Matt Richtel and Andrew Jacobs

The numbers show just how widespread drug resistant infections have become, with the latest projection of deaths in America double previous estimates.

“A lot of progress has been made, but the bottom line is that antimicrobial resistance is worse than we previously thought,” said Michael Craig, senior adviser on antibiotic resistance for the Centers for Disease Control and Prevention, which released the updated death toll Wednesday. “Every 11 seconds someone in the United States gets a resistant infection, and someone dies every 15 minutes.”

The CDC report came on the same day that New York became the first state to release the names of the medical facilities that have treated patients with Candida auris, a fungus that is resistant to major medicines and has been spreading globally under a cloak of secrecy.

C. auris is one of the newer and more mysterious examples of such infections. The New York Times has spent the past year documenting its rise as multiple governments declined to identify or confirm the names of hospitals and nursing homes with the presence of C. auris. Some hospitals, including major academic institutions, declined to discuss cases even when family members or physicians confirmed them.

New York health officials said they decided to break with that practice and disclose the names of the institutions with cases in the state over the past three years because of how rapidly C. auris has spread. Their aim, they said, was to provide transparency to consumers and encourage hospitals and nursing homes to help stop its spread.

The state found that the heaviest concentration of C. auris patients was in Manhattan, Brooklyn and Queens. It did not say how many cases were at each institution and or identify patients.

The new CDC report, a comprehensive look at the nation’s battle against antimicrobial resistance, said that 2.8 million people are sickened each year in the United States from pathogens that have learned to outsmart antimicrobial drugs, an increase of 800,000 per year since the previous report was issued in 2013. Officials said the updated figures reflected advances in data collection made possible by electronic medical records.

The findings were not entirely dire. The agency documented a 30% decline in deaths among patients who acquire drug-resistant infections in hospitals, a reduction it attributed to better hygiene among nurses and doctors who in recent years have been bombarded with messages about the importance of hand washing.

Among the greatest threats the report cites are a form of drug-resistant gonorrhea that has been spreading among young people and gay men; tough-to-treat urinary tract infections that strike otherwise healthy women; and Clostridioides difficile, or C. diff, a deadly bacterial infection that ravages the guts of hospitalized patients, sickening 224,000 and killing 12,800 each year.

On the flip side, the CDC reported substantial declines in cases of MRSA, a bacterial infection sometimes referred to as a “superbug,” and infections like Pseudomonas aeruginosa, an infection that often strikes nursing home residents on ventilators and patients recovering from surgery.

The C. auris cases identified in New York on Wednesday included patients who were infected and those who are “colonized,” which means they have it on their skin but are not showing symptoms. Some colonized patients eventually become ill, and some do not, but all have the potential to spread the germ. The state also listed several cases of patients believed to be possibly colonized.

The germ, which is typically resistant to one or more major antifungal medications, preys on people with compromised immune systems and spreads with ease on equipment, clothing and skin.

About half of patients who contract C. auris die within 90 days, although the patients are typically infirm, and so it is not clear whether they die from the fungus or it merely is among an ultimately lethal combination of poor health factors. There have been 806 confirmed cases of C. auris infection in the United States; 388 are in New York.

In releasing the hospital and nursing home data, New York state officials implored patients not to avoid going to medical facilities just because they have treated C. auris patients. In fact, the hospitals and nursing homes listed may well be doing a good job of containing the fungus, said Dr. Howard Zucker, commissioner of the New York State Department of Health.

At the same time, he said the germ has spread so quickly that hospitals and nursing homes need to acknowledge its presence and address it as they would other major drug-resistant infections tracked and made public by the state. Consumers, he argued, deserve to know “to help them make an educated decision for their life or someone dear to them.”

For hospitals and nursing homes, he said, there was a benefit, too. “If you can’t measure it, you can’t improve it,” he said.

New York is the first state to provide such data, said Michael Osterholm, director for infectious disease research and policy at the University of Minnesota, where he runs a clearinghouse for information on drug-resistant infection.

“One of the challenges we’ve had is this climate of secrecy,” he said. “I applaud this,” he added, “It’s potentially a game changer because of the unique nature and consequences of dealing with this infection.”

The reports from the CDC and New York, which also found improvements in hospital performance at the state level in dealing with drug-resistant infections, suggest that intensified scrutiny is making at least modest inroads into a worldwide challenge.

Drug resistance is a vexing, seemingly intractable problem owing to the powerful forces driving it: the biological reality that germs will develop defenses when threatened with extinction and modern medical, pharmaceutical and farming economies are built on the use of millions of tons of antibiotics and antifungal drugs.

Without change, the United Nations estimates that drug-resistant infections will kill 10 million people in the year 2050, more than the number projected to die that year from cancer.

C. auris has become an object lesson in many of the core policy debates and challenges, and that includes discussion about whether to disclose health care institutions that are battling the germ.

