H5N1

With all eyes on Covid-19, drug-resistant infections crept in

Via The New York Times: With All Eyes on Covid-19, Drug-Resistant Infections Crept In.

As Covid-19 took hold over the last year, hospitals and nursing homes used and reused scarce protective equipment — masks, gloves, gowns. This desperate frugality helped prevent the airborne transfer of the virus. 

But it also appears to have helped spread a different set of germs — drug-resistant bacteria and fungi — that have used the chaos of the pandemic to grow opportunistically in health care settings around the globe. 

These bacteria and fungi, like Covid-19, prey on older people, the infirm and those with compromised immune systems. They can cling tenaciously to clothing and medical equipment, which is why nursing homes and hospitals before the pandemic were increasingly focused on cleaning rooms and changing gowns to prevent their spread. 

That emphasis all but slipped away amid an all-consuming focus on the coronavirus. In fact, experts warn, the changes in hygiene and other practices caused by the Covid-19 fight are likely to have contributed to the spread of these drug-resistant germs.  

“Seeing the world as a one-pathogen world is really problematic,” said Dr. Susan S. Huang, an infectious disease specialist at the University of California at Irvine Medical School, noting that the nearly singular focus on the pandemic appears to have led to more spread of drug-resistant infection. “We have every reason to believe the problem has gotten worse.”  

A few data points reinforce her fears, including isolated outbreaks of various drug-resistant infections in Florida, New Jersey and California, as well as in India, Italy, Peru and France. Overall figures have been hard to track because many nursing homes and hospitals simply stopped screening for the germs as resources were diverted to Covid-19.  

When even modest screening picked up again early in the summer, the results suggested that certain drug-resistant organisms had taken root and spread. Particularly troublesome have been growing case counts of a fungus called Candida auris, which authorities had tried to fight before the pandemic with increased screening, isolation of infected patients and better hygiene.

A breeding ground for a fatal scourge: Nursing homes

Via The New York Times: A Breeding Ground for a Fatal Scourge: Nursing Homes. Excerpt:

Maria Davila lay mute in a nursing home bed, an anguished expression fixed to her face, as her husband stroked her withered hand. Ms. 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.  

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 Ms. Davila’s nursing home, Palm Gardens Center for Nursing and Rehabilitation in Brooklyn, 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.

Canada: Doctors and scientists mystified by spread of Candida auris superbug

Via CBC News: Doctors and scientists mystified by spread of Candida auris superbug. Excerpt:

The emergence of a partially drug-resistant fungal infection in Canadian hospitals and elsewhere has doctors and scientists scrambling to understand the pathogen and stop its spread.

Candida auris was virtually unknown until 2009, but the past decade has seen outbreaks of infection in hospitals and long-term care facilities around the world, predominantly among patients with weakened immune systems, such as people receiving chemotherapy or surgery and those who receive medication through large intravenous lines.

So far C. auris remains relatively rare, said Dr. Isaac Bogoch, an infectious disease physician at Toronto General Hospital. But the fungus, which can cause infections, including of the blood, of wounds and ears, has three main features that make it worrisome to health-care professionals:  

• It's tricky for some laboratories to identify. 

• It can be hard to treat successfully when it invades the bloodstream. 

• It's frequently resistant to one or more classes of antifungal medications that doctors turn to first. 

"It poses a bit of challenge to treat, and the reason is there can be delays in diagnosis: conventional labs might not be able to detect that it's Candida auris right away," said Bogoch. 

"With the delayed diagnosis, that can often delay appropriate treatment — and if we delay treatment for fungal infection, especially when they're in the blood, people can get very sick, very quickly." 

Serious infection 

In Canada, provincial laboratories and the National Microbiology Laboratory in Winnipeg are able to identify the specific infection. In the developing world, detection isn't always possible, according to the U.S. Centers for Disease Control and Prevention. 

Symptoms may not be noticeable because patients with C. auris infection are often already sick in the hospital. 

Based on information from a limited number of patients, the CDC estimates more than one in three patients with invasive C. auris die. 

Canada has had a total of 20 cases of C. auris from 2012 to June 2019, the Public Health Agency of Canada (PHAC) said: 

• 6 cases in Central Canada (Quebec or Ontario) between 2012 and 2017.  

