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During Pandemic, Clinical Laboratories Should Be Alert for Drug Resistant Infections That Pose High Risk to COVID-19 Patients

On top of everything else during this pandemic, drug-resistant infections are threatening the most vulnerable patients in COVID-19 ICUs

New study by researchers at the University of Minnesota highlights the continuing need for microbiologists and clinical laboratories to stay alert for COVID-19 patients with drug-resistant infections. In their study, researchers highlighted CDC statistics about the number of Candida auris (C. auris) infections reported in the United States during 2020, for example.

In a paper, titled, “Three Cases of Worrisome Pan-Resistant C Auris Found in New York,” the Center for Infectious Disease Research and Policy (CIDRAP) at the University of Minnesota reported that “As of Dec 11, the CDC said 941 confirmed and probable C. auris cases have been reported in 13 states, and an additional 1,830 patients have been found to be colonized with the multidrug-resistant fungus. Most of the cases have been detected in the New York City area, New Jersey, and the Chicago area.”

Candida auris is a particularly nasty fungus. It spreads easily, is difficult to remove from surfaces, and can kill. Worst of all, modern drugs designed to combat this potentially deadly fungus are becoming less effective at eradicating it, and COVID-19 ICU patients appear especially vulnerable to C. auris infections.

In “Potentially Fatal Fungus Invades Hospitals and Public Is Not Informed,” Dark Daily reported how Candida auris’ ability to elude detection makes decontamination of hospital rooms far more complicated. And in “CDC Ranks Two More Drug-Resistant Microbes as ‘Urgent Threat’ to Americans; Clinical Laboratories Are Advised to Increase Awareness of Antimicrobial Resistance,” we covered how the federal Centers for Disease Control and Prevention (CDC) added C. auris to its “Biggest Threats and Data: Antibiotic Resistance Threats in the United States” report for 2019.

COVID-19 and C. auris a Potentially Devastating Combination

Hospitals in many areas are at a critical capacity. Thus, hospital-acquired infections such as sepsis can be particularly dangerous for COVID-19 patients. Adding to the problem, C. auris requires special equipment to identify, and standard medical laboratory methods are not always enough. Misidentification is possible, even probable.

A paper in the Journal of Global Antimicrobial Resistance (JGAR), titled, “The Lurking Scourge of Multidrug Resistant Candida Auris in Times of COVID-19 Pandemic,” notes that “A particularly disturbing feature of COVID-19 patients is their tendency to develop acute respiratory distress syndrome that requires ICU admission, mechanical ventilation, and/or extracorporeal membrane oxygenation. … This haunting facet of COVID-19 pandemic has severely challenged even the most advanced hospital settings. Yet one potential confounder, not in the immediate attention of most healthcare professionals, is the secondary transmission of multidrug resistant organisms like the fungus Candida auris in COVID-19 ICUs. … C. auris outbreaks occur in critically ill hospitalized patients and can result in mortalities rates ranging from 30% to 72%. … Both C. auris and SARS-CoV-2 have been found on hospital surfaces including on bedrails, IV poles, beds, air conditioner ducts, windows and hospital floors. Therefore, the standard COVID-19 critical care of mechanical ventilation and protracted ventilator-assisted management makes these patients potentially susceptible to colonization and infections by C. auris.”

One study mentioned in the JGAR paper conducted in New Delhi, India, looked at 596 cases where patients were admitted to the ICU with COVID-19. Fifteen of them had infections caused by C. auris. Eight of those patients died. “Of note, four patients who died experienced persistent fungemia and despite five days of micafungin therapy, C. auris again grew in blood culture,” according to reporting on the study in Infection Control Today (ICT).

Some C. auris mortality rates are as high as 72%. And patients with weakened immune systems are at particular risk, “making it an even more serious concern when 8% to 9% of roughly 530,000 ICU patients in the United States have COVID-19,” ICT reported.

Apparently, the COVID-19 pandemic has created circumstances that are particularly suited for C. auris to spread. “Given the nosocomial transmission of SARS-CoV-2 by those infected, many hospital environments may serve as venues for C. auris transmission as it is a known environmental colonizer of ICUs,” wrote the JGAR paper authors.