Loretta Willis, vice president for quality advocacy with the Healthcare Association of New York, which represents about 100 nursing homes in the state, said she worried New York’s disclosure could unnerve patients and their families. “Without a fuller understanding about what’s happening and what’s going on with these emerging infections, it may cause unnecessary panic,” she said.

“I’m worried it will be taken out of context,” said Willis, who is also a nurse, asserting that there are many germs these institutions deal with, that they are equipped to handle the situation and that it would be to the detriment of patients and their families to look at a list of facilities and say, “‘That’s horrible, I’ll never go there.’”

Brian Conway, a spokesman for the Greater New York Hospital Association, said, “While we have some reservations about hospitals being named, the hospital community is committed to doing everything we can to eliminate C. auris.”

He added that this week the group is releasing a five-minute training video for hospital and nursing cleaning crews about how to clean a room where a patient has tested positive for C auris. New York City, a major travel hub, can be among the first to face new germs and be forced to consider new policy positions.

But C. auris is growing elsewhere with institutions treating it still unknown.

California confirmed this week that the number of colonized patients has jumped in Southern California — from fewer than five this summer to 181. But California health officials declined to be interviewed by phone about the subject and responded in an email, “The California Department of Public Health (CDPH) is in the process of determining if facility names can be released.”

The state of Connecticut declined earlier this year to identify the hospital where one of the first C. auris patients was detected in the United States; a hospital in Chicago, Northwestern Memorial Hospital, also would not comment or provide any acknowledgment of the situation, for an article that was published about a patient with C. auris who had died; doctors at several institutions around the world told The New York Times they could not speak about the patients they had seen or the spread of C. auris at hospitals where they worked, fearing reprisals from administration.

Zucker, the New York state health commissioner, said he hoped that other states would follow New York’s lead.

“We really live in an information-centric world and patients should have data,” he said.

This article originally appeared in

New York Discloses Finding Deadly Fungus at 167 Medical Facilities

Nearly 35,000 people in the United States are dying each year from drug-resistant infections, public health officials said Wednesday, an alarming problem that New York state underscored by revealing that it had found one particularly new and virulent fungus in 64 hospitals and 103 nursing homes.

NEW YORK — Maria Davila lay mute in a nursing home bed, an anguished expression fixed to her face, as her husband stroked her withered hand. Davila, 65, suffers from a long list of ailments — respiratory failure, kidney disease, high blood pressure, an irregular heartbeat — and is kept alive by a gently beeping ventilator and a feeding tube in her neck.

Doctors recently added another diagnosis to her medical chart: Candida auris, a highly contagious, drug-resistant fungus that has infected nearly 800 people since it arrived in the United States four years ago, with half of patients dying within 90 days.

At least 38 other patients at Davila’s nursing home, Palm Gardens Center for Nursing and Rehabilitation in Brooklyn, New York, have been infected with or carry C. auris, a germ so virulent and hard to eradicate that some facilities will not accept patients with it. Now, as they struggle to contain the pathogen, public health officials from cities, states and the federal government say that skilled nursing facilities like Palm Gardens are fueling its spread.

“They are the dark underbelly of drug-resistant infection,” said Dr. Tom Chiller, who heads the fungal division at the Centers for Disease Control and Prevention, speaking about skilled nursing facilities, particularly those with ventilated patients, but not Palm Gardens specifically.

Such nursing homes are playing a key role in the spread in New York, where 396 people are known to be infected and another 496 are carrying the germ without showing symptoms, according to public health officials. In Chicago, half of patients living on dedicated ventilator floors in the city’s skilled nursing homes are infected with or harboring C. auris on their bodies, said Dr. Allison Arwady, the acting commissioner of the city’s Department of Public Health.

Much of the blame for the rise of drug-resistant infections like C. auris, as well as efforts to combat them, has focused on the overuse of antibiotics in humans and livestock, and on hospital-acquired infections. But public health experts say that nursing facilities, and long-term hospitals, are a dangerously weak link in the health care system, often understaffed and ill-equipped to enforce rigorous infection control, yet continuously cycling infected patients, or those who carry the germ, into hospitals and back again.

“They are caldrons that are constantly seeding and reseeding hospitals with increasingly dangerous bacteria,” said Betsy McCaughey, a former lieutenant governor of New York who leads the nonprofit Committee to Reduce Infection Deaths. “You’ll never protect hospital patients until the nursing homes are forced to clean up.”

The story is far bigger than one nursing home or one germ. Drug-resistant germs of all types thrive in such settings where severely ill and ventilated patients like Davila are prone to infection and often take multiple antibiotics, which can spur drug resistance. Resistant germs can then move from bed to bed, or from patient to family or staff, and then to hospitals and the public because of lax hygiene and poor staffing.

