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Clinical Laboratories and Pathology Groups

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Researchers Find That Antibiotic-Resistant Bacteria Can Persist in the Body for Years

Study results from Switzerland come as clinical laboratory scientists seek new ways to tackle the problem of antimicrobial resistance in hospitals

Microbiologists and clinical laboratory scientists engaged in the fight against antibiotic-resistant (aka, antimicrobial resistant) bacteria will be interested in a recent study conducted at the University of Basel and University Hospital Basel in Switzerland. The epidemiologists involved in the study discovered that some of these so-called “superbugs” can remain in the body for as long as nine years continuing to infect the host and others.

The researchers wanted to see how two species of drug-resistant bacteria—K. pneumoniae and E. coli—changed over time in the body, according to a press release from the university. They analyzed samples of the bacteria collected from patients who were admitted to the hospital over a 10-year period, focusing on older individuals with pre-existing conditions. They found that K. pneumoniae persisted for up to 4.5 years (1,704 days) and E. coli persisted for up to nine years (3,376 days).

“These patients not only repeatedly become ill themselves, but they also act as a source of infection for other people—a reservoir for these pathogens,” said Lisandra Aguilar-Bultet, PhD, the study’s lead author, in the press release.

“This is crucial information for choosing a treatment,” explained Sarah Tschudin Sutter, MD, Head of the Division of Infectious Diseases and Hospital Epidemiology, and of the Division of Hospital Epidemiology, who specializes in hospital-acquired infections and drug-resistant pathogens. Sutter led the Basel University study.

The researchers published their findings in the journal Nature Communications titled, “Within-Host Genetic Diversity of Extended-Spectrum Beta-Lactamase-Producing Enterobacterales in Long-Term Colonized Patients.”

“The issue is that when patients have infections with these drug-resistant bacteria, they can still carry that organism in or on their bodies even after treatment,” said epidemiologist Maroya Spalding Walters, MD (above), who leads the Antimicrobial Resistance Team in the Division of Healthcare Quality Promotion at the federal Centers for Disease Control and Prevention (CDC). “They don’t show any signs or symptoms of illness, but they can get infections again, and they can also transmit the bacteria to other people.” Clinical laboratories working with microbiologists on antibiotic resistance will want to follow the research conducted into these deadly pathogens. (Photo copyright: Centers for Disease Control and Prevention.)

COVID-19 Pandemic Increased Antibiotic Resistance

The Basel researchers looked at 76 K. pneumoniae isolates recovered from 19 patients and 284 E. coli isolates taken from 61 patients, all between 2008 and 2018. The study was limited to patients in which the bacterial strains were detected from at least two consecutive screenings on admission to the hospital.

“DNA analysis indicates that the bacteria initially adapt quite quickly to the conditions in the colonized parts of the body, but undergo few genetic changes thereafter,” the Basel University press release states.

The researchers also discovered that some of the samples, including those from different species, had identical mechanisms of drug resistance, suggesting that the bacteria transmitted mobile genetic elements such as plasmids to each other.

One limitation of the study, the authors acknowledged, was that they could not assess the patients’ exposure to antibiotics.

Meanwhile, recent data from the World Health Organization (WHO) suggests that the COVID-19 pandemic might have exacerbated the challenges of antibiotic resistance. Even though COVID-19 is a viral infection, WHO scientists found that high percentages of patients hospitalized with the disease between 2020 and 2023 received antibiotics.

“While only 8% of hospitalized patients with COVID-19 had bacterial co-infections requiring antibiotics, three out of four or some 75% of patients have been treated with antibiotics ‘just in case’ they help,” the WHO stated in a press release.

WHO uses an antibiotic categorization system known as AWaRe (Access, Watch, Reserve) to classify antibiotics based on risk of resistance. The most frequently prescribed antibiotics were in the “Watch” group, indicating that they are “more prone to be a target of antibiotic resistance and thus prioritized as targets of stewardship programs and monitoring.”

