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.
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.”
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;
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.
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.
Owlstone Medical’s breath biopsy platform takes aim at breath biomarkers for an earlier diagnosis of cancer; could it supplant tissue biopsies sent to pathology labs?
For many years, medical laboratory scientists and pathologists have known that human breath contains molecules and substances that have the potential to be used as biomarkers for detecting different diseases and health conditions. The challenge was always how to create clinical laboratory test technology that could use human breath samples to produce accurate and clinically useful information.
Stated differently, breath, the essence of life, may contain medical laboratory test biomarkers that could provide early-detection advantages to pathology groups in their fight against cancer. Now diagnostics company Owlstone Medical—developer of the Breath Biopsy platform—is about to conduct a clinical study in collaboration with the United Kingdom’s (UK’s) National Health Service (NHS) and others to demonstrate the effectiveness of its breath-based diagnostic tests.
Anatomic pathology groups and clinical laboratory leaders know human breath contains volatile organic compounds (VOCs) that can be useful diagnostic biomarkers for medical laboratory testing. Many possible breath tests have been researched. One such test, the urea breath test for detecting Helicobacter pylori (H. pylori), has been in clinical use for 20 years. As part of the test, patients with suspect stomach ulcers or other gastric concerns, swallow a tablet with urea and exhale carbon dioxide that is measured for H. pylori bacteria.
According to an Owlstone Medical news release, the new study, called the “PAN Cancer Trial for Early Detection of Cancer in Breath,” will explore the ability of Owlstone Medical’s Breath Biopsy platform to detect cancers of the:
Current medical care standards call for these cancers to be diagnosed by analyzing biopsied tissue specimens. If Owlstone Medical’s breath test performs well during trial, it could provide advantages over traditional tissue-based cancer testing that include:
A non-invasive approach to finding cancer earlier;
A lower price point as compared to a tissue biopsy cancer test; and
Faster return of test results, since tissue would not need to be collected from patients during surgical procedures and sent to medical laboratories for analysis.
“By 2030, the number of new cancer cases per year is expected to rise to around 22-million globally. Some cancers are diagnosed very late when there are few treatment options available. Non-invasive detection of cancer in breath could make a real difference to survival,” stated Richard Gilbertson, PhD, Li Ka Shing Chair of Oncology, Director of the CRUK Cambridge Center, and Oncology Department Head at University of Cambridge, in the news release.
How the Breath Biopsy Platform Works
The Breath Biopsy platform relies on Owlstone Medical’s Field Asymmetric Ion Mobility Spectrometry (FAIMS) technology, which the diagnostics company explains is a “fast means to identifying volatile organic compound biomarkers in breath.”
Billy Boyle (above), co-founder and Chief Executive Officer at Owlstone Medical, demonstrates the ReCIVA Breath Sampler. “Positive results from the PAN cancer trial could be game-changing in the fight against cancer,” he noted in the news release. “Success in this study supports our vision of saving 100,000 lives and $1.5 billion in healthcare costs.” This technology has the potential to be disruptive to anatomic pathology, which relies on the analysis of biopsied tissue to detect cancer. (Photo copyright: Owlstone Medical.)
Here is how FAIMS works in the Breast Biopsy platform, according to the Owlstone Medical website:
Gases are exchanged between circulating blood and inhaled fresh air in the lungs;
VOC biomarkers in the body’s circulation system pass into air in the lungs, along with oxygen, carbon dioxide, and other gases;
Exhaled breath contains those biomarkers exiting the body;
Because it takes one minute for blood to flow around the body, a breath sample during that time makes possible collection and analysis of VOC biomarkers of any part of the body touched by the circulatory system.
One publication compared the capture of VOCs to liquid biopsies, another possible non-invasive cancer diagnostic technique being widely researched.
“The advantage to VOCs is that they can be picked up earlier than signatures searched for in liquid biopsies, meaning cancer can be diagnosed earlier and treated more effectively,” reported Pharmaphorum in its analysis of five technology companies fighting cancer.
As part of the clinical trial, breath samples will be collected in clinic settings with the hand-held Owlstone Medical ReCIVA Breath Sampler (equipped with a dime-sized FAIMS silicon chip). The samples will come from people with a suspected cancer diagnosis who are seeking care at Cambridge University Hospital’s Addenbrooke’s Hospital. To test reliability of the biomarkers, breath samples from patients with cancer and without cancer will be analyzed.