These issues have also vexed long-term, acute-care hospitals, where patients typically stay for a month or less before going to a skilled nursing home or a different facility.

A recent inquiry by the New York state Department of Health found that some long-term hospitals grappling with C. auris were failing to take basic measures, such as using disposable gowns and latex gloves, or to post warning signs outside the rooms of infected patients. At one unnamed facility, it said, “hand sanitizers were completely absent.”

Officials at the 240-bed Palm Gardens did not respond to repeated requests for comment. Over the past year, the number of patients who were infected with or were carrying C. auris there grew to 38 from six, according to a nurse there and public health officials. The tally has now fallen into the high 20s after some patients died or moved elsewhere.

The New York Health Department issued a statement in response to queries from The New York Times: “The Department of Health has made controlling the spread of C. auris a high priority and has conducted extensive training and education on infection control policies and procedures for Palm Gardens and other nursing home providers throughout this region. The health and well-being of nursing home residents is our primary concern and we take complaints regarding quality of care very seriously.”

Scientific research on nursing homes and drug resistance is sparse, but some recent studies offer evidence of the problem. A study published in June in the Journal of Clinical Infectious Diseases found that patients and residents in long-term care settings have alarmingly high rates of drug-resistant colonization, which means they carry the germs on their skin or in their bodies, usually without knowing it, and can pass them invisibly to staff members, relatives or other patients. Elderly or severely ill people with weakened immune systems who carry the germ are at high risk of becoming infected. (Health officials in New York state said 14% of those now infected started out carrying it and then developed symptoms).

The study, which focused on Southern California, found that 65% of nursing home residents in that region harbored a drug-resistant germ, as did 80% of residents of long-term acute-care hospitals, where their “status is frequently unknown to the facility.” By comparison, only 10% to 15% of hospital patients carried such germs, the study found.

The phenomenon is global. A study published in 2017 found that elderly residents of long-term care facilities in Britain were four times as likely to be infected with drug-resistant urinary tract infections as elderly residents living at home. Soaring levels of resistance were found in long-term care facilities in Italy, a 2018 paper found. And a 2019 study found that long-term care facilities in Israel are “a major reservoir” of carbapenem-resistant Enterobacteriaceae, or CRE — a major family of drug-resistant germs — contributing to their “rapid regional dissemination.”

Experts said the problem is pronounced in the United States, given changing economics that push high-risk patients out of hospitals and into skilled nursing homes. The facilities are reimbursed at a higher rate to care for these patients, they said, providing an economic incentive for poorly staffed or equipped facilities to care for vulnerable patients.

C. auris, which is resistant to major antifungal medications, was first identified in 2009 in Japan and, as of July 31, had infected 796 people in the United States, largely in New York, Chicago and New Jersey, since its arrival here in 2015, according to the CDC. Another 1,540 people have been identified as carrying the germ on their skin or in their bodies without showing symptoms.

C. auris Up Close

On Palm Gardens’ second floor, where Davila and other ventilated patients reside, signs posted outside nearly every room warn visitors and staff members to wear gloves, gowns and masks — a state requirement for those infected with C. auris.

But during two recent visits to Palm Gardens by a Times reporter, accompanying Davila’s husband as his guest, orderlies and nurses moved in and out of her room without the required protection.

“The nurses and janitors are just spreading this thing from room to room,” her husband, Anthony Hernandez, said on a visit in August, shortly after a nurse, who was wearing gloves but no mask or gown, poured liquid nourishment into his wife’s feeding tube. During a brief interview in the lobby, Pamela Delacuadra, the center’s director of nursing, said employees had initially struggled with the infection-control protocols required for C. auris.

“It was overwhelming at first but with help from the Health Department, we’ve gotten much better,” she said.

Davila’s medical records, reviewed by The Times, do not identify the specific date when she got C. auris, but a chart written by a Palm Gardens doctor in December 2018 includes a note listing her as a carrier of the fungus. She was put in isolation for C. auris patients, and her records subsequently referred to her as having the infection and taking antifungal medications for it.

Palm Gardens occupies a nondescript seven-story brick building in a working-class neighborhood in central Brooklyn. Magenta banners promote its dialysis center and adult day care services, as well as a “respiratory pavilion” for patients on mechanical life support.

A high-level official from a local hospital that has seen a number of C. auris patients from nursing homes said Palm Gardens was a major source. He declined to be named because his employer had not authorized any comment.

Palm Gardens’ performance is poorly rated by the federal government; it received two stars, a below-average rating for staffing and overall care, from the Centers for Medicare and Medicaid Services, an agency that ranks nursing home care on a scale from one star to five. In 2018, the agency investigated the deaths of two ventilator patients at Palm Gardens, finding that employees had failed to turn their ventilators back on after performing mechanical checks. The patients died within minutes of each other, the report said.

CMS declined to comment on Palm Gardens.

