The Mysterious Reason Hospitals Won’t Reveal Dangerous Pathogens


The U.S. Centers for Disease Control and Prevention has three levels of travel health notices. Watch Level 1 asks travelers to take precautions; Alert Level 2 recommends taking enhanced precautions; and Warning Level 3 warns U.S. residents to avoid nonessential travel.1

In January, the agency sent an urgent public warning2 of an Alert Level 2 when an antibiotic-resistant bacteria — Pseudomonas aeruginosa — affected at least 12 Americans3 having elective surgery in Tijuana, Mexico. Half of the 12 infected in Mexico had their surgery at Grand View Hospital.

The alert continued to outline the current situation and what travelers to Mexico may do to prevent the drug-resistant infection. However, when similar outbreaks occurred on U.S. soil, the agency did not warn citizens. A New York Times reporter stumbled on a compelling example in Alaska of a woman infected with a drug-resistant bacteria that nearly killed her and required multiple surgeries.4

As the reporter searched for an answer, he was turned away by the medical community. Digging deeper, the Times discovered this was not uncommon, but rather standard operating procedure as hospitals appear more intent on protecting their reputation than on transparency.5

Culture of Secrecy Affects Your Health Care

After contacting hospitals in New York, Chicago, Texas, England and India, the Times reporter realized the issue about secrecy was a big part of the story of antibiotic resistance. A physician in Spain commented the hospital didn’t want bad press by seeming to be a hotbed for outbreaks of antifungal-resistant infections now responsible for a rising number of deaths.

The reporter commented,6 “One doctor in New York told me that patients, and their families, don’t like being associated with the illness, as if they had a scarlet letter — ‘A’ for auris.” The fungus they are referring to is Candida auris (C. auris). The CDC7 calls this an “emerging fungus that presents a serious global health threat,” for three reasons:8

  1. The fungus is often multidrug-resistant, including several antifungal drugs commonly used to treat Candida infections
  2. The fungus is difficult to identify using standard lab methods. Additionally, it may be misidentified without specific technology, leading to inappropriate management
  3. Candida auris has caused outbreaks in health care settings, making quick identification necessary to stop the spread

Unfortunately, despite the CDC’s outline of why the fungus is particularly virulent and dangerous, they have collaborated with U.S. hospitals to maintain confidentiality.

Kevin Kavanagh,9 board chairman of the advocacy group Health Watch USA, contrasted the difference in handling the infections in Tijuana against a 2016 outbreak of a drug-resistant pathogen, carbapenem-resistant Enterobacteriaceae at a rural hospital in Kentucky.

It wasn’t until January 2018, nearly two years after the outbreak in Kentucky that the CDC10 reported it. Even then, the hospital remained unnamed. This infection has been dubbed a “nightmare” bacteria as they’re resistant to most antibiotics and spread easily from person to person.11

Despite its virulence, the CDC and the Kentucky hospital chose not to inform the public. The focus of a second New York Times report, about a rising number of drug-resistant fungal infections from C. auris, is raising more questions about the secrecy behind infectious disease outbreaks in hospitals.12

Candida Auris — The Fungus Hospitals Are Not Talking About

In the fight against antibiotic-resistant infections, C. auris is an example of a new intractable threat. The New York Times tells the tale of a man admitted to Mount Sinai Hospital in New York who died after 90 days.

Tests showed C. auris was everywhere in his room, so special equipment was brought in to clean it. Some of the ceiling and floor tiles were even ripped out. The hospital president commented:13

“Everything was positive — the walls, the bed, the doors, the curtains, the phones, the sink, the whiteboard, the poles, the pump. The mattress, the bed rails, the canister holes, the window shades, the ceiling, everything in the room was positive.”

In 2015, infectious disease expert Johanna Rhodes from Imperial College in London was contacted by Royal Brompton Hospital. Three months earlier, C. auris had taken root and the hospital had been unable to clear it. Under her direction, the hospital used a special device using aerosolized hydrogen peroxide.14

Working under the theory that the vapor could get into nooks and crannies where scrub brushes cannot, they left the device going for a week. After testing the room, only one organism grew back — C. auris. Although the infection was spreading, word about it was not.

