As the U.S. health care system weathered blow after blow of the COVID pandemic, diseases of all kinds, from HIV to congenital syphilis, surged across the country. Last week a national survey by the Centers for Disease Control and Prevention showed that outbreaks of emerging drug-resistant fungi also grew at an “alarming” rate in hospitals from 2019 to 2020.

Annual cases of the opportunistic, hard-to-treat yeast Candida auris nearly tripled from 476 in 2019 to 1,471 in 2021, according to the CDC’s recent report, which was published in Annals of Internal Medicine. Infectious disease experts say that the COVID pandemic likely exacerbated the already growing fungal outbreak by diverting the focus and resources needed to slow C. auris transmission. In some instances, the practices necessary to protect health care workers and patients from COVID, such as reusing high-demand masks, may have increased the risk of spreading the fungus.

“Problems with [C. auris] infection control were present before COVID-19,” says Meghan Lyman, an epidemiologist who specializes in mycology at the CDC and lead author of the study. “But I think some of the changes to fit this weird world had consequences we didn’t know at the time.”

As C. auris becomes more widespread, it will make recovering from catastrophic injuries or illnesses more dangerous for vulnerable patients, such as people who are immunocompromised and have preexisting conditions. “Almost everyone is going to be hospitalized or have a loved one hospitalized at some point in their life,” says Lucy Witt, an infectious disease physician at Emory University, who was not involved in the recent research. “It’s everybody’s problem.”

C. auris is closely related to a handful of common yeasts that live in human digestive tracts such as Candida albicans, which causes minor infections. But C. auris is more worrisome than its cousins. The yeast lives on skin rather than in the gut, which allows it to spread easily from person to person. In a 2021 survey of one skilled-nursing facility conducted by the CDC and the Chicago Department of Public Health (CDPH), swabs turned up the fungus on windowsills, bed handrails and doorknobs both inside and outside the rooms of patients. It lasts for weeks on surfaces and is immune to several common disinfectants.

For most healthy individuals, C. auris doesn’t progress throughout the body from the skin. It only becomes a deadly problem in people with a weakened immune system. In such cases, “patients are generally really sick at baseline,” Lyman says.

According to the new CDC report, transmission in health care facilities is responsible for most, if not all, C. auris cases in the U.S., with most diagnosed in long-term acute care hospitals and skilled-nursing facilities. Patients treated in those facilities tend to have an intravenous line, a catheter or other invasive medical devices, which create a pathway between the skin and internal organs. Once inside the body, the yeast can cause opportunistic illness: for instance, it strikes those recovering from organ transplants, chemotherapy or other medical treatments that wipe out the body’s innate immune defenses. Sepsis and fever are common symptoms, and studies have found a case fatality rate ranging from 30 to 60 percent. Since C. auris was first identified in the U.S. in 2016, reported hospital infections have almost doubled.

And “to add insult to injury, [C. auris] is able to withstand many antifungals,” says Ilan Schwartz, who specializes in fungal infections at Duke University’s School of Medicine.

There are only three classes of drugs used to treat patients with C. auris versus roughly half a dozen classes of antibiotics employed to treat bacterial infections. Resistance to any one drug drastically limits clinicians’ options to suppress infection. According to the new research, by 2020 nine patients in the U.S. had infections that were resistant to echinocandins, a first-option antifungal that doctors use against C. auris. By 2021 the CDC identified 27 echinocandin-resistant cases, seven of which were resistant to all antifungals.

Pharmaceutical companies are currently testing several new antifungals, making it “a really, really exciting time to study fungal infections,” Schwartz says. An oral drug that is similar to the frontline echinocandins and already approved for vaginal yeast infections is in trials for use against systemic Candida infections.

But the best way to control the spread of a drug-resistant organism is to clean constantly.

Chicago’s health care system has been on the front lines against C. auris infections since 2016, when its hospitals experienced the first multipatient outbreaks in the U.S. The city’s public health department began tracking facilities that reported the fungus. At one skilled-nursing facility in 2018, 43 percent of tested residents had traces on their skin. Over eight months of subsequent testing, that number grew to 71 percent. The rapid rise in cases pushed city health officials to coordinate a response, which included trainings on handwashing and using fluorescent markers to assess how thoroughly rooms were being cleaned.

“A lot of what came out of this was a recognition that people are doing more than cleaning a room; they are really helping to care for residents,” says Stephanie Black, medical director of CDPH’s communicable disease program. It was also crucial to convince administrators that “you need to spend your resources on cleaning the environment,” she says. Prior to the outbreak at this nursing facility, employees were using the right cleaning materials, but they weren’t necessarily letting those materials sit on surfaces long enough to take effect. Improvement also came from simply clarifying cleaning responsibilities, such as by “identifying who’s cleaning the IV poles, who’s cleaning the IV machine,” Black says. In response to CDPH’s outreach, the nursing facility added dozens of hand sanitizer dispensers and hired another full-time cleaner to focus on fungus. Fungal rates at the facility plateaued over the course of the study. (In an e-mail to Scientific American, CDPH said that it couldn’t disclose more recent facility-specific prevalence data.)

The control measures helped slow the outbreak, but “you can see how that would get lost in all of the issues around COVID,” Black says. She adds that many of the nurses that CDPH had trained had left their job, “so it’s a lot of reeducation.” The nursing workforce, hit hard by the COVID pandemic, is essential for controlling outbreaks. Across the country, nurses quit or took traveling posts, and a quarter of nursing facilities reported staffing shortages in March 2022.

Although Witt says that the new report doesn’t get into the “granular details” on what exactly drove the rapid surge in C. auris, the researchers say the pandemic is likely exacerbating outbreaks. COVID has caused an increase in many health-care-associated infections. Organ damage from the virus that causes the disease makes people vulnerable to opportunistic infections, and the steroids and antibiotics used to treat COVID complications can increase the risk of fungal infections. Health care workers who resorted to reusing masks and gloves to slow transmission of a respiratory illness may have created a vector for an organism that traveled on surfaces. “Everyone was trying to do the best they could in dire circumstances,” Lyman says.

Even as the COVID burden lifts, staffing shortages and burnout are likely to be continuing sources of risk. “But we don’t want people to be hopeless,” Lyman says. “There are definitely facilities that are able to control [C. auris] outbreaks.” Researchers say, however, that replicating that success is likely to take significant investment in the health departments that coordinate responses, as well as the health care workers scrubbing away on the ground.