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Deadly germs, Lost cures

A Mysterious Infection, Spanning the Globe in a Climate of Secrecy

The rise of Candida auris embodies a serious and growing public health threat: drug-resistant germs.

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Revenge of the Bacteria: Why We’re Losing the War

Bacteria are rebelling. They’re turning the tide against antibiotics by outsmarting our wonder drugs. This video explores the surprising reasons.

There once was a man named Albert Alexander. He was a policeman — “[American accent] Hey.” — in England. “[British accent] Hello.” One day on patrol, he cut his cheek — “Ouch!” — which led to a terrible infection. See, this was back in 1941, before patients had antibiotics. These were the days when a little scratch could kill you. “Or you got an ear infection and you died. A cat bite and you died. Or you stepped on a stick and you died. All of a sudden, antibiotics come along and bang.” The antibiotic era had begun. Soon a slow and painful death became a seven-day course of antibiotics and a $10 copay. And Albert? Albert was the first patient in the world to receive the antibiotic — penicillin. And it worked. “We just came up with a lifesaving, life-extending drug, one of the greatest developments in human history. Except not.” That’s Matt Richtel, a science reporter for The New York Times. For the past year, Matt’s been talking to health experts to find out if we are reaching the end of the antibiotic era. Modern medicine depends on the antibiotic. “And having used it so much, we’re now putting it at risk. Is our fate sealed?” “First off, I don’t think people respect bacteria enough.” This is Ellen Silbergeld, one of the leading scientists studying antibiotic resistance. “Bacteria rule the world. We are just a platform for bacteria. Within the human body, there are more bacterial cells than there are human cells. So we are, in fact, mostly bacteria.” “Alexander Fleming —” the man who discovered penicillin “— in his Nobel speech said, hang on, be aware. When you start killing this stuff off, it’s going to fight back.” “Did we pay any attention to that? No.” “The C.D.C. got our attention today with a warning about what it calls ‘nightmare bacteria.’” “These are bacteria that are resistant to most, if not all, antibiotics.” When we take antibiotics to kill infections, some bacteria survive. It used to be they’d replicate, and eventually resistance would grow. But now, they’re way more efficient and share drug-resistant genes among themselves. So every time we take an antibiotic, we risk creating stronger, more resistant bacteria. And stronger, more resistant bacteria means less and less effective antibiotics. And this is a problem because we take lots of antibiotics. “Money gets made over the sale of antibiotics.” Big money. Globally, the antibiotics market is valued at $40 billion. And in the U.S., the C.D.C. estimates that about 30 percent of all prescribed antibiotics are not needed at all. That’s 47 million excess prescriptions. And in many places outside of the U.S., you don’t even need a prescription. “You can walk into a pharmacy. A pharmacist will diagnose you and give you antibiotics. I tend to think of it as a story of Darwinian forces multiplied by the pace and scale of global capitalism. In an interconnected world — travel, import, export — we’re moving the bugs with us.” “I can go to a meeting in China or Vietnam or some place —” This is Lance Price, the director of the Antibiotic Resistance Action Center. “I can become colonized by untreatable E. coli. And I might not have any symptoms. But you can get colonized. And you can become this sort of long-term host.” So you could be healthy and still spreading bad bacteria without even knowing it. “Drug-resistant bacteria have never been able to travel the world as fast as they do today.” And that’s just part of the problem. “You should know that about 80 percent of antibiotic production in this country goes into agriculture.” “Why on earth did somebody think putting antibiotics in agriculture was a great idea?” “We’ve said, hey, look, cram these animals together. Don’t worry too much about hygiene or trying to keep them healthy. Just give them antibiotics. And then in a couple weeks, you’re going to have full-grown animals that you can chop up and eat. Right? And you can make money off of that.” “Nobody was making the connection between feeding animals antibiotics and the fact that the food would be carrying drug-resistant bacteria.” So Ellen did a study. She compared different kinds of store-bought chicken. And she found that poultry raised with antibiotics had nine