The medical community and governments have been reluctant to publicize the outbreak of resistant infections believing there’s no point in scaring patients, or prospective ones. In June 2016, a scientific paper15 reported an ongoing outbreak of 50 cases of C. auris in a European Hospital. Royal Brompton then took the extraordinary step of shutting down the ICU for 11 days, but without announcing why.

The New York Times reports an even bigger outbreak had begun in Valencia, Spain, responsible for 41.4% mortality rate in 30 days.16 The hospital in Spain has not made any announcement of the infections. Instead, they put out a statement saying:17

“It is very difficult to discern whether patients die from the pathogen or with it, since they are patients with many underlying diseases and in very serious general condition.”

The collaboration between the CDC and states to hide outbreaks is promoted as a way to avoid frightening patients about a situation where the risks are unclear. However, knowledge of an outbreak in a hospital is important when you’re making decisions about nonurgent matters, such as elective surgery.

The New York Times reports hospitals have hidden outbreaks even when disclosure could have saved lives. At a Seattle Hospital, 18 people died after being infected with a drug-resistant organism from a contaminated medical scope, but the outbreak was not disclosed at the time.18

Art Caplan, bioethicist at New York University, discussed the issue of full disclosure with the Times reporter. When the hospital is a treatment of last resort, he believes there will be patients with tough infections and yet he thinks there is greater value in promoting transparency, since public awareness could place pressure on hospitals to change the way they deal with infection control.19

Agricultural Fungicide Use Tied to Rising Infections

Antibiotics are used widely in farm animals and antifungals are applied to crops to prevent plants from rotting. In recent years, farmers have grown to rely on triazoles, a class of chemical used to fight fungi in humans. Globally, they’re the most widely used fungicides and Europe and North America use the largest volumes.20

According to the CDC,21 500 metric tons of triazole were used in 1992, as compared to an estimated 2,500 metric tons in 2015; however, data from 2015 do not include estimates for seed treatment applications, so this number may be higher.

To date, there is no definitive link between agricultural use of fungicide treatment and the sudden emergence of C. auris. While its emergence is still a mystery, the coincidence is not lost on scientists. Farm-based fungicides have been under suspicion. According to the Times, Dr. Tom Chiller, chief of the CDC’s mycotic diseases branch, believes C. auris has benefited from the heavy use of triazoles.22

Chiller theorizes the fungus has existed for thousands of years, hidden away, as it is not a particularly aggressive pathogen. However, as fungicides began destroying more prevalent fungi, C. auris was able to gain advantage. As a germ with the ability to resist fungicides and antifungal treatments, it is fully capable of resisting attack.23

In an interview with Mother Jones,24 Chiller reiterated the possibility of a link between triazole fungicides and the emergence of C. auris. He again stressed there is little known about the origin of the fungi and added he’s not aware of any current research analyzing farm fields. Instead, researchers have been scrambling to determine how to control it. He commented:25

“[T]he ones that are going to survive are the ones that are resistant — and they’re going to flourish. And so you could see how that could select for a relatively rare Candida like Candida auris.”

A Second Fungus Linked to Fungicide Use

A second fungus linked to the rising tonnage of triazole dumped on agricultural lands is Aspergillus fumigatus (A. fumigatus). Like C. auris, A. fumigatus is triggering drug-resistant infections in immunocompromised patients.26 Fortunately, the infections appear to be isolated and do not travel from patient to patient.

By 2013, Europe had established the link between A. fumigatus infections and the use of triazole fungicides.27 While it is a ubiquitous organism, the spores are breathed in every day without people getting sick, according to the CDC.28

However, the spores may trigger serious infections in those with compromised immune systems. A study by the CDC29 found since the organism can withstand antifungal medications, mortality may exceed 50%.

