News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel

News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel
Sign In

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

Genomic analysis of pipes and sewers leading from the National Institutes of Health Clinical Care Center in Bethesda, Md., reveals the presence of carbapenem-resistant organisms; raises concern about the presence of multi-drug-resistant bacteria previously undetected in hospital settings

If hospitals and medical laboratories are battlegrounds, then microbiologists and clinical laboratory professionals are frontline soldiers in the ongoing fight against hospital-acquired infections (HAIs) and antibiotic resistance. These warriors, armed with advanced testing and diagnostic skills, bring expertise to antimicrobial stewardship programs that help block the spread of infectious disease. In this war, however, microbiologists and medical laboratory scientists (AKA, medical technologists) also often discover and identify new and potential strains of antibiotic resistance.

One such discovery involves a study published in mBio, a journal of the American Society for Microbiology (ASM), conducted by microbiologist Karen Frank, MD, PhD, D(AMBB), Chief of the Microbiology Service Department at the National Institutes of Health (NIH), and past-president of the Academy of Clinical Laboratory Physicians and Scientists (ACLPS). She and her colleagues identified a surprising source of carbapenem-resistant organisms—the plumbing, sewers, and wastewater beneath the National Institutes of Health Center (NIHCC) in Bethesda, Md. And they theorize similar “reservoirs” could exist beneath other healthcare centers as well.

Potential Source of Superbugs and Hospital-Acquired Infections

According to the mBio study, “Carbapenemase-producing organisms (CPOs) are a global concern because of the morbidity and mortality associated with these resistant Gram-negative bacteria. Horizontal plasmid transfer spreads the resistance mechanism to new bacteria, and understanding the plasmid ecology of the hospital environment can assist in the design of control strategies to prevent nosocomial infections.”

Karen Frank, MD, PhD

Karen Frank, MD, PhD (above), is Chief of the Microbiology Service Department at the National Institutes of Health and past-president of the Academy of Clinical Laboratory Physicians and Scientists. She suggests hospitals begin tracking the spread of the bacteria. “In the big picture, the concern is the spread of these resistant organisms worldwide, and some regions of the world are not tracking the spread of the hospital isolates.” (Photo copyright: National Institutes of Health.)

Frank’s team used Illumina’s MiSeq next-generation sequencer and single-molecule real-time (SMRT) sequencing paired with genome libraries, genomics viewers, and software to analyze the genomic DNA of more than 700 samples from the plumbing and sewers. They discovered a “potential environmental reservoir of mobile elements that may contribute to the spread of resistance genes, and increase the risk of antibiotic resistant ‘superbugs’ and difficult to treat hospital-acquired infections (HAIs).”

Genomic Sequencing Identifies Silent Threat Lurking in Sewers

Frank’s study was motivated by a 2011 outbreak of antibiotic-resistant Klebsiella pneumoniae bacteria that spread through the NIHCC via plumbing in ICU, ultimately resulting in the deaths of 11 patients. Although the hospital, like many others, had dedicated teams working to reduce environmental spread of infectious materials, overlooked sinks and pipes were eventually determined to be a disease vector.

In an NBC News report on Frank’s study, Amy Mathers, MD, Director of The Sink Lab at the University of Virginia, noted that sinks are often a locus of infection. In a study published in Applied and Environmental Microbiology, another journal of the ASM, Mathers noted that bacteria in drains form a difficult to clean biofilm that spreads to neighboring sinks through pipes. Mathers told NBC News that despite cleaning, “bacteria stayed adherent to the wall of the pipe” and even “splashed out” into the rooms with sink use.

During the 2011-2012 outbreak, David Henderson, MD, Deputy Director for Clinical Care at the NIHCC, told the LA Times of the increased need for surveillance, and predicted that clinical laboratory methods like genome sequencing “will become a critical tool for epidemiology in the future.”

