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. 

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.

Multiple introductions of multidrug-resistant Candida auris in the USA

Via The Lancet: Multiple introductions and subsequent transmission of multidrug-resistant Candida auris in the USA: a molecular epidemiological survey. The summary:

Background 

Transmission of multidrug-resistant Candida auris infection has been reported in the USA. To better understand its emergence and transmission dynamics and to guide clinical and public health responses, we did a molecular epidemiological investigation of C auris cases in the USA. 

Methods 

In this molecular epidemiological survey, we used whole-genome sequencing to assess the genetic similarity between isolates collected from patients in ten US states (California, Connecticut, Florida, Illinois, Indiana, Maryland, Massachusetts, New Jersey, New York, and Oklahoma) and those identified in several other countries (Colombia, India, Japan, Pakistan, South Africa, South Korea, and Venezuela). We worked with state health departments, who provided us with isolates for sequencing. 

These isolates of C auris were collected during the normal course of clinical care (clinical cases) or as part of contact investigations or point prevalence surveys (screening cases). We integrated data from standardised case report forms and contact investigations, including travel history and epidemiological links (ie, patients that had shared a room or ward with a patient with C auris). Genetic diversity of C auris within a patient, a facility, and a state were evaluated by pairwise differences in single-nucleotide polymorphisms (SNPs). 

Findings 

From May 11, 2013, to Aug 31, 2017, isolates that corresponded to 133 cases (73 clinical cases and 60 screening cases) were collected. Of 73 clinical cases, 66 (90%) cases involved isolates related to south Asian isolates, five (7%) cases were related to South American isolates, one (1%) case to African isolates, and one (1%) case to east Asian isolates. Most (60 [82%]) clinical cases were identified in New York and New Jersey; these isolates, although related to south Asian isolates, were genetically distinct. 

Genomic data corroborated five (7%) clinical cases in which patients probably acquired C auris through health-care exposures abroad. Among clinical and screening cases, the genetic diversity of C auris isolates within a person was similar to that within a facility during an outbreak (median SNP difference three SNPs, range 0–12). 

Interpretation 

Isolates of C auris in the USA were genetically related to those from four global regions, suggesting that C auris was introduced into the USA several times. The five travel-related cases are examples of how introductions can occur. Genetic diversity among isolates from the same patients, health-care facilities, and states indicates that there is local and ongoing transmission.

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. 

Essential reading on Candida auris

Via Controversies in Hospital Infection Prevention, Dr. Dan Diekema writes: Essential reading on Candida auris. Click or tap through to read the whole post and use the links. Excerpt:

During my intern rotation on the University of Virginia bone marrow transplant unit, I convinced myself that a Candida krusei epidemic was brewing. One of my patients was infected, and the bug was (and is inherently) resistant to fluconazole, a drug that had only recently been introduced (yes, I’m old—the year was 1990). This never really came to pass—despite 30 years of widespread fluconazole use, C. krusei still accounts for < 5% of invasive candidiasis, and outbreaks are rare.  

Now, a Candida species that wasn’t even described a decade ago is emerging as a major problem in ICUs around the world. The Candida auris story is fascinating, puzzling, and concerning. For reasons nobody understands, the species emerged (or began to recognized) almost simultaneously on three different continents. 

Although risk factors for invasive C. auris are similar to those for other causes of invasive candidiasis (ICU stay, antibiotic exposure, device use), it also features high rates of antifungal resistance, persistence on environmental surfaces, resistance to commonly used disinfectants, frequent transmission in ICU environments, and has thus caused several large, difficult-to-control outbreaks.

Rapid genome sequencing for outbreak analysis of the emerging human fungal pathogen Candida auris

Via bioRxiv: Rapid genome sequencing for outbreak analysis of the emerging human fungal pathogen Candida auris. The abstract:

Background: 

Candida auris was first described in 2009, and has since caused nosocomial outbreaks, invasive infections and fungaemia across 11 countries in five continents. An outbreak of C. auris occurred in a specialised cardiothoracic London hospital between April 2015 and November 2016, which to date has been the largest outbreak reported worldwide, involving a total of 72 patients. 

Methods: 

To understand the epidemiology of C. auris infection within this hospital, we sequenced the genomes of outbreak isolates using Oxford Nanopore Technologies and Illumina in order to type antifungal resistance alleles and to explore the outbreak within its local and global context. 

Findings: 

Phylogenomic analysis placed the UK outbreak in the India/Pakistan clade, demonstrating an Asian origin. The outbreak showed similar diversity to that of the entire clade and limited local spatiotemporal clustering was observed. One isolate displayed resistance to both echinocandins and 5-flucytosine; the former was associated with a serine to tyrosine amino acid substitution in the gene FKS1, and the latter was associated with a phenylalanine to isoleucine substitution in the gene FUR1. These mutations are novel for this pathogen. 

Interpretation: 

Multiple differential episodic selection of antifungal resistant genotypes has occurred within a genetically heterogenous population across this outbreak, creating a resilient pathogen and making it difficult to define local-scale patterns of transmission as well as implementing outbreak control measures.

Rare fungus found in 200 patients in 55 UK hospitals

Via Reuters: Rare fungus found in 200 patients in 55 UK hospitals. Excerpt:

A rare fungus that can cause drug-resistant infections has been found in around 200 patients in more than 55 hospitals across Britain, health officials said on Tuesday.  

Around a quarter of the cases of Candida auris have caused infections with symptoms, Public Health England (PHE) said, including in 27 patients who developed blood stream infections.

The fungus, also known as C. auris and first identified in Japan eight years ago, is rare and low-risk, but has a propensity to spread between hospital patients.  

"Most cases detected have not shown symptoms or developed an infection as a result of the fungus," said Colin Brown, a microbiologist with PHE's national infection service.  

He said health service staff were working with PHE experts to limit the fungus's spread. 

First isolated from the ear of a patient in Japan in 2009, C. auris has since been linked with bloodstream and wound infections, and with ear infections known as otitis, in at least eight other countries including South Africa, Kuwait, India and Venezuela. 

The first case of infection in Britain was in 2013.