Fungus May Be Tied to Inflammatory Diseases

No one really knows how many species of fungi inhabit the earth. One estimate published in Microbiology Spectrum30 suggests there may be 2.2 million to 3.8 million different species, only 120,000 of which have been documented.31

Many play a role in breaking down plant matter and redistributing nutrients. Less well appreciated and studied is the influence fungal infections have on human health. In the past few decades there’s been a rising tide of fungal infections acquired, many of which are superficial, such as athlete’s foot and thrush. These are relatively easy to diagnose and treat.32

However, as we’ve discussed, several species have developed resistance against antifungal medications and may trigger life threatening infections. Researchers are also learning fungi are linked to diseases we don’t yet fully understand, such as allergy and asthma.33

Animal studies suggest alterations in the fungi living in your gut may affect the severity of ulcerative colitis, Crohn’s disease34 and even alcoholic liver disease.35 There are also reports linking fungi to neurological disorders, such as Alzheimer’s disease.36

David Underhill is a research chair for inflammatory bowel disease at Cedars-Sinai Medical Center. His team is investigating links between fungi and inflammatory bowel diseases like Crohn’s. One fungus at the center of his research is Malassezia, a species of fungi specialized to live on your skin that is associated with eczema and dandruff.37

Underhill and his colleagues found a link between Malassezia and Crohn’s disease. Those suffering from Crohn’s had a higher concentration of the fungi on their intestinal walls, while those who had no evidence of Crohn’s had almost none.38

The researchers were then able to demonstrate that adding this fungi to the gut in mice was enough to exacerbate the inflammatory response in much the same way as it is seen in Crohn’s. His work is building on a growing body of scientific evidence linking fungi to other types of inflammatory bowel diseases.39

Health of Your Gut Microbiome Vital to Your Health

Your gastrointestinal tract is often referred to as your “second brain” as it is considered one of the most complex microbial ecosystems on Earth. Nearly 100 trillion bacteria, fungi, viruses and other microorganisms live in your gut microbiome. Advancing science finds these organisms play a major role in your health, and in fact you have more bacterial DNA than human DNA.

Up to 80% of your immune system is located in your gut, so a healthy gut is your first defense against major diseases and a factor in helping you maintain optimal health. In some cases, fungal infections are opportunistic and easily infect those who are immunocompromised.

By taking care of your gut microbiome and maintaining a balance of beneficial bacteria, you help to support your immune system and reduce your potential for infections. For a discussion of how to optimize your gut health, see my previous article, “Gut Microbiome May Be a Game-Changer for Cancer Prevention and Treatment.”

How to Protect Yourself During a Hospital Stay

Also remember that hospitals are a primary source of many drug-resistant infections, so avoid going there unless absolutely necessary. According to 2017 statistics, 1 in 31 patients in the U.S. ends up contracting at least one health care-associated infection every day.40 While this number is going down by the year — in 201441 it was 1 in 25 — the CDC said “[M]ore needs to be done to prevent health care-associated infections in a variety of settings.”42

To help safeguard your health, ask all personnel to wash their hands and change gloves before touching you or anything in your room at each visit. Visitors should also wash their hands, as should you, if you venture off your bed.

If you’re having a colonoscopy or any other procedure using a flexible endoscope done, you can significantly reduce your risk of contracting an infection by asking the hospital or facility how the scope is cleaned, and which cleaning agent is used.

Some esophagoscopes and bronchoscopes have sterile sheaths with disposable air-water and biopsy channels, but many others do not, and must be cleaned between each use. If the hospital or clinic uses glutaraldehyde, or the brand name Cidex, cancel your appointment and go elsewhere.

About 80 percent of clinics use glutaraldehyde because it’s a less expensive alternative; however, it does not do a good job of sterilizing the equipment. If they use peracetic acid, your likelihood of contracting an infection from a previous patient is slim. To learn more about this, see my interview with David Lewis, Ph.D., in “How Improper Sterilization of Endoscopes Could Put Your Health at Risk.”

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