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.
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.
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.
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.
“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.
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.
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.
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 Dailyhas 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?
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.
New bioinformatic tool finds gut microbiota may be ‘potential reservoir of bloodstream pathogens’ suggesting patients’ own bodies can be source of infections
Clinical laboratories in hospitals and health networks throughout the nation are collaborating in the priority effort to reduce deaths from sepsis and related blood infections. Now comes news that researchers at Stanford have identified an unexpected source of bloodstream infections. This finding may help medical laboratories contribute to faster and more accurate diagnoses of blood infections, particularly for hospital inpatients.
Lax infection-control practices often are blamed for hospital-acquired infections (HAIs). And HAIs certainly have been responsible for many tragic avoidable deaths. However, new research from Stanford University School of Medicine shows that hospital staff, other patients, or unclean instruments may not be solely responsible for all infections that present during hospital stays. According to Stanford researchers, a patient’s own digestive tract can be the surprising culprit for many bloodstream infections. This finding confirms a common belief that the patient’s microbiome probably is involved in many blood infections.
The researchers published their findings in Nature Medicine.
Bacteria Causing Blood Infections Found in Patients’ Stool Samples After Bone Marrow Transplants
Using a new bioinformatic computational tool called StrainSifter, the Stanford University team rapidly and accurately identified a surprising infection source in a group of hospitalized patients—microbes already living in the patients’ large intestines—a Stanford University news release explained.
The researchers analyzed blood and stool samples from 30 patients who developed bloodstream infections after receiving bone marrow transplants between October 2015 and June 2017 at Stanford Hospital. The researchers sought to determine whether the bacteria isolated from the patients’ blood also was found in stool specimens that had been collected prior to the transplants. The process required sequencing not only the patients’ DNA, but also analyzing the genomes of all the individual microbial strains resident in each patient’s stool.
“Just finding E. coli in a patient’s blood and again in the patient’s stool doesn’t mean they’re the same strain,” Ami Bhatt, MD, PhD, Assistant Professor of Hematology and Genetics at Stanford, explained in the news release. Bhatt served as senior author of the study. (Photo copyright: Stanford University.)
Analysis found that more than one-third of the patients’ stool samples (11) contained detectable levels of the same bacterial strain that had caused those patients’ bloodstream infections.
“Because the gut normally harbors more than 1,000 different bacterial strains, it’s looked upon as a likely culprit of bloodstream infections, especially when the identified pathogen is one known to thrive inside the gut,” Ami Bhatt, MD, PhD, Assistant Professor of Hematology and Genetics at Stanford, said in the news release. “But while this culpability has been assumed—and it’s an entirely reasonable assumption—it’s never been proven. Our study demonstrates that it’s true.”
Clinical and DNA data confirmed the gastrointestinal presence of Escherichia coli and Klebsiella pneumonia, common causes of pneumonia, urinary tract infections, and other potentially serious conditions. In addition, they found other disease-causing pathogens in the gut that they would not have expected to be there.
“We also find cases where typically nonenteric [outside the intestine] pathogens, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, are found in the gut microbiota, thereby challenging the existing informal dogma of these infections originating from environmental or skin sources,” Fiona Tamburini, a senior graduate student, and postdoctoral scholar Tessa Andermann, MD, MPH, Infectious Disease Medical Fellow, wrote in Nature Medicine.
New Tool for Precision Medicine
Bhatt believes being able to trace the source of bloodstream infections will help doctors provide more targeted treatments for HAIs and potentially lead to effective prevention methods. This will create a new opportunity for microbiology laboratories to provide the necessary diagnostic tests designed to guide therapeutic choices of attending physicians.
“Until now, we couldn’t pinpoint those sources with high confidence,” Bhatt said in the news release. “That’s a problem because when a patient has a bloodstream infection, it’s not enough simply to administer broad-spectrum antibiotics. You need to treat the source, or the infection will come back.”
Bhatt says the computational tool has the potential to allow medical practitioners to quickly identify whether a pathogen responsible for a patient’s bloodstream infection came from a break in the skin, leaked through the intestinal wall into the blood, or was passed on through an inserted catheter or other object.
Bhatt’s team focused on the intestines for their study because it’s the home of 1,000 to 2,000 different germs. Dark Daily has reported often on developments involving human gut bacteria (AKA, microbiome) in e-briefings going back to 2013. While these gut bacteria do not typically cause problems, Bhatt said, “It’s only when they show up in the wrong place—due, for example, to leaking through a disrupted intestinal barrier into the bloodstream—that they cause trouble.”
Because nearly 40% of immunocompromised patients who spend up to six weeks in a hospital develop bloodstream infections, the Stanford findings could signal a major breakthrough in preventing HAIs. However, larger studies are needed to validate the researchers’ contention that the gut is a “potential reservoir of bloodstreams pathogens.”
If true, microbiologists and clinical pathologists may in the future have a new method for helping hospitals identify, track, and treat blood-born infections as well as and preventing HAIs.