• 14 cases in Western Canada (Manitoba, Saskatchewan, Alberta or British Columbia) between 2014 and June 2019. 

Canada's first case of multidrug-resistant C. auris was diagnosed in July 2017, imported by a returning traveller, said PHAC spokesperson Anna Maddison. 

Some — but not all — of the resistant infections were acquired in hospitals outside Canada, Maddison said. It's not known how the others acquired it.

"We absolutely will be seeing more cases," Bogoch said. 

What superbug hunters know that we don’t

Via The New York Times, an opinion piece by Dr. Matt McCarthy: What Superbug Hunters Know That We Don’t. Excerpt:

Antibiotic-resistant superbugs are everywhere. If your hospital claims it doesn’t have them, it isn’t looking hard enough. 

Hospitals are losing an important public relations battle over the expanding threat of superbugs, including the deadly fungus Candida auris. Though states are tasked with conducting outbreak investigations, they aren't required to disclose their findings to the Centers for Disease Control and Prevention (and in many cases they haven’t). Grieving families are pushing for more transparency, while patient advocates smell a cover-up, likening the scenario to a restaurant failing to report an outbreak of food poisoning. In the midst of all this mistrust, hospital spokesmen are declining to comment. This is a mistake. 

I hate to be the bearer of bad news, but these microbes are in our homes, cars and grocery stores. One study found that even after the use of disinfectant, more than half of hospital rooms still contain a superbug. Nurses and doctors carry these things around, too. Roughly 5 percent of health care workers are colonized with MRSA, a bacterium that kills thousands of people in the United States every year, and another study found that 10 percent of patients entering a hospital had a multidrug-resistant species on their hands. You don’t want to know what’s hiding on a handkerchief.  

Here’s the thing: You almost certainly don’t need to worry about any of this. Potentially deadly bacteria and fungi live harmlessly on our hands, feet, and faces, and may never cause a problem. There are trillions of bacteria living inside all of us. Why are we pretending they aren’t on our gurneys, blood pressure cuffs and X-ray machines? 

Demanding that hospitals release lists of every superbug they find within their walls, however, as many transparency advocates want, is not the answer. The irony is that the hospitals that see the most superbugs are often the best ones we have, for the simple reason that they have the most sophisticated diagnostic platforms, the most powerful antibiotics and the experts to administer them.  

Compelling a world-class hospital like Massachusetts General Hospital, where I saw my first superbug as a medical student, to reveal a microbe list would only freak patients out. It wouldn’t explain where the microbes came from, whether any patients were infected, and how they were cured. 

In a worst-case scenario, more transparency could lead to patients avoiding medical care out of a misplaced fear of encountering drug-resistant bacteria. Hospitals might start refusing patients with certain infections, especially those coming from nursing facilities where these microbes are common, out of a concern that the patient’s bacteria could be added to the list. This would do everyone a disservice: Patients wouldn’t receive optimal care and superbugs would multiply.  

But hospital administrators and government officials do need to be honest about the microbes in our medical centers and explain what is really going on. No comment will no longer suffice. People have questions and this story is not going away. To ensure that patients are well-informed, hospitals should train spokesmen to address these issues and states should revisit their reluctance to disclose information. Above all, health care workers and administrators should speak openly about the measures their hospitals are already employing to keep people safe.  

I’m not particularly interested in the microbes that dwell inside of a given hospital; what matters is whether its employees follow the strict protocols that prevent these organisms from going where they shouldn’t.

The scary shortage of infectious-disease doctors

Via The New York Times, an op-ed: The Scary Shortage of Infectious-Disease Doctors. Is this also true of countries with reasonable health-insurance systems? Excerpt:

Many have heard of the rise of drug-resistant infections. But few know about an issue that’s making this threat even scarier in the United States: the shortage of specialists capable of diagnosing and treating those infections. 

Infectious diseases is one of just two medicine subspecialties that routinely do not fill all of their training spots every year in the National Resident Matching Program (the other is nephrology). Between 2009 and 2017, the number of programs filling all of their adult-infectious-disease training positions dropped by more than 40 percent. 