“When a patient requires antibiotics, the benefits often outweigh the risks associated with side effects or antibiotic resistance,” said Silvia Bertagnolio, MD, Unit Head in the Antimicrobial resistance (AMR) Division at the WHO in the press release. “However, when they are unnecessary, they offer no benefit while posing risks, and their use contributes to the emergence and spread of antimicrobial resistance.”

Citing research from the National Institutes of Health (NIH), NPR reported that in the US, hospital-acquired antibiotic-resistant infections increased 32% during the pandemic compared with data from just before the outbreak.

“While that number has dropped, it still hasn’t returned to pre-pandemic levels,” NPR noted.

Search for Better Antimicrobials

In “Drug-Resistant Bacteria Are Killing More and More Humans. We Need New Weapons,” Vox reported that scientists around the world are researching innovative ways to speed development of new antimicrobial treatments.

One such scientist is César de la Fuente, PhD, Presidential Assistant Professor at University of Pennsylvania, whose research team developed an artificial intelligence (AI) system that can look at molecules from the natural world and predict which ones have therapeutic potential.

The UPenn researchers have already developed an antimicrobial treatment derived from guava plants that has proved effective in mice, Vox reported. They’ve also trained an AI model to scan the proteomes of extinct organisms.

“The AI identified peptides from the woolly mammoth and the ancient sea cow, among other ancient animals, as promising candidates,” Vox noted. These, too, showed antimicrobial properties in tests on mice.

These findings can be used by clinical laboratories and microbiologists in their work with hospital infection control teams to better identify patients with antibiotic resistant strains of bacteria who, after discharge, may show up at the hospital months or years later.

—Stephen Beale

Related Information:

Resistant Bacteria Can Remain in The Body for Years

‘Superbugs’ Can Linger in the Body for Years, Potentially Spreading Antibiotic Resistance

Superbug Crisis Threatens to Kill 10 Million Per Year by 2050. Scientists May Have a Solution

Drug-Resistant Bacteria Are Killing More and More Humans. We Need New Weapons.

How the Pandemic Gave Power to Superbugs

WHO Reports Widespread Overuse of Antibiotics in Patients Hospitalized with COVID-19

Measles Cases in the US, Europe, and Other Countries are Increasing, Slowing Progress on Efforts to Eliminate the Disease

Clinical laboratory managers should prepare for an increase in demand for measles testing, especially for children

Clinical laboratory managers should be on the alert for new cases of measles. The US Centers for Disease Control and Prevention (CDC) has reported a surge in the highly infectious disease. Public health experts pointed to declining vaccination coverage as the primary cause. Officials in other countries have also reported outbreaks.

In 2000, the US declared that measles had been eliminated, meaning it “is no longer constantly present in this country,” the CDC stated on its website. However, the agency noted travelers can still bring the disease into the country and that there have been sporadic outbreaks since then.

In a new study, published April 11, 2024, in the CDC’s Morbidity and Mortality Weekly Report (MMWR), the agency reported that it was notified of 97 confirmed cases in the first quarter of 2024. That compares to an average of five cases during the first quarters of 2020 through 2023, the agency stated. In total, 338 cases were reported to the CDC between Jan. 1, 2020, and March 28, 2024, so the latest outbreaks amount to 29%—nearly a third—of the total.

“While the risk for measles for the majority of the US population still remains low, it’s crucial that we take the necessary steps now to prevent the continued spread of measles and maintain elimination in the US,” Adria D. Mathis, MSPH, lead author of the CDC report, told Healthline. Mathis is affiliated with the CDC’s Division of Viral Diseases at the National Center for Immunization and Respiratory Diseases (NCIRD).

“We have seen, in the region, not only a 30-fold increase in measles cases, but also nearly 21,000 hospitalizations and five measles-related deaths. This is concerning,” Hans Henri P. Kluge, MD (above), WHO Regional Director for Europe, told BBC News. “Vaccination is the only way to protect children from this potentially dangerous disease.” Clinical laboratories in the US that identify a case of measles from a positive test must report that result to public health labs. Thus, wise lab managers will track the rise in measles cases and prepare for increased demand for measles testing. (Photo copyright: World Health Organization.)