times as much drug-resistant bacteria on it. “Now, let’s talk about the vegetarians. I just want you to understand, you’re not safe. You know all these outbreaks that take place among the lettuce and the things like that. Have you ever wondered how that happened? It’s because animal manure is used in raising crops. Organic agriculture lauds the use of animal manure.” “Unless you’re just a complete, ‘I’m a vegan, and I only hang out with vegans, and I eat sterilized vegetables,’ you know, it’s very likely that you’re picking up the same bacteria.” Resistant bacteria seep into the groundwater, fly off the back of livestock trucks and hitch a ride home on the hands of farm workers, all of which makes trying to pinpoint exactly where resistant bacteria is originating extremely difficult. And even when it seems like there is a clear source, things still aren’t so simple. “No one wants to be seen as a hub of an epidemic.” Say your grandmother makes you a rump roast. And then that rump roast makes you sick. Well, if you live in France, or Ireland, or pretty much anywhere in the E.U., packaged meat has a tracking label. You can figure out exactly what farm that meat came from. But in the U.S., not even the top public health officials can do that. “Most countries have animal ID laws. We don’t.” Pat Basu, former chief veterinarian for the U.S.D.A.’s Food Safety and Inspection Service, basically one of the top veterinarians in the country. “Let me start at the beginning. We got a case where we had resistant bacteria causing illness in people. There were sick people that C.D.C. identified.” “More than 50 people in eight counties have gotten an unusual strain of salmonella linked to pork.” “This is not your grandmother’s pathogen anymore. This is a new bug.” Health officials traced the outbreak back to the slaughterhouse and identified six potential farms where the outbreak could have come from. But then the investigation shut down. “The individual farmers have to agree voluntarily to share the data with these investigators who go out. We couldn’t go any further back. It was a dead end.” 192 people sick, 30 hospitalizations and zero access for health officials to investigate the farms. “The secrecy is maintained because there are big economic forces behind it. Farms are scared of losing their ability to get antibiotics. Hospitals are scared of driving away patients.” “Well, as a physician, I do get very upset. I get very upset, as a patient, that information is being withheld.” This is Kevin Kavanagh, a doctor and a consumer advocate for patients. “Drug-resistant bacteria is a huge problem. If it occurs at a restaurant, if it occurs in a cruise ship, you know about this immediately —” “A salmonella outbreak —” “within days or hours of an outbreak occurring.” “This morning, Chipotle is keeping dozens of its restaurants in the Pacific Northwest closed —” “But yet, in a hospital, it can take you months or even over a year until this data appears on a governmental website or reported by the C.D.C.” In the U.S., hospitals are under no obligation to inform the public when a bacterial outbreak occurs. “Defend and deny. They are very concerned about the short-term economic benefits, rather than looking at long-term problems.” “There’s always this response like, well, but there’s still a drug, right? Like, this isn’t the end.” Remember Albert Alexander? — “Hello. Ouch!” — the first patient to be given penicillin? Well, his story didn’t end there. Five days after he started recovering, the hospital ran out of the new drug, and Mr. Alexander died. Today, we don’t have to worry about antibiotics running out. We have to worry about using them so much that they stop working altogether. “— want to know why a metro health department didn’t shut down a restaurant —” “It’s a very resistant bacteria —” “We really need to change the way we use antibiotics. Because the way we use antibiotics is destroying them.” “It’s putting at risk the entire system of care that we depend on for lengthening our lives and improving the quality of our lives.” The British government commissioned a study which predicted a worst case scenario where more people will die by 2050 of these infections than will die of cancer. “That’s a generation from now.” “It takes 10 years to identify, develop, test and bring to market a new antibiotic. And it takes a billion dollars.” “This is a common issue for humanity.” “Very similar to global warming.” “You can’t control it as a single company. You can’t control this as a single government.” And because the bacteria are now working together so efficiently — “Unless the world acts consistently together, it doesn’t make a difference.”