This could not be happening at a worse time. Antibiotic-resistant microbes, known as superbugs, are pinballing around the world, killing hundreds of thousands of people every year. The Times recently reported on Candida auris, a deadly new fungus that has infected hospital patients in Illinois, New Jersey and New York. 

Everyone who works in health care agrees that we need more infectious-disease doctors, yet very few actually want the job. What’s going on?  

The problem is that infectious-disease specialists care for some of the most complicated patients in the health care system, yet they are among the lowest paid. It is one of the only specialties in medicine that sometimes pays worse than being a general practitioner. At many medical centers, a board-certified internist accepts a pay cut of 30 percent to 40 percent to become an infectious-disease specialist. 

 This has to do with the way our insurance system reimburses doctors. Medicare assigns relative value units to the thousands of services that doctors provide, and these units largely determine how much physicians are paid. The formula prioritizes invasive procedures over intellectual expertise.

The problem is that infectious-disease doctors don’t really do procedures. It is a cognitive specialty, providing expert consultation, and insurance doesn’t pay much for that. 

For example, I recently diagnosed a case of fungal pneumonia. To arrive at this diagnosis took hours: first, speaking with the patient’s primary care doctor and pulmonologist, followed by a long stretch reviewing chest X-rays and other imaging studies with a radiologist, before examining the cells in the patient’s lung tissue under a microscope to confirm the diagnosis and report back to the anxious patient and family. Most of this work was done free. 

A generation ago, most well-rounded doctors knew what to do when a patient developed a fever. Not anymore. New threats like Candida auris pop up all the time, and to identify a deadly pathogen, we often have to use a sophisticated technique called matrix-assisted laser desorption ionization time-of-flight mass spectrometry. As the name suggests, it requires a bit of expertise.

Back in the day, there were only a handful of reliable antibiotics to choose from. But as more bugs have emerged, and more have become resistant to standard treatments, we’ve had to develop new drugs to fight them. The good news is that in 2018, the Food and Drug Administration approved a cadre of new antibiotics to confront the rising threat of superbugs, including eravacycline, plazomicin and omadacycline, and we can expect even more this year. But very few physicians know how to use these powerful new drugs. Many don’t even know how to pronounce them.  

Infectious-disease specialists are often the only health care providers in a hospital — or an entire town — who know when to use all of the new antibiotics (and when to withhold them). These experts serve as an indispensable cog in the health care machine, but if trends continue, we won’t have enough of them to go around. 

The terrifying part is that most patients won’t even know about the deficit. Your doctor won’t ask a specialist for help because in some parts of the country, the service simply won’t be available. She’ll just have to wing it.

Culture of secrecy shields hospitals with outbreaks of drug-resistant infections

Via The New York Times: Culture of Secrecy Shields Hospitals With Outbreaks of Drug-Resistant Infections. Excerpt from a disturbing report:

In January, the Centers for Disease Control and Prevention sent out an urgent public alert about a deadly bacteria, resistant to virtually every known antibiotic, that sickened more than a dozen Americans who had elective surgery at Grand View Hospital in Tijuana, Mexico. 

But when similar outbreaks take place at hospitals on American soil, the C.D.C. makes no such public announcement. That is because under its agreement with states, the C.D.C. is barred from publicly identifying hospitals that are battling to contain the spread of dangerous pathogens.  

The rise of a deadly drug-resistant fungus called Candida auris, a focus of a New York Times report last weekend, has raised fresh questions about the secrecy enveloping infectious outbreaks at American medical institutions.

Patient advocates say hospitals and health authorities are often slow to alert the public about drug-resistant germs, potentially endangering patients. 

“They might not get up and go to another hospital, but patients and their families have the right to know when they are at a hospital where an outbreak is occurring,” said Lisa McGiffert of the Patient Safety Action Network. “That said, if you’re going to have hip replacement surgery, you may chose to go elsewhere.” 

Kevin Kavanagh, board chairman of the advocacy group Health Watch USA, contrasted the C.D.C.’s handling of the infections in Tijuana with a 2016 outbreak of a different drug-resistant pathogen, known as carbapenem-resistant Enterobacteriaceae, or CRE, at a rural hospital in Kentucky. It was not until early 2018 that the C.D.C. issued a report on that outbreak — and even then, the agency did not name the hospital where it occurred.  