The ownership of Palm Gardens is controlled by someone identified as Shimon Lefkowitz, according to public filings.

Lefkowitz did not respond to efforts to reach him through Palm Gardens. Calls to several law firms that represent Palm Gardens in lawsuits were not returned.

Not all Palm Gardens residents with C. auris contracted the germ there, and it is not clear how many did. One patient who died was infected at Maimonides Medical Center in Brooklyn, according to the man’s family.

A changing role in health care

Skilled nursing homes and long-term care facilities have been playing an increasingly important role in caring for seriously ill patients who used to stay longer in hospitals.

Advances in medical technology have made it possible to prolong the lives of desperately ill patients, while changes in Medicare reimbursement rates created a financial incentive for the expansion of such facilities, said Neale Mahoney, an economist at the University of Chicago who studies the industry’s growth. There are now about 400 long-term care hospitals across the country, up from about 40 in the early 1980s, he said.

Since 2012, the number of skilled nursing homes with ventilator units rose to 436 from 367 — a significant jump but still a fraction of the nation’s 15,000 nursing homes — according to CMS.

“Ventilator units are the poster child, the best example of a place that has challenges,” said Dr. Alexander Kallen, an outbreak expert at the CDC.

The federal government reimburses facilities for ventilator patients at significantly higher rates than for other patients, according to CMS. Ventilated patients can bring in $531 a day compared to $200 for a standard patient. That’s about $16,000 a month compared to $6,000.

The reimbursement rates reflect the significant care required for vulnerable patients, and the cost of equipment.

CMS contends the majority of skilled nursing homes do well with staffing and overall care. Yet roughly 1,400 nursing homes received a one-star rating for staffing in 2018 from the agency.

“It is impossible for them to do a good job with the way their staffing is,” said Dr. Mary Hayden, a professor at Rush Medical College who studies the rise of drug-resistant infections in health care, adding of the challenges of curbing drug-resistant infection. “The way they’re set up, they can’t do it.”

Davila’s path

Davila carried C. auris with her on her journey through the health care system.

In early August, after a routine blood test found her white cell count plummeting, she was taken by ambulance to Methodist Hospital in Brooklyn for a blood transfusion. Doctors discovered an infection and put her on two different antibiotics. Heavy use of antibiotics, while often necessary, can kill off the nonresistant infections and allow resistant ones to thrive.

Her condition stabilized after two weeks and she returned to Palm Gardens. It was one of at least a dozen trips she had taken to the hospital from the facility.

Her sharp decline began in 2017 after pain from a suspected hernia sent her to the hospital. A lifelong smoker, Davila had emphysema, which led to a litany of complications and infections, according to a review of her medical records.

Now she spends her days frozen in bed, serenaded by a Latin music radio station and the mechanical whir of her respirator.

Hernandez doubts his wife will recover. “If I can take her home to die that would be a blessing,” he said.

He pulled the blanket higher, turned up the radio and told his wife he loved her. Momentarily alert, she fixed her eyes on his and then mouthed: “I love you, too.”

Nursing Homes Foster Spread of Virulent, Often Fatal Fungus

(Deadly Germs, Lost Cures)

The germ, a fungus called Candida auris, preys on people with weakened immune systems, and it is quietly spreading across the globe. Recently C. auris reached New York, New Jersey and Illinois, leading the federal Centers for Disease Control and Prevention to add it to a list of germs deemed “urgent threats.”

The man at Mount Sinai died after 90 days in the hospital, but C. auris did not. Tests showed it was everywhere in his room, so invasive that the hospital needed special cleaning equipment and had to rip out some of the ceiling and floor tiles to eradicate it.

C. auris is so tenacious, in part, because it is impervious to major antifungal medications, making it a new example of one of the world’s most intractable health threats: the rise of drug-resistant infections.

For decades, public health experts have warned that the overuse of antibiotics was reducing the effectiveness of drugs that have lengthened life spans by curing bacterial infections once commonly fatal. But lately, there has been an explosion of resistant fungi as well.

“It’s an enormous problem,” said Matthew Fisher, a professor of fungal epidemiology at Imperial College London. “We depend on being able to treat those patients with antifungals.”

Simply put, fungi, just like bacteria, are evolving defenses to survive modern medicines. A study the British government funded projects that if policies are not put in place to slow the rise of drug resistance, 10 million people could die worldwide of all such infections in 2050, eclipsing the 8 million expected to die that year from cancer.

Antibiotics and antifungals are essential to combat infections in people, but antibiotics are also used widely to prevent disease in farm animals, and antifungals are also applied to prevent agricultural plants from rotting. Some scientists cite evidence that rampant use of fungicides on crops is contributing to the surge in drug-resistant fungi infecting humans.