Renewed Threat to the US, Other Countries

The recent cases “represent a renewed threat to the US elimination status,” and “underscore the need for additional efforts to increase measles, mumps, and rubella (MMR) vaccination coverage, especially among close-knit and under-vaccinated communities,” Mathis told Healthline.

The MMWR report notes that most of the new cases were in persons under age 20, and that almost all were “in persons who were unvaccinated or whose vaccination status was unknown.” Most of the importations, the report states, were “among persons traveling to and from countries in the Eastern Mediterranean and African WHO [World Health Organization] regions; these regions experienced the highest reported measles incidence among all WHO regions during 2021–2022.”

In the US, vaccination coverage has been below 95% for three consecutive years. That is the “estimated population-level immunity necessary to prevent sustained measles transmission,” according to the federal agency. In 12 states and the District of Columbia, the coverage rate is below 90%. In total, “approximately 250,000 kindergarten children [are] susceptible to measles each year,” the CDC report states.

Measles vaccination coverage has declined globally, “from 86% in 2019 to 83% in 2022.” This left nearly 22 million children under the age of one susceptible to the disease, the report notes.

Earlier Measles Outbreaks in the US

The CDC performed its latest analysis following two larger measles outbreaks in 2019 among under-vaccinated populations in New York state.

The Associated Press (AP) reported that the 2019 epidemic, which totaled 1,274 cases nationwide, “was the worst in almost three decades and threatened the United States’ status as a country that has eliminated measles by stopping the continual spread of the measles virus.”

A vaccine for the disease first became available in 1963. Prior to its availability, “there were some three million to four million cases per year,” AP reported. Most people recover, but “in the decade before the vaccine was available, 48,000 people were hospitalized per year. … About 1,000 people developed dangerous brain inflammation from measles each year, and 400 to 500 died,” AP noted, citing CDC data.

US Not Alone in Fight against Measles

Other countries also are reporting spikes in measles cases. In a recently published rapid risk assessment, the Canadian government reported a total of 29 cases as of March 15, 2024, of which 21 were reported since Feb. 28.

“That’s already the largest annual total since 2019 and more than double the number of cases reported last year, as medical experts fear the number will rise while more Canadians travel in and out of the country this month for March break,” CBC News reported.

“New projections from a team at Simon Fraser University (SFU) in British Columbia show the grim possibilities,” CBC News reported. “The modelling suggests that vaccine coverage of less than 85% can lead to dozens of cases within small communities—or even hundreds if immunization rates are lower.”

Numbers are far worse in parts of Europe. In a February 2024 news release, the World Health Organization reported that in 2023, more than 58,000 people in its European region were infected by the disease, “resulting in thousands of hospitalizations and 10 measles-related deaths.”

According to WHO epidemiological data, countries in Central Asia, which is part of WHO’s European region, reported some of the highest numbers:

  • 15,111 in Kazakhstan,
  • 13,735 in Azerbaijan, and
  • 7,044 in Kyrgyzstan.

The Russian Federation reported 12,723 cases and Turkey reported 4,559.

A WHO European Region Measles and Rubella Monthly Update notes that more than half of the regionwide cases—31,428—were reported in the last three months of 2023. More than 15,000 cases were reported in December. That compares to just 163 cases reported in 2021 and 942 in 2022. Nearly half of the cases were among children under the age of five.

Lack of Vaccinations among Children Blamed for Outbreaks

One factor that has led to the increase in measles cases was the disruption to immunization services caused by the COVID-19 pandemic. “This has resulted in a significant accumulation of susceptible children who have missed their routine vaccinations against measles and other vaccine-preventable diseases,” the WHO reported.

Among the region’s 53 member states, 33 had eliminated measles, WHO reported, but “this achievement remains fragile. To retain this status, a country must ensure that transmission of the virus following any importation is stopped within 12 months from the first reported case.”

In the UK, which reported 231 cases last year, the National Health Service has launched a campaign to improve vaccination rates, the BBC reported, noting that “more than 3.4 million children aged under 16 are unprotected and at risk of becoming ill.”