CDC Reports and Recommendations

Along with being especially dangerous for people with weakened immune systems, C. auris infections also produce symptoms similar to those of COVID-19, “including fever, cough, and shortness of breath,” according to the CDC’s website. People admitted to ICUs with COVID-19 are especially vulnerable to bacterial and fungal co-infections. “These fungal co-infections are reported with increasing frequency and can be associated with severe illness and death,” says the CDC.

C. auris outbreaks in the United States have mostly been in long-term care facilities, but the pandemic seems to be changing that and more outbreaks have been detected in acute care facilities, the CDC reported. The lack of appropriate personal protective equipment (PPE), changes in infection control routines, and other factors could be to blame for the increase.

Just as community spread is an issue with COVID-19 variants, so too is it a concern with C. auris infections. “New C. auris cases without links to known cases or healthcare abroad have been identified recently in multiple states, suggesting an increase in undetected transmission,” the CDC noted.

As of January 19, 2021, according to the CDC the case count of C. auris infections in the US was 1,625, with California, Florida, Illinois, New Jersey, and New York having more than 100 cases each.

According to a CDC report, “Candida auris (C. auris) is an emerging multidrug-resistant yeast (a type of fungus). It can cause severe infections and spreads easily between hospitalized patients and nursing home residents.” The graphic above, taken from the report, illustrates how “C. auris began spreading in the United States in 2015. Reported cases increased 318% in 2018 when compared to the average number of cases reported in 2015 to 2017.” (Graphic copyright: Centers for Disease Control and Prevention.)

Using Clinical Laboratory Tests to Identify C. Auris

One of the big concerns about C. auris is that it is so difficult to detect, and that medical laboratories in some countries simply do not have the technology and resources to identify and tackle the infection.

“As C. auris diagnostics in resource-limited countries is yet another challenge, we feel that alerting the global medical community about the potential of C. auris as a confounding factor in COVID-19 is a necessity,” wrote the authors of the paper published in the Journal of Global Antimicrobial Resistance.

As if the COVID-19 pandemic has not been enough, drug resistant bacteria, viruses, and deadly fungi are threatening to wreak havoc among SARS-CoV-2 infected patients. Microbiologists and medical laboratory scientists know that testing for all types of infections is vitally important, but especially when it comes to infections caused by antibiotic-resistant bacteria (ARB) and other dangerous organisms that demonstrate antimicrobial resistance (AMR).

Microbiologists and clinical laboratory professionals will want to stay informed about the number of C. auris cases identified in the US and the locations and settings where the fungus was detected. They will want to be on the alert within their hospitals and health networks, as well as with the doctor’s offices served by their labs.

—Dava Stewart

Related Information:

Potentially Fatal Fungus Invades Hospitals and Public Is Not Informed

CDC Ranks Two More Drug-Resistant Microbes as ‘Urgent Threat to Americans; Clinical Laboratories Are Advised to Increase Awareness of Antimicrobial Resistance:

Biggest Threats and Data: Antibiotic Resistance Threats in the United States report for 2019

Three Cases of Worrisome Pan-Resistant C auris Found in New York

COVID Unleashes the ‘Lurking Scourge’ Candida Auris

The Lurking Scourge of Multidrug Resistant Candida auris in Times of COVID-19 Pandemic

CDC: Fungal Diseases and COVID-19

CDC: Candida auris

Doctors in India Sound Alarm: CRE Infections are Becoming Common in India and Killing Two-Thirds of Patients Who Contract Them While Undergoing Cancer Treatment!

As infectious bacteria become even more resistant to antibiotics, chronic disease patients with weakened immune systems are in particular danger

Microbiologists and clinical laboratory managers in the United States may find it useful to learn that exceptionally virulent strains of bacteria are causing increasing numbers of cancer patient deaths in India. Given the speed with which infectious diseases spread throughout the world, it’s not surprising that deaths due to similar hospital-acquired infections (HAIs) are increasing in the US as well.

Recent news reporting indicates that an ever-growing number of cancer patients in the world’s second most populous nation are struggling to survive these infections while undergoing chemotherapy and other treatments for their cancers.