Frank’s research fulfilled Henderson’s prediction and proved the importance of genomic sequencing and analysis in tracking new potential sources of infection. Frank’s team used the latest tools in genomic sequencing to identify and profile microbes found in locations ranging from internal plumbing and floor drains to sink traps and even external manhole covers outside the hospital proper. It is through that analysis that they identified the vast collection of CPOs thriving in hospital wastewater.

In an article, GenomeWeb quoted Frank’s study, noting that “Over two dozen carbapenemase gene-containing plasmids were identified in the samples considered” and CPOs turned up in nearly all 700 surveillance samples, including “all seven of the wastewater samples taken from the hospital’s intensive care unit pipes.” Although the hospital environment, including “high-touch surfaces,” remained free of similar CPOs, Frank’s team noted potential associations between patient and environmental isolates. GenomeWeb noted Frank’s findings that CPO levels were in “contrast to the low positivity rate in both the patient population and the patient-accessible environment” at NIHCC, but still held the potential for transmission to vulnerable patients.

Antibiotic-Resistance: A Global Concern

The Centers for Disease Control and Prevention (CDC) reports that more than two million illnesses and 23,000 deaths in the US are caused each year by antibiotic resistance, with 14,000 deaths alone linked to antibiotic resistance associated with Clostridium difficile infections (CDI). Worldwide those numbers are even higher.

Second only to CDI on the CDC’s categorized list of “18 drug-resistant threats to the United States” are carbapenem-resistant Enterobacteriaceae (CRE).

Since carbapenems are a “last resort” antibiotic for bacteria resistant to other antibiotics, the NIHCC “reservoir” of CPOs is a frightening discovery for physicians, clinical laboratory professionals, and the patients they serve.

The high CPO environment in NIHCC wastewater has the capability to spread resistance to bacteria even without the formal introduction of antibiotics. In an interview with Healthcare Finance News, Frank indicated that lateral gene transfer via plasmids was not only possible, but likely.

“The bacteria fight with each other and plasmids can carry genes that help them survive. As part of a complex bacterial community, they can transfer the plasmids carrying resistance genes to each other,” she noted. “That lateral gene transfer means bacteria can gain resistance, even without exposure to the antibiotics.”

The discovery of this new potential “reservoir” of CPOs may mean new focused genomic work for microbiologists and clinical laboratories. The knowledge gained by the discovery of CPOs in hospital waste water and sinks offers a new target for study and research that, as Frank concludes, will “benefit healthcare facilities worldwide” and “broaden our understanding of antimicrobial resistance genes in multi-drug resistant (MDR) bacteria in the environment and hospital settings.”

Amanda Warren

Related Information:

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

Snooping Around in Hospital Pipes, Scientists Find DNA That Fuels the Spread of Superbugs

CSI Bethesda: Sleuths Used Sequenced Genome to Track Down Killer

Antibiotic/Antimicrobial Resistance

Study Tracks How Superbugs Splash Out of Hospital Sink Drains

CDC: Biggest Threats

Antimicrobial Stewardship: How the Microbiology Laboratory Can Right the Ship

Superbugs Breeding in Hospital Plumbing Put Patients at Risk

Microbiologists at Weill Cornell Use Next-Generation Gene Sequencing to Map the Microbiome of New York City Subways

UCLA Device Enables Diagnosis of Antimicrobial Resistance in Any Setting; Could Save Lives Lost to Antimicrobial Resistant Bacteria

In studies, the automated microbial susceptibility testing device for smartphone performed with 98.2% accuracy, meeting FDA criteria

Imagine doing antimicrobial susceptibility testing outside a clinical laboratory. That’s the goal of researchers on the West Coast who are developing a smartphone-based diagnostic device with the capability of performing this type of point-of-care testing (POCT).

This new mobile POCT device is under development at the University of California-Los Angeles (UCLA). It promises to bring antimicrobial susceptibility testing—a routine procedure in the most medical laboratories—to remote, resource-limited areas of the world.

