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Clinical Laboratories and Pathology Groups

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Clinical Laboratories and Pathology Groups

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

In a separate study, HHS finds a 40% increase in sepsis cases, as more patients succumb to infections without effective antibiotics and antimicrobial drugs

Given the drastic steps being taken to slow the spread of the Coronavirus in America, it’s easy to forget that significant numbers of patients die each year due to antibiotic-resistant bacteria (ARB), other forms of antimicrobial resistance (AMR), and in thousands of cases the sepsis that follows the infections.

This is why the Centers for Disease Control and Prevention (CDC) issued the report “Antibiotic Resistance Threats in the United States, 2019 (2019 AR Threats Report)” last fall. The federal agency wants to call attention the emergence of new antibiotic-resistant bacteria and fungi. In its report, the CDC lists 18 bacteria and fungi that pose either urgent, serious, or concerning threats to humans. It also placed one fungus and two bacteria on a “watch” list.

The CDC’s website states that “more than 2.8 million antibiotic-resistant infections occur in the US each year, and more than 35,000 people die as a result.” And a CDC news release states, “on average, someone in the United States gets an antibiotic-resistant infection every 11 seconds and every 15 minutes someone dies.”

Those are huge numbers.

Clinical laboratory leaders and microbiologists have learned to be vigilant as it relates to dangerously infectious antimicrobial-resistant agents that can result in severe patient harm and death. Therefore, new threats identified in the CDC’s Antibiotic Resistance Threats in the United States report will be of interest.

Drug-resistant Microbes That Pose Severe Risk

The CDC has added the fungus Candida auris (C. auris) and carbapenem-resistant Acinetobacter (a bacteria that can survive for a long time on surfaces) to its list of “urgent threats” to public health, CDC said in the news release. These drug-resistant microbes are among 18 bacteria and fungi posing a greater threat to patients’ health than CDC previously estimated, Live Science reported.

In 2013, the CDC estimated that about two million people each year acquired an antibiotic-resistant (AR) infection that killed as many as 23,000. However, in 2019, the CDC reported that those numbers were low and that the number of deaths due to AR infections in 2013 was about twice that amount. During a news conference following the CDC announcement, Michael Craig (above), a Senior Adviser for the CDC’s Antibiotic Resistance Coordination and Strategy Unit said, “We knew and said [in 2013] that our estimate was conservative … and we were right,” Live Science reported. In 2019, CDC reported 2.8 million antibiotic-resistant infections annually with more than 35,000 related deaths in the US alone. (Photo copyright: Centers for Disease Control and Prevention.)

The CDC considers five threats to be urgent. Including the latest additions, they are:

Dark Daily has regularly covered the healthcare industry’s ongoing struggle with deadly fungus and bacteria that are responsible for hospital-acquired infections (HAI) and sepsis. This latest CDC report suggests healthcare providers continue to struggle with antimicrobial-resistant agents.

Acinetobacter Threat Increases and C. auris a New Threat since 2013

Carbapenem-resistant Acinetobacter, a bacterium that causes pneumonia and bloodstream and urinary tract infections, escalated from serious to urgent in 2013. About 8,500 infections and 700 deaths were noted by the CDC in 2017. 

C. auris, however, was not addressed in the 2013 report at all. “It’s a pathogen that we didn’t even know about when we wrote our last report in 2013, and since then it’s circumvented the globe,” said Michael Craig, Senior Adviser for the CDC’s Antibiotic Resistance Coordination and Strategy Unit, during a news conference following the CDC announcement, Live Science reported.

Today, C. auris is better understood. The fungus resists emerging drugs, can result in severe infections, and can be transmitted between patients, CDC noted.

Last year, Dark Daily reported on C. auris, noting that as of May 31 the CDC had tracked 685 cases. (See, “Potentially Fatal Fungus Invades Hospitals and Public Is Not Informed,” August 26, 2019.)

By year-end, CDC tracking showed 988 cases in the US.

More Patients Getting Sepsis as Antibiotics Fail: HHS Study

In a separate study published in Critical Care Medicine, a journal of the Society of Critical Care Medicine (SCCM), the US Department of Health and Human Services  (HHS) found that antibiotic-resistant bacteria and fungi are resulting in more people acquiring sepsis, a life-threatening condition, according to an HHS news release.

Sepsis increased by 40% among hospitalized Medicare patients from 2012 through 2018, HHS reported.   

“These (untreatable infections) are happening here and now in the United States in large numbers. This is isn’t some developing world thing. This isn’t a threat for 2050. It’s a threat for here and now,” Cornelius “Neil” Clancy, MD, Associate Chief of Veterans Affairs Pittsburg Health System (VAPHS) and Opportunistic Pathogens, told STAT.

It is troubling to see data about so many patient deaths related to antibiotic-resistant infections and sepsis cases when the world is transfixed by the Coronavirus. Nevertheless, it’s important that medical laboratory leaders and microbiologists keep track of how the US healthcare system is or is not responding to these new infectious agents. And, to contact infection control and environmental services colleagues to enhance surveillance, ensure safe healthcare environments and equipment, and adopt appropriate strategies to prevent antibiotic-resistant infections.   

—Donna Marie Pocius

Related Information:

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

More People in the U.S. Dying from Antibiotic-Resistant Infections Than Previously Estimated; Significant Progress Since 2013 Could be Lost Without More Action

These Two Drug-Resistant Microbes Are New “Urgent Threats” to Americans’ Health

CDC Report: 35,000 Americans Die of Antibiotic-Resistant Infections Each Year

The Superbug Candida Auris is Giving Rise to Warnings and Big Questions

On the Emergency of Candida Auris Climate Change, Azoles, Swamps, and Birds

Largest Study of Sepsis Cases Among Medicare Beneficiaries Finds Significant Burden

Sepsis Among Medicare Beneficiaries: The Burdens of Sepsis 2012 to 2018

Dark Daily: Hospital-Acquired Infection

Potentially Fatal Fungus Invades Hospitals and Public is Not Informed

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

Precision Healthcare Milestone Reached as Food and Drug Administration Clears New Multi-Marker Medical Laboratory Test to Detect Antibiotic-Resistant Bacteria

FDA issues press release following clearance of a clinical lab test to detect genetic markers that indicate the presence of Carbapenem-resistant Enterobacteriaceae

Clearance by the US Food and Drug Administration (FDA) of a new rapid, multi-marker genetic test designed to identify bacteria that are resistant to Carbapenem antibiotics was considered significant enough that the federal agency issued a press release announcing that the test was cleared and now available for use by physicians and clinical laboratories in the United States.

In the race to develop molecular assays and genetic tests for infectious disease that deliver improved sensitivity and specificity with a faster time-to-answer, this new test offers all three benefits. Results are available in just 48 minutes, for example.

It was on June 29, 2016, that the FDA cleared Cepheid’s Xpert Carba-R rapid-diagnostic test for marketing in the United States. This is the first clinical laboratory test cleared for market by the FDA that detects healthcare-associated infections (AKA, hospital-acquired infections or HAIs) through the use of genetic markers taken directly from clinical samples. The assay tests for genetic markers that indicate the presence of Carbapenem-resistant Enterobacteriaceae (CRE). (more…)

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