In some ways, this situation is the result of more powerful antibiotics. Today’s modern antibiotics help physicians, pathologists, and clinical laboratories protect patients from infectious disease. However, it’s a tragic fact that those same powerful drugs are making patients with chronic diseases, such as cancer, more susceptible to death from HAIs caused by bacteria that are becoming increasingly resistant to those same antibiotics.

India is a prime example of that devastating dichotomy. Bloomberg reported that a study conducted by Abdul Ghafur, MD, an infectious disease physician with Apollo Hospitals in Chennai, India, et al, concluded that “Almost two-thirds of cancer patients with a carbapenem-resistant infection are dead within four weeks, vs. a 28-day mortality rate of 38% in patients whose infections are curable.”

This news should serve as an alert to pathologists, microbiologists, and clinical laboratory leaders in the US as these same superbugs—which resist not only antibiotics but other drugs as well—may become more prevalent in this country.

 ‘We Don’t Know What to Do’

The dire challenge facing India’s cancer patients is due to escalating bloodstream infections associated with carbapenem-resistant enterobacteriaceae (CRE), a particularly deadly bacteria that has become resistant to even the most potent carbapenem antibiotics, generally considered drugs of last resort for dealing with life-threatening infections.

Lately, the problem has only escalated. “We are facing a difficult scenario—to give chemotherapy and cure the cancer and get a drug-resistant infection and the patient dying of infections.” Ghafur told Bloomberg. “We don’t know what to do. The world doesn’t know what to do in this scenario.”

Ghafur added, “However wonderful the developments in the field of oncology, they are not going to be useful, because we know cancer patients die of infections.”

Abdul Ghafur, MD (above), an infectious disease physician with Apollo Hospitals in Chennai, India, told The Better India that, “Indians, are obsessed with antibiotics and believe that they can cure almost all infections, including viral infections! Moreover, at least half of the prescriptions by Indian doctors include an antibiotic. Sadly, the public believes that whenever we get cold and cough, we need to swallow antibiotics for three days along with paracetamol [acetaminophen]! This is a myth that urgently needs to disappear!” (Photo copyright: Longitude Prize.)

The problem in India, Bloomberg reports, is exacerbated by contaminated food and water. “Germs acquired through ingesting contaminated food and water become part of the normal gut microbiome, but they can turn deadly if they escape the bowel and infect the urinary tract, blood, and other tissues.” And chemotherapy patients, who likely have weakened digestive tracts, suffer most when the deadly germs reach the urinary tract, blood, and surrounding tissues.

“Ten years ago, carbapenem-resistant superbug infections were rare. Now, infections such as carbapenem-resistant klebsiella bloodstream infection, urinary infection, pneumonia, and surgical site infections are a day-to-day problem in our (Indian) hospitals. Even healthy adults in the community may carry these bacteria in their gut in Indian metropolitan cities; up to 5% of people carry these superbugs in their intestines,” Ghafur told The Better India.

What are CRE and Why Are They So Deadly?

CRE are part of the enterobacteriaceae bacterial family, which also includes Escherichia coli (E. coli) and Klebsiella pneumoniae. CRE, according to the Centers for Disease Control and Prevention (CDC), are considered “antibiotic-resistant” because antibiotic agents known as carbapenems are becoming increasing less effective at treating enterobacteriaceae.

In fact, a 2018 study conducted by the All India Institute of Medical Sciences (AIIMS) in New Delhi, which was published in the Journal of Global Infectious Diseases (JGID), found that bloodstream infections due to CRE were the “leading cause” of illness and death in patients with hematological malignancies, such as leukemia.

“These patients receive chemotherapy during treatment, which lead to severe mucositis of gastrointestinal tract and myelosuppression. It was hypothesized that the gut colonizer translocate into blood circulation causing [bloodstream infection],” the AIIMS paper states.

US Cases of C. auris Also Linked to CRE

Deaths in the US involving the fungus Candida auris (C. auris) have been linked to CRE as well. And, people who were hospitalized outside the US may be at particular risk.

The CDC reported on a Maryland resident who was hospitalized in Kenya with a carbapenemase-producing infection, which was later diagnosed as C. auris. The CDC describes C. auris as “an emerging drug-resistant yeast of high public concern … C auris frequently co-occurs with carbapenemase-producing organisms like CRE.”