CRE sometimes kills up to half of people infected. No deaths were reported in the Kentucky outbreak, but at least two dozen patients at the hospital were colonized with the bug, meaning they were not sick but could have spread it to others.

The report identified a cleaning cart as a possible source for the spread of the pathogen, which had traveled between the hospital’s emergency room and its surgical ward. 

The C.D.C. declined to comment, but in the past officials have said their approach to confidentiality is necessary to encourage the cooperation of hospitals and nursing homes, which might otherwise seek to conceal infectious outbreaks.  

Those pushing for increased transparency say they are up against powerful medical institutions eager to protect their reputations, as well as state health officials who also shield hospitals from public scrutiny.

A mysterious infection, spanning the globe in a climate of secrecy

Via The New York Times: A Mysterious Infection, Spanning the Globe in a Climate of Secrecy. Excerpt:

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.”

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.

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.”

'We're holding up a floodgate': BC fights off superbugs brought home by medical tourists

Via CBC News: 'We're holding up a floodgate': B.C. fights off superbugs brought home by medical tourists. Excerpt:

The risks involved in medical tourism aren't just personal. Having surgery abroad could also mean bringing back a drug-resistant superbug and putting people in this country at risk, B.C. officials warn. 

That alert comes after the recent discovery that two patients at New Westminster's Royal Columbian Hospital had been colonized with the multidrug-resistant yeast Candida auris. Though neither patient is infected with the bug, the two join just a handful of cases that have been identified in B.C. since 2017.  

Dr. Linda Hoang, medical co-director for the Provincial Infection Control Network (PICNet), said most of these cases have come from travellers who have had treatment overseas, including medical tourists. 

It means patients need to do serious research on the facilities they're considering for surgeries or other treatments abroad, including looking for objective information about the presence of any drug-resistant microorganisms.  

"It's not only a problem in India or Southeast Asia. It is endemic in parts of the U.S. and parts of Europe," Hoang told CBC News.  

"It [antibiotic-resistant superbugs] is a global problem, and the only way to to be aware of them is to make sure that health-care professionals are informed and our residents are informed when they're seeking health care outside of British Columbia." 

It's a sobering reminder for those who travel abroad for medical treatments, whether it's to skip the surgery wait list in B.C., access therapies that aren't approved in Canada or save money on cosmetic therapy. Some of the top destinations for medical tourists from around the world include India, Mexico, Southeast Asia, Brazil and Turkey, according to the Medical Tourism Association.  

But facilities in other countries can sometimes take a more haphazard approach to prescribing antibiotics, and overuse can trigger the evolution of resistance to these crucial drugs.  

India a major source of bug 

The two colonized patients at Royal Columbian were isolated after the bug was discovered, and the hospital has been aggressively cleaning all areas they had visited, using UV light for disinfection, according to Fraser Health. 

C. auris was first identified in Japan in 2009, but it has popped up since then in countries around the world. 

It acts much like any other yeast species, causing infections in wounds, the bloodstream and the ears, but the real problem is how to treat it. 

"The only real reason why we're concerned or interested in monitoring Candida auris is because of that potential resistance profile, making it difficult to treat with the anti-fungal agent that we have," Hoang said. 

The biggest risk of infection right now seems to come from Indian facilities, Hoang said.

The bug was confirmed for the first time in B.C. in July 2017 in a patient who'd been treated in India. As it turned out, that traveller also came back with infections from multiple other drug-resistant organisms. 

B.C. doesn't track whether infected people travelled abroad as medical tourists or simply required medical treatment because of an emergency during their voyages. 

But patients who have had medical treatment outside B.C. for any reason are a major source of these superbugs, she said.

They include so-called CPOs — carbapenemase-producing organisms like Klebsiella, E. coli and Pseudomonas that have become resistant to broad-spectrum antibiotics, which Hoang describes as the "last resort" for treatment. 

In 2017-2018, PICNet recorded more CPO cases than ever before, and more than half of them were from people who had accessed health care overseas, Hoang said.

Breakthrough test screens for all known bacterial infections

Some very good news from Columbia University Mailman School of Public Health: Breakthrough Test Screens for All Known Bacterial Infections. Excerpt:

Scientists at the Center for Infection and Immunity (CII) in the Columbia University Mailman School of Public Health have developed the first diagnostic platform that can simultaneously screen for all known human pathogenic bacteria as well as markers for virulence and antibiotic resistance. A study in the journal mBio provides details on the performance of the BacCapSeq platform.  