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Bacteria are rebelling. They’re turning the tide against antibiotics by outsmarting our wonder drugs. This video explores the surprising reasons.

Last 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.

The germ, a fungus called Candida auris, preys on people with weakened immune systems, and it is quietly spreading across the globe. Over the last 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.”

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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.

“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.”

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.

Image
Dr. Shawn Lockhart, a fungal disease expert at the Centers for Disease Control and Prevention, holding a microscope slide with inactive Candida auris collected from an American patient.Credit...Melissa Golden for The New York Times

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 United Nations 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 eight million expected to die that year from cancer.

Image
Dr. Johanna Rhodes, an infectious disease expert at Imperial College London. "We are driving this with the use of antifungicides on crops," she said of drug-resistant germs.Credit...Tom Jamieson for The New York Times

In the United States, two million people contract resistant infections annually, and 23,000 die from them, according to the official C.D.C. 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 C.D.C., 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.

C. auris, which infected the man at Mount Sinai, is one of dozens of dangerous bacteria and fungi that have developed resistance.

Image
A projection of the C. auris fungus on a microscope slide.Credit...Melissa Golden for The New York Times

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 C.D.C. said.

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 identify,” she said.

Nearly half of patients who contract C. auris die within 90 days, according to the C.D.C. 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 C.D.C., which is spearheading a global detective effort to find treatments and stop the spread. “It bubbled up and now it is everywhere.”

Candida Auris

A deadly, drug-resistant fungus is infecting patients in hospitals and nursing homes around the world. The fungus seems to have emerged in several locations at once, not from a single source.

EUROPE

The first large outbreak in Europe involved 72 cases in a London hospital in 2015–16.

COUNTRIES WITH

Multiple cases of

Candida auris infection

One reported case

BRITAIN

RUSSIA

CANADA

FRANCE

GERMANY

UNITED

STATES

UNITED STATES

The country has had at least 587 Candida auris infections since 2013.

SPAIN

JAPAN

CHINA

ISRAEL

KUWAIT

PAKISTAN

SOUTH

KOREA

SAUDI

ARABIA

INDIA

OMAN

PANAMA

VENEZUELA

SINGAPORE

COLOMBIA

KENYA

INDIA AND PAKISTAN

The two countries have some of the highest case counts in the world. A distinct strain appeared in Pakistan as early as 2008 and in Delhi by 2009.

CENTRAL AND

SOUTH AMERICA

The first documented outbreak in the Americas was from 2012–13 at a medical center in Venezuela. Five of 18 infected patients died.

AUSTRALIA

SOUTH

AFRICA

SOUTH AFRICA

A genetically distinct strain of Candida auris in South Africa infected at least 451 patients from 2012–16.

JAPAN

Candida auris (left) was discovered in 2009 in the infected ear of a 70-year-old Japanese woman.

Candida

auris

COUNTRIES WITH

EUROPE

The first large outbreak in Europe involved 72 cases in a London hospital in 2015–16.

Multiple cases of

Candida auris infection

One reported case

BRITAIN

RUSSIA

CANADA

FRANCE

GERMANY

SOUTH

KOREA

UNITED

STATES

UNITED STATES

The country has had at least 587 Candida auris infections since 2013.

SPAIN

JAPAN

CHINA

ISRAEL

KUWAIT

PAKISTAN

SAUDI

ARABIA

INDIA

OMAN

VENEZUELA

PANAMA

SINGAPORE

COLOMBIA

KENYA

CENTRAL AND

SOUTH AMERICA

The first documented outbreak in the Americas was from 2012–13 at a medical center in Venezuela. Five of 18 infected patients died.

INDIA AND PAKISTAN

The two countries have some of the highest case counts in the world. A distinct strain appeared in Pakistan as early as 2008 and in Delhi by 2009.

AUSTRALIA

SOUTH

AFRICA

SOUTH AFRICA

A genetically distinct strain of Candida auris in South Africa infected at least 451 patients from 2012–16.

JAPAN

Candida auris (left) was discovered in 2009 in the infected ear of a 70-year-old Japanese woman.

Candida

auris

COUNTRIES WITH

Multiple cases of

Candida auris infection

EUROPE

The first large outbreak in Europe involved 72 cases in a London hospital in 2015–16.

One reported case

RUSSIA

CANADA

UNITED STATES

The country has had at least 587 Candida auris infections since 2013.

SOUTH

KOREA

UNITED

STATES

CHINA

PAKISTAN

JAPAN

INDIA

BRITAIN

INDIA AND PAKISTAN

The two countries have some of the highest case counts in the world. A distinct strain appeared in Pakistan as early as 2008 and in Delhi by 2009.