The graphic above, developed by the NYT from CDC data, shows that Candida auris is found globally and not restricted to poor or resource-strapped nations. “The fungus seems to have emerged in several locations at once, not from a single source,” the NYT reports. This means clinical laboratories can expect to be processing more tests to identify the deadly fungus. (Graphic copyright: New York Times/CDC.)

Drug-resistant germs are a public health threat that has grown beyond overuse of antibiotics to an “explosion of resistant fungi,” reported the New York Times (NYT).

“It’s an enormous problem. We depend on being able to treat those patients with antifungals,” Matthew Fisher, PhD, Professor of Fungal Disease Epidemiology at Imperial College London, told the NYT

The NYT article states that “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.”

Cases of C. auris in the US are showing up in New York, New Jersey, and Illinois and is arriving on travelers from many countries, including India, Pakistan, South Africa, Spain, United Kingdom, and Venezuela.  

“It is a creature from the black lagoon,” Tom Chiller, MD, Chief of the Mycotic Diseases Branch at the CDC told the NYT. “It bubbled up and now it is everywhere.”

Since antibiotics are used heavily in agriculture and farming worldwide, the numbers of antibiotic-resistant infections will likely increase. Things may get worse, before they get better.

Pathologists, microbiologists, oncologists, and clinical laboratories involved in caring for patients with antibiotic-resistant infections will want to fully understand the dangers involved, not just to patients, but to healthcare workers as well.

—Donna Marie Pocius

Related Information:

Superbugs Deadlier than Cancer Put Chemotherapy into Question

Taking Antibiotics for a Viral Infection? A Doc Shares Why You Should Think Twice

Healthcare-Associated Infections: CRE

Rectal Carriage of Carbapenem-resistant enterobacteriaceae: A Menace to Highly Vulnerable Patients

Clinical Study of Carbapenem Sensitive and Resistant Gram-negative Bacteria in Neutropenic and Nonneutropenic Patients: The First Series from India

Candida Auris in a U.S. Patient with Carbapenemase-Producing Organisms and Recent Hospitalization in Kenya

Deadly Germs, Lost Cures: A Mysterious Infection, Spanning the Globe in a Climate of Secrecy

University of Edinburgh Study Finds Antimicrobial Bacteria in Hospital Wastewater in Research That Has Implications for Microbiologists

Pathologists and Clinical Laboratories to Play Critical Role in Developing New Tools to Fight Antibiotic Resistance

Lurking Below: NIH Study Reveals Surprising New Source of Antibiotic Resistance That Will Interest Microbiologists and Medical Laboratory Scientists

Wellcome Sanger Institute Study Discovers New Strain of C. Difficile That Targets Sugar in Hospital Foods and Resists Standard Disinfectants

Researchers believe new findings about genetic changes in C. difficile are a sign that it is becoming more difficult to eradicate

Hospital infection control teams, microbiologists, and clinical laboratory professionals soon may be battling a strain of Clostridium difficile (C. difficile) that is even more resistant to disinfectants and other forms of infection control.

That’s the opinion of research scientists at the Wellcome Sanger Institute (WSI) and the London School of Hygiene and Tropical Medicine (LSHTM) in the United Kingdom who discovered the “genetic changes” in C. difficile. Their genomics study, published in Nature Genetics, shows that the battle against super-bugs could be heating up.

A WSI news release states the researchers “identified genetic changes in the newly-emerging species that allow it to thrive on the Western sugar-rich diet, evade common hospital disinfectants, and spread easily.”

Microbiologists and infectious disease doctors know full well that this means the battle to control HAIs is far from won.

C. difficile is currently forming a new species with one group specialized to spread in hospital environments. This emerging species has existed for thousands of years, but this is the first time anyone has studied C. difficile genomics in this way to identify it. This particular [bacterium] was primed to take advantage of modern healthcare practices and human diets,” said Nitin Kumar, PhD (above), in the news release. (Photo copyright: Wellcome Sanger Institute.) 