Yet as the problem grows, it is little understood by the public — in part because the very existence of resistant infections is often cloaked in secrecy. With bacteria and fungi alike, hospitals and local governments are reluctant to disclose outbreaks for fear of being seen as infection hubs.

C. auris, which infected the man at Mount Sinai, is one of dozens of dangerous bacteria and fungi that have developed resistance. Yet, like most of them, it is a threat that is virtually unknown to the public.

Other prominent strains of the fungus Candida — one of the most common causes of bloodstream infections in hospitals — have not developed significant resistance to drugs, but more than 90 percent of C. auris infections are resistant to at least one drug, and 30 percent are resistant to two or more drugs, the CDC said.

Nearly half of patients who contract C. auris die within 90 days, according to the CDC. Yet the world’s experts have not nailed down where it came from in the first place.

“It is a creature from the black lagoon,” said Dr. Tom Chiller, who heads the fungal branch at the CDC. “It bubbled up and now it is everywhere.”

‘No Need’ to Tell the Public

In late 2015, Dr. Johanna Rhodes, an infectious disease expert at Imperial College London, got a panicked call from the Royal Brompton Hospital outside London. C. auris had taken root there months earlier, and the hospital couldn’t clear it.

“‘We have no idea where it’s coming from. We’ve never heard of it. It’s just spread like wildfire,’” Rhodes said she was told. She agreed to help the hospital identify the fungus’ genetic profile and clean it from rooms.

It was spreading, but word of it was not. The hospital, a specialty lung and heart center that draws wealthy patients from the Middle East and around Europe, alerted the British government and told infected patients, but made no public announcement.

This hushed panic is playing out in hospitals around the world. Individual institutions and national, state and local governments have been reluctant to publicize outbreaks of resistant infections, arguing there is no point in scaring patients — or prospective ones.

Dr. Silke Schelenz, Royal Brompton’s infectious disease specialist, found the lack of urgency from the government and hospital in the early stages of the outbreak “very, very frustrating.”

“They obviously didn’t want to lose reputation,” Schelenz said. “It hadn’t impacted our surgical outcomes.”

By the end of June 2016, a scientific paper reported “an ongoing outbreak of 50 C. auris cases” at Royal Brompton, and the hospital took an extraordinary step: It shut down its ICU for 11 days, again with no announcement.

Days later the hospital finally acknowledged to a newspaper that it had a problem. A headline in The Daily Telegraph warned, “Intensive Care Unit Closed After Deadly New Superbug Emerges in the U.K.”

Yet the issue remained little known internationally, while an even bigger outbreak had begun in Valencia, Spain, at the Hospital Universitari i Politècnic La Fe. As with Royal Brompton, the hospital in Spain did not make any public announcement. It still has not.

The secrecy infuriates patient advocates, who say people have a right to know if there is an outbreak. “Why the heck are we reading about an outbreak almost a year and a half later — and not have it front-page news the day after it happens?” said Dr. Kevin Kavanagh, chairman of Health Watch USA, a nonprofit patient advocacy group.

Health officials say that disclosing outbreaks frightens patients about a situation they can do nothing about, particularly when the risks are unclear. “It’s hard enough with these organisms for health care providers to wrap their heads around it,” said Dr. Anna Yaffee, a former CDC outbreak investigator. “It’s really impossible to message to the public.”

Officials in London did alert the CDC to the Royal Brompton outbreak while it was occurring. And the CDC realized it needed to get the word to U.S. hospitals. On June 24, 2016, the CDC blasted a nationwide warning and set up an email address, candidaauris@cdc.gov, to field queries. Dr. Snigdha Vallabhaneni, a key member of the fungal team, expected to get a trickle — “maybe a message every month.”

Instead, within weeks, her inbox exploded. In the United States, 587 cases of people having contracted C. auris have been reported, according to the CDC. The symptoms — fever, aches and fatigue — are seemingly ordinary, but when a person gets infected, particularly someone already unhealthy, such commonplace symptoms can be fatal.

The Role of Pesticides?

As the CDC works to limit the spread of drug-resistant C. auris, its investigators have been trying to answer the vexing question: Where in the world did it come from?

The first time doctors encountered C. auris was in the ear of a woman in Japan in 2009 (auris is Latin for ear). It seemed innocuous at the time, a cousin of common, easily treated fungal infections. Three years later, it appeared in an unusual test result in the lab of Dr. Jacques Meis, a microbiologist in Nijmegen, Netherlands, who was analyzing a bloodstream infection in 18 patients from four hospitals in India. Soon, new clusters of C. auris seemed to emerge with each passing month in different parts of the world.

When the CDC investigators compared the entire genome of auris samples from India and Pakistan, Venezuela, South Africa and Japan, they found that its origin was not a single place, and there was not a single auris strain. The genome sequencing showed that there were four distinctive versions of the fungus, with differences so profound that they suggested that these strains had diverged thousands of years ago and emerged as resistant pathogens from harmless environmental strains in four different places at the same time.