VENEZUELA

PANAMA

GERMANY

FRANCE

COLOMBIA

SPAIN

ISRAEL

CENTRAL AND

SOUTH AMERICA

The first documented outbreak in the Americas was from 2012–13 at a medical center in Venezuela. Five of 18 infected patients died.

KUWAIT

SAUDI

ARABIA

OMAN

AUSTRALIA

KENYA

SOUTH AFRICA

A genetically distinct strain of Candida auris in South Africa infected at least 451 patients from 2012–16.

JAPAN

Candida auris (left) was discovered in 2009 in the infected ear of a 70-year-old Japanese woman.

SOUTH

AFRICA

COUNTRIES WITH

Multiple cases of

Candida auris infection

One reported case

CANADA

UNITED STATES

The country has had at least 587 Candida auris infections since 2013.

UNITED

STATES

VENEZUELA

PANAMA

COLOMBIA

EUROPE

The first large outbreak in Europe involved 72 cases in a London hospital in 2015–16.

CENTRAL AND

SOUTH AMERICA

The first documented outbreak in the Americas was from 2012–13 at a medical center in Venezuela. Five of 18 infected patients died.

BRITAIN

FRANCE

GERMANY

SPAIN

ISRAEL

KUWAIT

SAUDI

ARABIA

OMAN

KENYA

SOUTH AFRICA

A genetically distinct strain of Candida auris in South Africa infected at least 451 patients from 2012–16.

SOUTH

AFRICA

RUSSIA

JAPAN

CHINA

PAKISTAN

SOUTH

KOREA

INDIA AND PAKISTAN

The two countries have some of the highest case counts in the world. A distinct strain appeared in Pakistan as early as 2008 and in Delhi by 2009.

INDIA

SINGAPORE

CHINA

A study of a Shenyang hospital found 15 samples from 2011–17 that were misidentified as a different strain of fungus. Candida auris is hard to identify and may unreported in other hospitals around the world.

JAPAN

Candida auris was discovered in 2009 in the infected ear of a 70-year-old Japanese woman.

AUSTRALIA

COUNTRIES WITH

Multiple cases of

Candida auris infection

One reported case

UNITED STATES

The country has had at least 587 Candida auris infections since 2013.

CANADA

UNITED

STATES

PANAMA

VENEZUELA

COLOMBIA

CENTRAL AND

SOUTH AMERICA

The first documented outbreak in the Americas was from 2012–13 at a medical center in Venezuela. Five of 18 infected patients died.

EUROPE

The first large outbreak in Europe involved 72 cases in a London hospital in 2015–16.

BRITAIN

GERMANY

FRANCE

SPAIN

ISRAEL

KUWAIT

SAUDI

ARABIA

OMAN

SOUTH AFRICA

A genetically distinct strain of Candida auris in South Africa infected at least 451 patients from 2012–16.

KENYA

SOUTH

AFRICA

INDIA AND PAKISTAN

The two countries have some of the highest case counts in the world. A distinct strain appeared in Pakistan as early as 2008 and in Delhi by 2009.

RUSSIA

JAPAN

CHINA

PAKISTAN

SOUTH

KOREA

INDIA

SINGAPORE

JAPAN

Candida auris was discovered in 2009 in the infected ear of a 70-year-old Japanese woman.

AUSTRALIA

COUNTRIES WITH

Multiple cases of

Candida auris

infection

One reported case

CANADA

UNITED

STATES

UNITED STATES

The country has had at least 587 Candida auris infections since 2013.

PANAMA

VENEZUELA

COLOMBIA

CENTRAL AND

SOUTH AMERICA

The first documented outbreak in the Americas was at a medical center in Venezuela from 2012–13.

EUROPE

The first large outbreak in Europe involved 72 cases in a London hospital in 2015–16.

BRITAIN

GERMANY

FRANCE

SPAIN

ISRAEL

KUWAIT

SAUDI

ARABIA

OMAN

KENYA

SOUTH AFRICA

A genetically distinct strain of Candida auris in South Africa infected at least 451 patients from 2012–16.

SOUTH

AFRICA

INDIA AND PAKISTAN

The two countries have some of the highest case counts in the world.