Genomic Study Finds New Species of Bacteria Thrive in Western Hospitals

In the published paper, Nitin Kumar, PhD, Senior Bioinformatician at the Wellcome Sanger Institute and Joint First Author of the study, described a need to better understand the formation of the new bacterial species. To do so, the researchers first collected and cultured 906 strains of C. difficile from humans, animals, and the environment. Next, they sequenced each DNA strain. Then, they compared and analyzed all genomes.

The researchers found that “about 70% of the strain collected specifically from hospital patients shared many notable characteristics,” the New York Post (NYPost) reported.

Hospital medical laboratory leaders will be intrigued by the researchers’ conclusion that C. difficile is dividing into two separate species. The new type—dubbed C. difficile clade A—seems to be targeting sugar-laden foods common in Western diets and easily spreads in hospital environments, the study notes. 

“It’s not uncommon for bacteria to evolve, but this time we actually see what factors are responsible for the evolution,” Kumar told Live Science.

New C. Difficile Loves Sugar, Spreads

Researchers found changes in the DNA and ability of the C. difficile clade A to metabolize simple sugars. Common hospital fare, such as “the pudding cups and instant mashed potatoes that define hospital dining are prime targets for these strains”, the NYPost explained.

Indeed, C. difficile clade A does have a sweet tooth. It was associated with infection in mice that were put on a sugary “Western” diet, according to the Daily Mail, which reported the researchers found that “tougher” spores enabled the bacteria to fight disinfectants and were, therefore, likely to spread in healthcare environments and among patients.

“The new C. difficile produces spores that are more resistant and have increased sporulation and host colonization capacity when glucose or fructose is available for metabolism. Thus, we report the formation of an emerging C. difficile species, selected for metabolizing simple dietary sugars and producing high levels or resistant spores, that is adapted for healthcare-mediated transmission,” the researchers wrote in Nature Genetics.

Bacteria Pose Risk to Patients

The findings about the new strains of C. difficile bacteria now taking hold in provider settings are important because hospitalized patients are among those likely to develop life-threatening diarrhea due to infection. In particular, people being treated with antibiotics are vulnerable to hospital-acquired infections, because the drugs eliminate normal gut bacteria that control the spread of C. difficile bacteria, the researchers explained.

According to the Centers for Disease Control and Prevention (CDC), C. difficile causes about a half-million infections in patients annually and 15,000 of those infections lead to deaths in the US each year.

New Hospital Foods and Disinfectants Needed

The WSI/LSHTM study suggests hospital representatives should serve low-sugar diets to patients and purchase stronger disinfectants. 

“We show that strains of C. difficile bacteria have continued to evolve in response to modern diets and healthcare systems and reveal that focusing on diet and looking for new disinfectants could help in the fight against this bacteria,” said Trevor Lawley, PhD, Senior Author and Group Leader of the Lawley Lab at the Wellcome Sanger Institute, in the news release.

Microbiologists, infectious disease physicians, and their associates in nutrition and environmental services can help by understanding and watching development of the new C. difficile species and offering possible therapies and approaches toward prevention.

Meanwhile, clinical laboratories and microbiology labs will want to keep up with research into these new forms of C. difficile, so that they can identify the strains of this bacteria that are more resistant to disinfectants and other infection control methods.  

—Donna Marie Pocius

Related Information:

Adaptation of Host Transmission Cycle During Clostridium Difficile Speciation

Diarrhea-causing Bacteria Adapted to Spread in Hospitals

Sugary Western Diets Fuel Newly Evolving Superbug

New Carb-Loving Superbug is Primed to Target Hospital Food

Superbug C Difficile Evolving to Spread in Hospitals and Feeds on the Sugar-Rich Western Diet

CDC: Healthcare-Associated Infections-C. Difficile  

University of Edinburgh Study Finds Antimicrobial Bacteria in Hospital Wastewater in Research That Has Implications for Microbiologists

The highly infectious bacteria can survive treatment at local sewage plants and enter the food chain of surrounding populations, the study revealed

Researchers at the University of Edinburgh (UE) in Scotland found large amounts of antimicrobial-resistance (AMR) genes in hospital wastewater. These findings will be of interest to microbiologists and clinical laboratory managers, as the scientists used metagenomics to learn “how abundances of AMR genes in hospital wastewater are related to clinical activity.”