“You’re seeing a convergence of technology now, so we can actually run large-scale clinical studies to get the data to prove odor analysis has real utility,” stated Owlstone Medical co-founder and Chief Executive Officer Billy Boyle, in a New York Times article.
Breath Tests Popular Area for Research
The company’s Breath Biopsy platform is also being tested in a clinical trial for lung cancer being funded by the UK’s NHS. The study involves 3,000 people, the New York Times article reported.
Breath tests in general—because they generally are non-invasive, fast, and cost-effective—have been the subject of several other Dark Daily e-briefings as well, including those about:
Owlstone Medical’s ability to get backing from Britain’s NHS, as well as investments to the tune of $23.5 million (the most recent coming from Aviva Ventures) is a positive sign. That Owlstone Medical’s Breath Biopsy platform is credible enough to attract such respected collaborators in the cancer trials as the Cancer Research UK Cambridge Institute (CRUK), University of Cambridge, and Cambridge University Hospitals (CUH) NHS Foundation Trust is evidence that the company’s diagnostic technology is considered to have good potential for use in clinical care.
Medical laboratory managers and pathology group stakeholders will want to monitor these developments closely. Once proven in clinical trials such as those mentioned above, breath tests have the potential to supplant other medical laboratory diagnostics and perhaps lower the number of traditional biopsies sent to labs for diagnosis of cancer.
Decline in hospital-acquired conditions (HACs) overall since 2010 attributed to increased attention to safety protocols and practices by hospital staff in cooperation with clinical laboratory services
It’s now been almost nine years since the Medicare Program stopped paying hospitals and other providers for certain hospital-acquired conditions (HACs). Included in this list are hospital-acquired infections (HAIs). The goal is to substantially reduce the number of HACs and HAIs, thus improving patient outcomes, while substantially reducing the healthcare costs associated with these conditions.
So, almost nine years into these programs, has there been progress on these goals? This is a question of key interest to Medical laboratories and pathology groups because they have a front-line role in working with clinicians to diagnose and treat HAIs, while also looking to identify the transmission of HAIs within the hospital.
A recent report by the Agency for Healthcare Research and Quality (AHRQ), a division of the US Department of Health and Human Service (HHS), indicates that there has been progress in the goal of reducing HACs. The AHRQ report noted a 21% decline in HACs between 2010 and 2015. Data collected during that time indicates a reduction of more than 3.1 million HACs and nearly 125,000 patient deaths due to HACs.
In 2015 alone, nearly one million fewer HAC incidents occurred. The reduction saved “approximately $28 billion in healthcare costs,” an outcome which, the AHRQ report notes, is the result of increased attention to safety protocols in hospitals and a “period of concerted effort by hospitals throughout the country to reduce adverse events.”
Clinical Pathologists/Laboratories Play Key Role in HAI Prevention
Though many reported incidents are associated with adverse drug events, HAIs have been significantly reduced in recent years due to focused efforts on infection prevention. The report notes that clinical pathologists have become vital players in infection prevention programs, and that increased coordination between hospital medical laboratories and clinicians played a crucial role in the reduction.
Eileen O’Rourke is an Infection Preventionist at the Lankenau Medical Center in Philadelphia. And she has served as a leader and consultant for hospital-based infection prevention programs in Pennsylvania since 1984. In an article on the Wolters Kluwer Pharmacy OneSource blog, O’Rourke noted that successful infection prevention and control requires development of “a highly visible and administratively supported infection prevention and control program with qualified and trained personnel.” Clinical pathologists are part of that support team, providing surveillance, testing, and interpretation of data essential for identifying epidemiological origins of infection and pathogen distribution. And the vital services that clinical laboratories provide to reduce HAIs center on surveillance, prevention, and control.
The chart above was calculated on US Dollars in 2012. Since then, thanks to contributions by medical laboratories and pathologists in collaboration with hospitals, those costs have decreased significantly. (Image copyright: MLive.com.)