RUSSIA

JAPAN

CHINA

PAKISTAN

SOUTH

KOREA

INDIA

SINGAPORE

JAPAN

Candida auris was discovered in 2009 in the infected ear of a 70-year-old Japanese woman.

AUSTRALIA

By The New York Times | Sources: Centers for Disease Control and Prevention; Emerging Infectious Diseases; Emerging Microbes & Infections; Clinical Infectious Diseases; Journal of Infection; Mycoses; Doherty Institute. Image from Kazuo Satoh et al., Microbiology and Immunology

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 in 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,’” Dr. 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, Dr. Rhodes said.

Only one organism grew back. C. auris.

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.

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

Image
"Somehow, it made a jump almost seemingly simultaneously, and seemed to spread and it is drug resistant, which is really mind-boggling," said Dr. Snigdha Vallabhaneni, a fungal expert and epidemiologist at the C.D.C.Credit...Melissa Golden for The New York Times

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,” Dr. 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 I.C.U. 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.

Image
Outside the Royal Brompton Hospital near London. By June 2016, the hospital had seen at least 50 “proven or possible” cases of C. auris, and decided to shut down its intensive care unit for 11 days to address the contamination.Credit...Tom Jamieson for The New York Times

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 C.D.C. 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 C.D.C. to the Royal Brompton outbreak while it was occurring. And the C.D.C. realized it needed to get the word to American hospitals. On June 24, 2016, the C.D.C. 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.

Image
Glo Gel under a black light in a room at Mount Sinai Hospital, before a simulation “terminal” cleaning of that room. Hospital workers place the gel in unexpected places to check that a room has been deeply cleaned — a necessary precaution after the hospital had to spend $1 million on cleaning equipment to protect against C. auris.Credit...Hilary Swift for The New York Times

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 C.D.C.

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 C.D.C. after reading the agency’s June 2016 advisory.

Candida Auris by State

Most cases in the United States have been in nursing homes in New York City, Chicago and New Jersey.

Mass.

N.Y.

Conn.

N.J.

Ill.

Ind.

Md.

Calif.

Va.

Okla.

200

Tex.

100

Fla.

25

Confirmed and

probable cases,

2013–19

1

Mass.

N.Y.

Conn.

N.J.

Ill.

Ind.

Md.

Calif.

Va.

Okla.

200

Tex.

100

Fla.

Confirmed and

probable cases,

2013–19

25

1

N.Y.

N.J.

Ill.

Md.

Ind.

Calif.

Va.

Okla.

200

Tex.

100

Fla.

25

Confirmed and probable cases, 2013–19

1

By The New York Times | Source: Centers for Disease Control and Prevention

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 C.D.C. 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.”

Image
Dr. Tom Chiller, head of the fungal branch at the C.D.C. “It is a creature from the black lagoon,” he said of C. auris.Credit...Melissa Golden for The New York Times

As the C.D.C. 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, the 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 C.D.C. 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.

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

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The C.D.C. in miniature. In the United States, two million people contract resistant infections each year, and 23,000 die from them, according to the official C.D.C. estimate.Credit...Melissa Golden for The New York Times

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

Dr. 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.”

Dr. Meis visited the C.D.C. 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 Dr. Rhodes, the infectious disease specialist who worked on the London outbreak. “We are driving this with the use of antifungicides on crops.”

Dr. 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.

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

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An empty hospital bed at Mount Sinai.Credit...Hilary Swift for The New York Times

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. Ms. 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.

Ana Harrero contributed reporting from Caracas, Venezuela, and Raphael Minder from Valencia, Spain.

Matt Richtel is a best-selling author and Pulitzer Prize-winning reporter based in San Francisco. He joined The Times staff in 2000, and his work has focused on science, technology, business and narrative-driven storytelling around these issues. More about Matt Richtel

Andrew Jacobs is a health and science reporter, based in New York. He previously reported from Beijing and Brazil and had stints as a metro reporter, Styles writer and national correspondent, covering the American South. More about Andrew Jacobs

A version of this article appears in print on  , Section A, Page 1 of the New York edition with the headline: Fungus Immune to Drugs Quietly Sweeps the Globe. Order Reprints | Today’s Paper | Subscribe

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