was invisible to humans. From C. auris had only been considered medically relevant in the 21st century, no one was looking for it.
It was not necessary. Until there is. “We know that new species don’t just appear” Shawn Lockhart, a CDC researcher, told JAMA in 2022. “We just didn’t understand where it was hiding until it started showing up in hospitals around the world. There’s a lot of speculation.” Lockhart’s best guess is that C. auris coexisted quietly with humans in the ear canal – until it increased the volume. Body temperature may have long protected us from fungus, but we will quickly learn that C. auris was different. Unlike most of its fungal cousins, it can grow in temperatures as high as 42 degrees Celsius (107.6 degrees Fahrenheit).
This is what makes it so deadly for some humans with weakened immune systems. At one level, we have not appreciated the protective role of temperature in fungal infections, because most viral and bacterial diseases currently affecting animals and humans are usually acquired from other warm hosts, which means that they are already adapted to mammalian temperatures and can be transmitted with relative ease. For example, we get the flu, COVID-19, tuberculosis, and more from other humans (and perhaps other mammals), and these microbes have a habit of replicating to our higher body temperatures.
But things change when we focus on environmentally acquired microbes, particularly fungi. Although many fungi still cannot survive normal human temperatures, some can and do. C. auris is Exhibit A. In a 2010 article, published in the journal mBiomicrobiologist Mónica García-Solache and I predicted that a fungal threat like C. auris was coming, even if we didn’t know his name yet.
“Global warming could have a significant effect on fungal populations,” we write. “First, a warmer climate could alter the distribution of heat-sensitive and heat-tolerant species by favoring those that are more thermotolerant and creating conditions that allow more environmental fungi to spread and come into closer contact with Second, under strong selective pressure, the prevalence of species adapted to heat tolerance could increase.
It wasn’t a question of whether the fungi would adapt to temperatures high enough to threaten humans, we warned, but when.
Extract of What if the mushrooms won? by Arturo Casadevall, MD, PhD, with Stephanie Desmon, MA. Copyright 2024. Published with permission of Johns Hopkins University Press.
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