The UE study sheds light on the types of bacteria in wastewater that goes down hospital pipes to sewage treatment plants. The study also revealed that not all infectious agents are killed after passing through waste treatment plants. Some bacteria with antimicrobial (or antibiotic) resistance survive to enter local food sources. 

The scientists concluded that the amount of AMR genes found in hospital wastewater was linked to patients’ length-of-stays and consumption of antimicrobial resistant bacteria while in the hospital.

Using Metagenomics to Surveille Hospital Patients

Antimicrobial resistance is creating super bacteria that are linked to increases in hospital-acquired infections (HAIs) nationwide. Dark Daily has reported many times on the growing danger of deadly antimicrobial resistant “super bugs,” which also have been found in hospital ICUs (see “Potentially Fatal Fungus Invades Hospitals and Public Is Not Informed,” August 26, 2019.)

In a paper the University of Edinburgh published on medRxiv, the researchers wrote: “There was a higher abundance of antimicrobial-resistance genes in the hospital wastewater samples when compared to Seafield community sewage works … Sewage treatment does not completely eradicate antimicrobial-resistance genes and thus antimicrobial-resistance genes can enter the food chain through water and the use of [processed] sewage sludge in agriculture. As hospital wastewater contains inpatient bodily waste, we hypothesized that it could be used as a representation of inpatient community carriage of antimicrobial resistance and as such may be a useful surveillance tool.”

Additionally, they wrote, “Using metagenomics to identify the full range of AMR genes in hospital wastewater could represent a useful surveillance tool to monitor hospital AMR gene outflow and guide environmental policy on AMR.”

AMR bacteria also are being spread by human touch throughout city subways, bus terminals, and mass transportation, making it difficult for the Centers for Disease Control and Prevention (CDC) to identify the source of the outbreak and track and contain it. This has led microbiologists to conduct similar studies using genetic sequencing to identify ways to track pathogens through city infrastructures and transportation systems. (See, “Microbiologists at Weill Cornell Use Next-Generation Gene Sequencing to Map the Microbiome of New York City Subways,” December 13, 2013.)

Antimicrobial stewardship programs are becoming increasingly critical to preventing the spread of AMR bacteria. “By having those programs, [there are] documented cases of decreased antibiotic resistance within organisms causing these infections,” Paul Fey, PhD, of the University of Nebraska Medical Center, told MedPage Today. “This is another indicator of how all hospitals need to implement stewardship programs to have a good handle on decreasing antibiotic use.” [Photo copyright: University of Nebraska.]

Don’t Waste the Wastewater

Antibiotic resistance occurs when bacteria change in response to medications to prevent and treat bacterial infections, according to a World Health Organization (WHO) fact sheet. The CDC estimates that more than 23,000 people die annually from two million antibiotic-resistance infections.

Wastewater, the UE scientists suggest, should not go to waste. It could be leveraged to improve hospitals’ detection of patients with antimicrobial resistance, as well as to boost environment antimicrobial-resistance polices.

They used metagenomics (the study of genetic material relative to environmental samples) to compare the antimicrobial-resistance genes in hospital wastewater against wastewater from community sewage points. 

The UE researchers:

  • First collected samples over a 24-hour period from various areas in a tertiary hospital;
  • They then obtained community sewage samples from various locations around Seafield, Scotland;
  • Finally, they complete the genetic sequencing on an Illumina HiSeq4000 System.

The researchers reported these findings:

  • 181 clinical isolates were identified in the samples of wastewater;
  • 1,047 unique bacterial genes were detected across all samples;
  • 19 genes made up more than 60% of bacteria in samples;
  • Overriding bacteria identified as Pseudomonas and Acinetobacter environmental samples (Pseudomonas fluorescens and Acinetobacter johnsonii) were most likely from hospital pipes;
  • Gut-related bacteria—Faecalibacterium, Bacteroides, Bifidobacterium, and Escherichia, were more prevalent in the hospital samples than in those from the community;
  • Antimicrobial-resistance genes increased with longer length of patient stays, which “likely reflects transmission amongst hospital inpatients,” researchers noted. 

Fey suggests that further research into using sequencing technology to monitor patients is warranted.