In an article for Lab Testing Matters, John Daly MD, Chief Medical Officer at the Commission on Office Laboratory Accreditation, and former Director of Clinical Laboratories for the Duke University Health System, highlights the importance of surveillance. He states that it is “an essential element of an infection control program” providing “data to identify infected patients and determine the site of infection” as well as “factors that contributed to the infection.” Medical laboratories must, Daly stresses, provide “easy access to high-quality and timely data and give guidance and support on how to use its resources for epidemiologic purposes.”
Daly argues that medical laboratories function as liaisons to clinical services, working to “improve the quality of specimens sent to the laboratory and promoting appropriate use of cultures and other laboratory tests.” The laboratory should, according to Daly, be involved in all aspects of the infection control programs. This ensures:
Proper specimen collection;
Accurate and rapid testing; and
Accurate reporting of laboratory data.
Laboratory Data Provide ‘Early Warning’ for HAI Surveillance Systems
Robert A. Weinstein, MD, wrote in his 1978 article, “The Role of the Microbiology Laboratory in Surveillance and Control of Nosocomial Infections,” that medical laboratories and pathologists are central to prevention and control of HAIs. Laboratory records, Weinstein remarked, serve as important data sources that can identify early spread of infection, thus becoming an “early warning system” for a potential outbreak of infections. The sampling that laboratories perform identifies not only the strain of infection, but the method by which infection is spread, and the best treatment options. Nearly 40 years later his statements ring truer than ever, as anatomic pathology laboratory data continues to reveal patterns of infection faster and more precisely than ever before.
Sarah Mahoney, PhD, is a research scientist at Navitor Pharmaceuticals in Cambridge, Mass. In an article published in the American Journal of Clinical Pathology, she states that in surveilling patterns of infection, pathologists also decipher the source of infection. Mahoney wrote that it is “necessary to identify the causative organism” for surveillance and management control of HAIs. She also noted that pathologists must strive to discriminate between “hospital- and community-acquired infection” in order to provide clinicians with guidance for treatment, and to map “infection transmission within a clinical setting.”
Hospitals Rely on Medical Laboratories and Pathologists to Help Reduce HAIs
The concerted effort to reduce HACs and HAIs was inspired by incentives put forth by the US government. In 2008-2009, the Centers for Medicare and Medicaid Services (CMS) ceased paying for hospital-acquired conditions, including HAIs. Since that time, hospitals have worked to prevent and better manage HAIs. In the years since those incentives went into effect, hospitals have increasingly relied on medical laboratories and pathologists to provide necessary testing to prevent HAIs.
The CDC’s Antimicrobial Stewardship Programs create a further need for lab professionals to be involved in the identification, prevention, and treatment of HAIs. The core elements of the program state that the role of diagnostic laboratory testing—especially rapid diagnostic tests—is imperative in providing the necessary data needed to combat HAIs. The pressure is on for hospitals to reduce HAIs further to save lives and reduce costs. Thus, there is increased pressure on medical laboratories as well.
Larry Massie, MD, Professor of Pathology at the University of New Mexico, and Chair of Pathology and Laboratory Medicine for the New Mexico VA Health Care System in Albuquerque, states that turn-around time is crucial for HAIs, but that laboratories often have difficulty keeping up with large volumes of samples. Massie suggests the use of new technologies could speed up turnaround time, particular for large healthcare providers.
The fight to reduce HAIs and HACs is showing significant progress, and clinical laboratories, working in tandem with clinicians and prevention programs, are a fundamental part of the success of HAI reduction. Clinical pathologists and laboratories often are the front line in prevention and management of HAIs, and the work they do in identifying infections is essential in the assessment and control of those infections.
Latest research provides new opportunities for clinical laboratories to demonstrate how testing can help curb hospital-acquired infections
Pathologists, microbiologists, and other healthcare providers have long been aware that hospital patients taking antibiotics are at higher risk of contracting the potentially deadly Clostridium difficile infection (C. diff). But new research adds an interesting twist to this issue.
Recent research indicates that being a “second user” of a bed may be another risk factor for acquiring the disease. This will give clinical laboratory professionals, microbiologists, and others on the front lines of hospital infection control programs another factor to consider when working to halt the spread of hospital-acquired infections (HAIs).
The recent study was published online in JAMA Internal Medicine. It shows that patients put in a hospital bed previously occupied by someone given antibiotics are 22% more likely to develop the C. difficile infection, even if they do not themselves receive antibiotics. (more…)