However, a public health campaign built on vaccination is successful only if a high rate of individuals get vaccinated. The Baby Boomer and Gen X generations had high rates of vaccination for smallpox, polio, etc. because the parents saw individuals in their family and neighborhood who became infected and suffered lifechanging consequences. They recognized that vaccination was a simple thing to provide protection from a potentially deadly infection.

Clinical laboratory managers and pathologists will want to follow the CDC’s ongoing reports of the number of cases of measles in this country. Today, the absolute number of new measles cases is relatively small. At the same time, in communities experiencing an outbreak of even a few measles cases, physicians may want to increase the volume of measles tests they order for their patients.

—Stephen Beale

Related Information:

Canada Heading Toward Major Measles Outbreak without Vaccine Boost, New Modelling Suggests

A Review of the Resurgence of Measles, a Vaccine-Preventable Disease, as Current Concerns Contrast with Past Hopes for Measles Elimination

Alarming 45-Fold Rise in Measles in Europe-WHO

US Declared Measles Gone in 2000—New Outbreaks May Change That

US Measles Cases Are Up in 2024. What’s Driving the Increase?

CDC Warns That Measles Spike Poses A ‘Renewed Threat’ To the Disease’s Elimination

Measles Vaccine Campaign Targets Unprotected Millions

UK Study Claims AI Reading of CT Scans Almost Twice as Accurate at Grading Some Cancers as Clinical Laboratory Testing of Sarcoma Biopsies

Radiological method using AI algorithms to detect, locate, and identify cancer could negate the need for invasive, painful clinical laboratory testing of tissue biopsies

Clinical laboratory testing of cancer biopsies has been the standard in oncology diagnosis for decades. But a recent study by the Institute of Cancer Research (ICR) and the Royal Marsden NHS Foundation Trust in the UK has found that, for some types of sarcomas (malignant tumors), artificial intelligence (AI) can grade the aggressiveness of tumors nearly twice as accurately as lab tests, according to an ICR news release.

This will be of interest to histopathologists and radiologist technologists who are working to develop AI deep learning algorithms to read computed tomography scans (CT scans) to speed diagnosis and treatment of cancer patients.

“Researchers used the CT scans of 170 patients treated at The Royal Marsden with the two most common forms of retroperitoneal sarcoma (RPS)—leiomyosarcoma and liposarcoma—to create an AI algorithm, which was then tested on nearly 90 patients from centers across Europe and the US,” the news release notes.

The researchers then “used a technique called radiomics to analyze the CT scan data, which can extract information about the patient’s disease from medical images, including data which can’t be distinguished by the human eye,” the new release states.

The scientists published their findings in The Lancet Oncology titled, “A CT-based Radiomics Classification Model for the Prediction of Histological Type and Tumor Grade in Retroperitoneal Sarcoma (RADSARC-R): A Retrospective Multicohort Analysis.”

The research team sought to make improvements with this type of cancer because these tumors have “a poor prognosis, upfront characterization of the tumor is difficult, and under-grading is common,” they wrote. The fact that AI reading of CT scans is a non-invasive procedure is major benefit, they added.

Christina Messiou, MD

“This is the largest and most robust study to date that has successfully developed and tested an AI model aimed at improving the diagnosis and grading of retroperitoneal sarcoma using data from CT scans,” said the study’s lead oncology radiologist Christina Messiou, MD, (above), Consultant Radiologist at The Royal Marsden NHS Foundation Trust and Professor in Imaging for Personalized Oncology at The Institute of Cancer Research, London, in a news release. Invasive medical laboratory testing of cancer biopsies may eventually become a thing of the past if this research becomes clinically available for oncology diagnosis. (Photo copyright: The Royal Marsden.)

Study Details

RPS is a relatively difficult cancer to spot, let alone diagnose. It is a rare form of soft-tissue cancer “with approximately 8,600 new cases diagnosed annually in the United States—less than 1% of all newly diagnosed malignancies,” according to Brigham and Women’s Hospital.

In their published study, the UK researchers noted that, “Although more than 50 soft tissue sarcoma radiomics studies have been completed, few include retroperitoneal sarcomas, and the majority use single-center datasets without independent validation. The limited interpretation of the quantitative radiological phenotype in retroperitoneal sarcomas and its association with tumor biology is a missed opportunity.”