“I think that monitoring each patient and sequencing their bowel flora is more likely where we’ll be able to see if there’s a significant carriage of antibiotic-resistant organisms,” Fey told MedPage Today. “In five years or so, sequencing could become so cheap that we could monitor every patient like that.”

Fey was not involved in the University of Edinburgh research.

Given the rate at which AMR bacteria spreads, finding antibiotic-resistance genes in hospital wastewater may not be all that surprising. Still, the University of Edinburgh study could lead to cost-effective ways to test the genes of bacteria, which then could enable researchers to explore different sources of infection and determine how bacteria move through the environment.

And, perhaps most important, the study suggests clinical laboratories have many opportunities to help eliminate infections and slow antibiotic resistance. Microbiologists can help move their organizations forward too, along with infection control colleagues.  

—Donna Marie Pocius

Related Information:

Secrets of the Hospital Underbelly: Abundance of Antimicrobial-Resistance Genes in Hospital Wastewater Reflects Hospital Microbial Use and Inpatient Length of Stay

Antibiotic-Resistance Genes Trouble Hospital Water; Study Emphasizes Importance of Antibiotic Stewardship Programs, Expert Says

Fact Sheet: Antibiotic Resistance

United States Gathers 350 Commitments to Combat Antibiotic Resistance, Action Must Continue

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenemase Resistance

Dark Daily E-briefings: Hospital-Acquired Infections

NIH Study Reveals Surprising New Source of Antibiotic Resistance that Will Interest Microbiologists and Medical Laboratory Scientists

Potentially Fatal Fungus Invades Hospitals and Public Is Not Informed

Clinical laboratories and microbiologists will want to be on the alert for this deadly infectious agent that has killed patients through blood infections

Healthcare continues to struggle with the issue of how much to disclose to the public when new and deadly infectious agents are identified in a limited number of patients. Timely disclosure of new pathogens is a matter of great concern to clinical laboratory scientists, microbiologists, and clinical pathologists because their laboratories get specimens from infected patients and they must correctly identify rare or emerging pathogens to help minimize the spread of disease.

This is why many medical laboratory professionals were surprised to see national news headlines recently about a particularly deadly new form of a pathogen. The Centers for Disease Control and Prevention (CDC) has been dealing with one particularly nasty example of Candida auris, or C. auris. This “superbug” fungus has been appearing in hospitals and healthcare clinics across the globe and it has killed people.

The news coverage of C. auris focused on two elements:

  • First, how the pathogen was recognized by such healthcare agencies as the CDC.
  • Second, why CDC and others did not issue a public alert to hospitals, physicians, and other caregivers once it was known that C. auris was responsible for the death of several patients.

Once C. auris takes hold, it can enter a patient’s bloodstream or wounds and cause life- threatening complications like sepsis. When hospitals rooms are not properly decontaminated, life-threatening hospital-acquired infections (HAIs), also known as nosocomial infections, can occur.

Incidences of HAIs have been on the rise in the past few years. Dark Daily has reported on this disturbing trend many times.

The New York Times (NYT) reported on one such HAI that had tragic consequences. A patient admitted to Mount Sinai Hospital in New York for abdominal surgery was later discovered to have contracted C. auris. He was immediately isolated and spent 90 days in the hospital before passing away. Tests showed that Candida auris was everywhere in his room.

“Everything was positive—the walls, the bed, the doors, the curtains, the phones, the sink, the whiteboard, the poles, the pump,” Scott Lorin, MD, President and Chief Operating Officer at Mount Sinai Brooklyn Hospital, told the NYT. “The mattress, the bed rails, the canister holes, the window shades, the ceiling, everything in the room was positive,” he said.

The hospital had to use special cleaning equipment to sterilize the room and even found it necessary to tear out some ceiling and floor tiles to annihilate the fungus, the NYT reported.

Media News Coverage of ‘Culture of Secrecy’ 

When this deadly fungus first emerged in America, it was not disclosed to the public for a lengthy period of time. Then, when details of deaths in hospitals due to the superbug went public, the national news media reacted but then went silent. Why?