“Somehow, it made a jump almost seemingly simultaneously, and seemed to spread and it is drug-resistant, which is really mind-boggling,” Vallabhaneni said.

There are different theories as to what happened with C. auris. Meis, the Dutch researcher, said he believed that drug-resistant fungi were developing thanks to heavy use of fungicides on crops.

Meis became intrigued by resistant fungi when he heard about the case of a 63-year-old patient in the Netherlands who died in 2005 from a fungus called Aspergillus. It proved resistant to a front-line antifungal treatment called itraconazole. That drug is a virtual copy of the azole pesticides that are used to dust crops the world over.

Chiller of the CDC theorizes that C. auris may have benefited from the heavy use of fungicides. His idea is that C. auris actually has existed for thousands of years, a not particularly aggressive bug. But as azoles began destroying more prevalent fungi, an opportunity arrived for C. auris to enter the breach.

The mystery of C. auris’ emergence remains unsolved, and its origin seems, for the moment, to be less important than stopping its spread.

This article originally appeared in <a id="2add23e3-24f6-4fd7-998b-aa8caab10de3" href="https://www.nytimes.com/2019/04/06/health/drug-resistant-candida-auris.html">The New York Times</a>.

Fungus Immune to Drugs Secretly Sweeps the Globe

In May, an elderly man was admitted to the Brooklyn branch of Mount Sinai Hospital for abdominal surgery. A blood test revealed that he was infected with a newly discovered germ as deadly as it was mysterious.

Fungus immune to drugs secretly sweeps the globe

The germ, a fungus called Candida auris, preys on people with weakened immune systems, and it is quietly spreading across the globe. Over the past five years, it has hit a neonatal unit in Venezuela, swept through a hospital in Spain, forced a prestigious British medical center to shut down its intensive care unit, and taken root in India, Pakistan and South Africa.

Recently C. auris reached New York, New Jersey and Illinois, leading the federal Centers for Disease Control and Prevention to add it to a list of germs deemed “urgent threats.”

“Everything was positive — the walls, the bed, the doors, the curtains, the phones, the sink, the whiteboard, the poles, the pump,” said Dr. Scott Lorin, the hospital’s president. “The mattress, the bed rails, the canister holes, the window shades, the ceiling, everything in the room was positive.”

For decades, public health experts have warned that the overuse of antibiotics was reducing the effectiveness of drugs that have lengthened life spans by curing bacterial infections once commonly fatal. But lately, there has been an explosion of resistant fungi as well, adding a new and frightening dimension to a phenomenon that is undermining a pillar of modern medicine.

“It’s an enormous problem,” said Matthew Fisher, a professor of fungal epidemiology at Imperial College London, who was a co-author of a recent scientific review on the rise of resistant fungi. “We depend on being able to treat those patients with antifungals.”

Simply put, fungi, just like bacteria, are evolving defenses to survive modern medicines.

Yet even as world health leaders have pleaded for more restraint in prescribing antimicrobial drugs to combat bacteria and fungi — convening the U.N. General Assembly in 2016 to manage an emerging crisis — gluttonous overuse of them in hospitals, clinics and farming has continued.

Resistant germs are often called “superbugs,” but this is simplistic because they don’t typically kill everyone. Instead, they are most lethal to people with immature or compromised immune systems, including newborns and the elderly, smokers, diabetics and people with autoimmune disorders who take steroids that suppress the body’s defenses.

Scientists say that unless more effective new medicines are developed and unnecessary use of antimicrobial drugs is sharply curbed, risk will spread to healthier populations. A study the British government funded projects that if policies are not put in place to slow the rise of drug resistance, 10 million people could die worldwide of all such infections in 2050, eclipsing the 8 million expected to die that year from cancer.

In the United States, 2 million people contract resistant infections annually, and 23,000 die from them, according to the official CDC estimate. That number was based on 2010 figures; more recent estimates from researchers at Washington University School of Medicine put the death toll at 162,000. Worldwide fatalities from resistant infections are estimated at 700,000.

Antibiotics and antifungals are both essential to combat infections in people, but antibiotics are also used widely to prevent disease in farm animals, and antifungals are also applied to prevent agricultural plants from rotting. Some scientists cite evidence that rampant use of fungicides on crops is contributing to the surge in drug-resistant fungi infecting humans.

Yet as the problem grows, it is little understood by the public — in part because the very existence of resistant infections is often cloaked in secrecy.

With bacteria and fungi alike, hospitals and local governments are reluctant to disclose outbreaks for fear of being seen as infection hubs. Even the CDC, under its agreement with states, is not allowed to make public the location or name of hospitals involved in outbreaks. State governments have in many cases declined to publicly share information beyond acknowledging that they have had cases.