The device, which attaches directly to a smartphone, contains an automated diagnostic test reader that examines the body’s antimicrobial resistance, according to a UCLA news release. (more…)

Clinical Laboratories and Pharmacies Scramble to Be Ready for the Era of Hospital Antimicrobial Stewardship Programs That Starts on January 1, 2017

All hospital laboratories will be part of these programs, and it is an opportunity for medical laboratory professionals to deliver considerable value, as hospitals take steps to improve the utilization of antibiotics

Clinical laboratories and pharmacies in the nation’s hospitals and health systems have a huge opportunity to deliver substantial value in patient care. That’s because, at the start of 2017, hospitals must put effective antimicrobial stewardship programs (ASPs) in place to meet the new accreditation requirements of Medicare and The Joint Commission.

Overuse and inappropriate use of antibiotics is now considered one of the biggest problems in medicine. “Antibiotics are lifesaving drugs, and if we continue down the road of inappropriate use we’ll lose the most powerful tool we have to fight life-threatening infections,” stated Tom Frieden, MD, MPH, Director, Centers for Disease Control and Prevention (CDC) and Administrator, Agency for Toxic Substances and Disease Registry (ATSDR), in a press release issued by the CDC last May. “Losing these antibiotics would undermine our ability to treat patients [who have] deadly infections, cancer, provide organ transplants, and save victims of burns and trauma.”

Much publicity is devoted to the rise of the increase of antibiotic-resistant organisms. In recognition of this problem, the Centers for Medicare and Medicaid Services (CMS), and The Joint Commission (TJC), took steps to add antimicrobial stewardship program requirements to their respective hospital accreditation programs. (more…)

Researchers at the Stanford University School of Medicine Develop Cutting-Edge Test to Identify Whether an Infection is Bacterial or Viral

Early results are promising and this technology could lead to a clinical laboratory test that would give microbiologists and pathologists a new tool for helping diagnose infections

Infectious disease physicians and clinical laboratory scientists will be interested to learn that researchers at the Stanford University School of Medicine recently developed a new blood test that can identify whether the source of an infection is bacterial or viral.

These findings were published in Science Translational Medicine in July. The paper was authored by Stanford staff members Timothy Sweeney, MD, PhD, and Purvesh Khatri, PhD, Assistant Professor (Research) of Medicine (Biomedical Informatics Research-ITI Institute) and of Biomedical Data Science. Hector Wong, MD, of the University of Cincinnati was the third co-author of the study.

These findings are timely because, starting on January 1, 2017, hospitals and health systems will need to implement more rigorous antimicrobial stewardship programs to comply with new requirements of the Centers for Medicare & Medicaid Services (CMS) and The Joint Commission (TJC). A clinical laboratory test that makes it easier to determine whether the cause of an infection is bacterial or viral would be a welcome tool for physicians, pharmacists, pathologists, and microbiologists involved in a hospital’s infection control program. (more…)

More Use of Whole Gene Sequencing Poised to Play Important New Roles in Microbiology and Medical Laboratory Testing

Cheaper, faster, and more accurate rapid gene sequencing technologies show great promise in identifying infectious disease agents

In clinical laboratories across the nation, microbiology has greatly benefited from the introduction of molecular diagnostics in clinical practice. Now the field of microbiology is poised to undergo a more profound transformation of clinical practice, due to advances in whole genome sequencing.

Leaders in this field are calling these developments “transformative” and say they have the potential to change “all aspects of microbiology.” The driver to this emerging trend is advanced technology that makes it possible to sequence the whole gene sequence of an organism in a day or less, for a cost that is $1,000 and falling rapidly.

In the past six months, microbiologists and pathologists at such hospitals as Methodist Hospital in Houston, Texas, have begun to do whole genome sequencing of microbes found in specimens collected from patients arriving in the emergency room. The New York Times wrote about these developments in a story titled “The New Generation of Microbe Hunters,” that it published on August 29, 2011.

(more…)

;