“Once approved for clinical use, BacCapSeq will give physicians a powerful tool to quickly and precisely screen for all known pathogenic bacteria, including those that cause sepsis, the third leading cause of death in the United States,” says first author Orchid M. Allicock, PhD, a post-doctoral researcher at CII. “This platform is 1,000 times more sensitive than traditional unbiased testing, at a level comparable to tests that screen one bacterium at a time.” 

Currently, the most common method used to test for sepsis can take as long as three days, and even longer to provide information on antibiotic resistance. While physicians wait for a result, they usually prescribe broad-spectrum antibiotics, a practice that contributes to the growth of antibiotic resistance. BacCapSeq provides results in 70 hours, but the researchers believe that the platform will become faster with advances in computing power. 

Each year, antibiotic-resistant infections claim 100,000 lives in the United States, and 700,000 globally, with the highest burden in the developing world, according to World Economic Forum estimates. The direct annual impact of antibiotic resistance in the U.S. is $20-35 billion with an additional $35 billion in lost productivity, according to the U.S. Center for Disease Control and Prevention. Absent an effective response to limit further growth in antimicrobial resistance, the challenge will continue to increase. The World Bank issued a report in 2017 projecting an impact on the GDP between $1.1 trillion and $3.4 trillion. 

BacCapSeq contains 4.2 million genetic probes used to detect the signature DNA of all 307 pathogenic bacteria, as well as biomarkers for antibiotic resistance and virulence. Each probe binds to a corresponding sequence; when a particular bacterium and biomarker is present in a sample, a magnetic process “pulls out” its unique sequences, which can then be used to identify the bacterium and its characteristics. 

To date, even the most advanced multiplexed polymerase chain reaction systems are only able to screen for up to 19 pathogenic bacteria, and none can assess virulence and antimicrobial resistance.

ECDC: Emerging spread of new fungal species poses risk for healthcare settings in the EU/EEA

ECDC has published Emerging spread of new fungal species poses risk for healthcare settings in the EU/EEA.

The rise in Europe of Candida auris infections, a difficult-to-control fungus, is of concern. The fungus spreads easily in healthcare settings, can cause invasive infections, and is also associated with resistance to multiple classes of anti-fungal medication. Difficulties with laboratory identification, and lack of awareness of this new Candida species might result in transmission and outbreaks remaining unnoticed. 

The first discovered case of infection of the fungus was reported in 2009 in Japan. Since then, there have been several outbreaks in five continents, making the emerging spread of the fungus a global public health issue within just a few years. During 2013–2017, 620 cases of Candida auris were reported in the European Union/European Economic Area (EU/EEA). 

“There is a need to raise awareness in European healthcare facilities for them to adapt their laboratory testing strategies, and implement enhanced control measures early enough to prevent further hospital outbreaks” says Dominique Monnet, Head of the Antimicrobial Resistance and Healthcare-associated Infections Disease Programme at ECDC. “The occurrence of new outbreaks can be expected. It is therefore of concern that some countries lack national laboratory reference capacity for mycology, or have no information on Candida auris cases available at national level”. Candida auris can cause invasive infections in patients, especially in those who are suffering from severe underlying diseases and suppressed immune systems. 

Candida auris can survive on surfaces for weeks and requires special disinfectants, as some of the disinfectants commonly used in hospitals are not effective. The fungus is associated with resistance to fluconazole, a common antifungal medication, and multidrug-resistant isolates have also been identified. 

Early detection of the fungus is necessary for preventing further cases and outbreaks. However, identification of Candida auris requires specialised laboratory methodology as traditional identification methods may lead to misidentification. Due to a lack of laboratory capability for routine detection and surveillance in some EU/EEA countries, recognition of Candida auris introduction to a healthcare facility might be delayed until spread has already occurred.  

ECDC issued a Rapid Risk Assessment on 23 April 2018, which contains options for response to EU/EEA countries on possible measures to reduce identified risks, including laboratory detection, infection control measures as well as improvement of surveillance and preparedness.