All the while, the germs are easily spread — carried on hands and equipment inside hospitals; ferried on meat and manure-fertilized vegetables from farms; transported across borders by travelers and on exports and imports; and transferred by patients from nursing home to hospital and back.

Dr. Lynn Sosa, Connecticut’s deputy state epidemiologist, said she now saw C. auris as “the top” threat among resistant infections. “It’s pretty much unbeatable and difficult to identity,” she said.

“It is a creature from the black lagoon,” said Dr. Tom Chiller, who heads the fungal branch at the CDC, which is spearheading a global detective effort to find treatments and stop the spread. “It bubbled up and now it is everywhere.”

‘No Need’ to Tell the Public

In late 2015, Dr. Johanna Rhodes, an infectious disease expert at Imperial College London, got a panicked call from the Royal Brompton Hospital, a British medical center outside London. C. auris had taken root there months earlier, and the hospital couldn’t clear it.

“‘We have no idea where it’s coming from. We’ve never heard of it. It’s just spread like wildfire,’” Rhodes said she was told. She agreed to help the hospital identify the fungus’s genetic profile and clean it from rooms.

Under her direction, hospital workers used a special device to spray aerosolized hydrogen peroxide around a room used for a patient with C. auris, the theory being that the vapor would scour each nook and cranny. They left the device going for a week. Then they put a “settle plate” in the middle of the room with a gel at the bottom that would serve as a place for any surviving microbes to grow, Rhodes said.

Only one organism grew back. C. auris.

“There was no need to put out a news release during the outbreak,” said Oliver Wilkinson, a spokesman for the hospital.

By the end of June 2016, a scientific paper reported “an ongoing outbreak of 50 C. auris cases” at Royal Brompton, and the hospital took an extraordinary step: It shut down its ICU for 11 days, moving intensive care patients to another floor, again with no announcement.

Days later the hospital finally acknowledged to a newspaper that it had a problem. A headline in The Daily Telegraph warned, “Intensive Care Unit Closed After Deadly New Superbug Emerges in the U.K.” (Later research said there were eventually 72 total cases, though some patients were only carriers and were not infected by the fungus.)

Yet the issue remained little known internationally, while an even bigger outbreak had begun in Valencia, Spain, at the 992-bed Hospital Universitari i Politècnic La Fe. There, unbeknown to the public or unaffected patients, 372 people were colonized — meaning they had the germ on their body but were not sick with it — and 85 developed bloodstream infections. A paper in the journal Mycoses reported that 41 percent of the infected patients died within 30 days.

A statement from the hospital said it was not necessarily C. auris that killed them. “It is very difficult to discern whether patients die from the pathogen or with it, since they are patients with many underlying diseases and in very serious general condition,” the statement said.

As with Royal Brompton, the hospital in Spain did not make any public announcement. It still has not.

One author of the article in Mycoses, a doctor at the hospital, said in an email that the hospital did not want him to speak to journalists because it “is concerned about the public image of the hospital.”

The secrecy infuriates patient advocates, who say people have a right to know if there is an outbreak so they can decide whether to go to a hospital, particularly when dealing with a nonurgent matter, like elective surgery.

“Why the heck are we reading about an outbreak almost a year and a half later — and not have it front-page news the day after it happens?” said Dr. Kevin Kavanagh, a physician in Kentucky and board chairman of Health Watch USA, a nonprofit patient advocacy group. “You wouldn’t tolerate this at a restaurant with a food poisoning outbreak.”

Health officials say that disclosing outbreaks frightens patients about a situation they can do nothing about, particularly when the risks are unclear.

“It’s hard enough with these organisms for health care providers to wrap their heads around it,” said Dr. Anna Yaffee, a former CDC outbreak investigator who dealt with resistant infection outbreaks in Kentucky in which the hospitals were not publicly disclosed. “It’s really impossible to message to the public.”

Officials in London did alert the CDC to the Royal Brompton outbreak while it was occurring. And the CDC realized it needed to get the word to U.S. hospitals. On June 24, 2016, the CDC blasted a nationwide warning to hospitals and medical groups and set up an email address, candidaauris@cdc.gov, to field queries. Dr. Snigdha Vallabhaneni, a key member of the fungal team, expected to get a trickle — “maybe a message every month.”

Instead, within weeks, her inbox exploded.

Coming to America

In the United States, 587 cases of people having contracted C. auris have been reported, concentrated with 309 in New York, 104 in New Jersey and 144 in Illinois, according to the CDC.

The symptoms — fever, aches and fatigue — are seemingly ordinary, but when a person gets infected, particularly someone already unhealthy, such commonplace symptoms can be fatal.

The earliest known case in the United States involved a woman who arrived at a New York hospital on May 6, 2013, seeking care for respiratory failure. She was 61 and from the United Arab Emirates, and she died a week later, after testing positive for the fungus. At the time, the hospital hadn’t thought much of it, but three years later, it sent the case to the CDC after reading the agency’s June 2016 advisory.