The New York Times (NYT) covered the debate over public disclosure of outbreaks involving drug-resistant infections at healthcare facilities in “Culture of Secrecy Shields Hospitals with Outbreaks of Drug-Resistant Infections.”

In that article, the NYT states that “under its agreement with states, the CDC is barred from publicly identifying hospitals that are battling to contain the spread of dangerous pathogens.” So, the CDC is prevented from revealing to the public the names and locations of facilities that are dealing with C. auris. And state governments typically do not share that information either. 

The NYT article also states, “The CDC 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.”

And that, “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.”

“Who’s speaking up for the baby that got the flu from the hospital worker or for the patient who got MRSA from a bedrail? The idea isn’t to embarrass or humiliate anyone, but if we don’t draw more attention to infectious disease outbreaks, nothing is going to change,” Arthur Caplan, PhD (above), told the NYT. Caplan is Drs. William F and Virginia Connolly Mitty Professor and founding head of the Division of Medical Ethics at NYU School of Medicine in New York City. (Photo copyright: NYU Langone Health.)

Common Yeast Infection or Killer Superbug? Both!

C. auris grows as a common yeast infection. However, it can be life threatening if it enters the bloodstream.

“The average person calls Candida infections yeast infections,” William Schaffner, MD, Professor and Chair, Department of Preventative Medicine at Vanderbilt University Medical Center, told Prevention. “However, Candida auris infections are much more serious than your standard yeast infection. They’re a variety of so-called superbugs [that] can complicate the therapy of very sick people.”

The CDC reports that, as of May 31, 2019, there have been a total of 685 cases of C. auris reported in the US. The majority of those cases occurred in Illinois (180), New Jersey (124), and New York (336). Twenty more cases were reported in Florida, and eight other states—California, Connecticut, Indiana, Maryland, Massachusetts, Oklahoma, Texas, and Virginia—each had less than 10 confirmed cases of C. auris.

The CDC states the infection seems to be most prominent among populations that have had extended stays in hospitals or nursing facilities. Patients who have had lines or tubes such as breathing tubes, feeding tubes, or central venous catheters entering their body, and those who have recently been given antibiotics or antifungal medications, seem to be the most vulnerable to contracting C. auris.

The fungus typically attacks people who are already sick or have weakened immune systems, which can make it challenging to diagnose, the CDC notes. C. auris infections are typically diagnosed with special clinical laboratory testing of blood specimens or other body fluids. Infections have been found in patients of all ages, from infants to the elderly.

Data from the CDC indicates that C. auris can cause bloodstream infections, wound infections, and ear infections. Common symptoms that indicate a person has Candida auris include fever, chills, weakness, low blood pressure, and general malaise that do not improve with antibiotics.

“A patient’s temperature may go up, their blood pressure can go down, and they have complications of a pre-existing illness because of Candida auris,” Schaffner told Prevention.

The CDC reports that more than one in three patients with invasive C. auris dies. Even though the mortality rates for Candida auris are high, it is unclear whether patients are dying from the infection or from their underlying illnesses. “Whatever the cause, having Candida auris doesn’t help a patient in any way,” Schaffner noted.

The CDC states that it and its public health partners are working hard to discover more about this fungus, and to devise ways to protect people from contracting it. Average healthy people probably don’t need to worry about becoming infected with Candida auris. However, individuals who are at high risk, and healthcare professionals, microbiologists, and pathologists, should be on the alert for this new superbug strain of fungus. 

—JP Schlingman

Related Information:

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

Culture of Secrecy Shields Hospitals with Outbreaks of Drug-Resistant Infections

Candida auris: A Drug-Resistant Germ That Spreads in Healthcare Facilities

A Deadly Superbug Fungus Called Candida auris Has Been Detected in 12 States—Here’s What You Need to Know

A Deadly Fungal Infection Called Candida auris Is Spreading across the Globe, and No One Knows How to Stop It

Study: Colonized Candida auris Patients Shed Fungus via Skin

The Deadly Yeast Infection You Must Know About

What You Need to Know Candida auris, a Dangerous Fungal Infection That’s on the Rise

With Candida auris, a Lack of Transparency Could Make Things Worse

Could Proximity of Toilets to Sinks in Medical Intensive Care Units Contribute to Hospital-Acquired Infections?

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