This woman probably was not America’s first C. auris patient. She carried a strain different from the South Asian one most common here. It killed a 56-year-old American woman who had traveled to India in March 2017 for elective abdominal surgery, contracted C. auris and was airlifted back to a hospital in Connecticut that officials will not identify. She was later transferred to a Texas hospital, where she died.

The germ has spread into long-term care facilities. In Chicago, 50 percent of the residents at some nursing homes have tested positive for it, the CDC has reported. The fungus can grow on intravenous lines and ventilators.

Workers who care for patients infected with C. auris worry for their own safety. Dr. Matthew McCarthy, who has treated several C. auris patients at Weill Cornell Medical Center in New York, described experiencing an unusual fear when treating a 30-year-old man.

“I found myself not wanting to touch the guy,” he said. “I didn’t want to take it from the guy and bring it to someone else.” He did his job and thoroughly examined the patient, but said, “There was an overwhelming feeling of being terrified of accidentally picking it up on a sock or tie or gown.”

The Role of Pesticides?

The first time doctors encountered C. auris was in the ear of a woman in Japan in 2009 (auris is Latin for ear). It seemed innocuous at the time, a cousin of common, easily treated fungal infections.

Three years later, it appeared in an unusual test result in the lab of Dr. Jacques Meis, a microbiologist in Nijmegen, Netherlands, who was analyzing a bloodstream infection in 18 patients from four hospitals in India. Soon, new clusters of C. auris seemed to emerge with each passing month in different parts of the world.

The CDC investigators theorized that C. auris started in Asia and spread across the globe. But when the agency compared the entire genome of auris samples from India and Pakistan, Venezuela, South Africa and Japan, it found that its origin was not a single place, and there was not a single auris strain.

The genome sequencing showed that there were four distinctive versions of the fungus, with differences so profound that they suggested that these strains had diverged thousands of years ago and emerged as resistant pathogens from harmless environmental strains in four different places at the same time.

Meis became intrigued by resistant fungi when he heard about the case of a 63-year-old patient in the Netherlands who died in 2005 from a fungus called Aspergillus. It proved resistant to a front-line antifungal treatment called itraconazole. That drug is a virtual copy of the azole pesticides that are used to dust crops the world over and account for more than one-third of all fungicide sales.

A 2013 paper in PLoS Pathogens said that it appeared to be no coincidence that drug-resistant Aspergillus was showing up in the environment where the azole fungicides were used. The fungus appeared in 12 percent of Dutch soil samples, for example, but also in “flower beds, compost, leaves, plant seeds, soil samples of tea gardens, paddy fields, hospital surroundings, and aerial samples of hospitals.”

Meis visited the CDC last summer to share research and theorize that the same thing is happening with C. auris, which is also found in the soil: Azoles have created an environment so hostile that the fungi are evolving, with resistant strains surviving.

This is similar to concerns that resistant bacteria are growing because of excessive use of antibiotics in livestock for health and growth promotion. As with antibiotics in farm animals, azoles are used widely on crops.

“On everything — potatoes, beans, wheat, anything you can think of, tomatoes, onions,” said Rhodes, the infectious disease specialist who worked on the London outbreak. “We are driving this with the use of antifungicides on crops.”

Chiller theorizes that C. auris may have benefited from the heavy use of fungicides. His idea is that C. auris actually has existed for thousands of years, hidden in the world’s crevices, a not particularly aggressive bug. But as azoles began destroying more prevalent fungi, an opportunity arrived for C. auris to enter the breach, a germ that had the ability to readily resist fungicides now suitable for a world in which fungi less able to resist are under attack.

Resistance and Denial

For now, the uncertainty around C. auris has led to a climate of fear, and sometimes denial.

Last spring, Jasmine Cutler, 29, went to visit her 72-year-old father at a hospital in New York City, where he had been admitted because of complications from a surgery the previous month.

When she arrived at his room, she discovered that he had been sitting for at least an hour in a recliner, in his own feces, because no one had come when he had called for help to use the bathroom. Cutler said it became clear to her that the staff was afraid to touch him because a test had shown that he was carrying C. auris.

“I saw doctors and nurses looking in the window of his room,” she said. “My father’s not a guinea pig. You’re not going to treat him like a freak at a show.”

He was eventually discharged and told he no longer carried the fungus. But he declined to be named, saying he feared being associated with the frightening infection.

In May, an elderly man was admitted to the Brooklyn branch of Mount Sinai Hospital for abdominal surgery. A blood test revealed that he was infected with a newly discovered germ as deadly as it was mysterious. Doctors swiftly isolated him in the intensive care unit.

Matt Richtel and Andrew Jacobs

Articles written by the author

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