According to the ICR news release, “The [AI] model accurately graded the risk—or how aggressive a tumor is likely to be—[in] 82% of the tumors analyzed, while only 44% were correctly graded using a biopsy.”

Additionally, “The [AI] model also accurately predicted the disease type [in] 84% of the sarcomas tested—meaning it can effectively differentiate between leiomyosarcoma and liposarcoma—compared with radiologists who were not able to diagnose 35% of the cases,” the news release states.

“There is an urgent need to improve the diagnosis and treatment of patients with retroperitoneal sarcoma, who currently have poor outcomes,” said the study’s first author Amani Arthur, PhD, Clinical Research Fellow at The Institute of Cancer Research, London, and Registrar at The Royal Marsden NHS Foundation Trust, in the ICR news release.

“The disease is very rare—clinicians may only see one or two cases in their career—which means diagnosis can be slow. This type of sarcoma is also difficult to treat as it can grow to large sizes and, due to the tumor’s location in the abdomen, involve complex surgery,” she continued. “Through this early research, we’ve developed an innovative AI tool using imaging data that could help us more accurately and quickly identify the type and grade of retroperitoneal sarcomas than current methods. This could improve patient outcomes by helping to speed up diagnosis of the disease, and better tailor treatment by reliably identifying the risk of each patient’s disease.

“In the next phase of the study, we will test this model in clinic on patients with potential retroperitoneal sarcomas to see if it can accurately characterize their disease and measure the performance of the technology over time,” Arthur added.

Importance of Study Findings

Speed of detection is key to successful cancer diagnoses, noted Richard Davidson, Chief Executive of Sarcoma UK, a bone and soft tissue cancer charity.

“People are more likely to survive sarcoma if their cancer is diagnosed early—when treatments can be effective and before the sarcoma has spread to other parts of the body. One in six people with sarcoma cancer wait more than a year to receive an accurate diagnosis, so any research that helps patients receive better treatment, care, information and support is welcome,” he told The Guardian.

According to the World Health Organization, cancer kills about 10 million people worldwide every year. Acquisition and medical laboratory testing of tissue biopsies is both painful to patients and time consuming. Thus, a non-invasive method of diagnosing deadly cancers quickly, accurately, and early would be a boon to oncology practices worldwide and could save thousands of lives each year.

—Kristin Althea O’Connor

Related Information:

AI Twice as Accurate as a Biopsy at Grading Aggressiveness of Some Sarcomas

AI Better than Biopsy at Assessing Some Cancers, Study Finds

AI Better than Biopsies for Grading Rare Cancer, New Research Suggests

A CT-based Radiomics Classification Model for the Prediction of Histological Type and Tumor Grade in Retroperitoneal Sarcoma (RADSARC-R): A Retrospective Multicohort Analysis

AMA Issues Proposal to Help Circumvent False and Misleading Information When Using Artificial Intelligence in Medicine

Pathologists and clinical laboratory managers will want to stay alert to the concerns voiced by tech experts about the need to exercise caution when using generative AI to assist medical diagnoses

Even as many companies push to introduce use of GPT-powered (generative pre-trained transformer) solutions into various healthcare services, both the American Medical Association (AMA) and the World Health Organization (WHO) as well as healthcare professionals urge caution regarding use of AI-powered technologies in the practice of medicine. 

In June, the AMA House of Delegates adopted a proposal introduced by the American Society for Surgery of the Hand (ASSH) and the American Association for Hand Surgery (AAHS) titled, “Regulating Misleading AI Generated Advice to Patients.” The proposal is intended to help protect patients from false and misleading medical information derived from artificial intelligence (AI) tools such as GPTs.

GPTs are an integral part of the framework of a generative artificial intelligence that creates text, images, and other media using generative models. These neural network models can learn the patterns and structure of inputted information and then develop new data that contains similar characteristics.

Through their proposal, the AMA has developed principles and recommendations surrounding the benefits and potentially harmful consequences of relying on AI-generated medical advice and content to advance diagnoses.

Alexander Ding, MD

“We’re trying to look around the corner for our patients to understand the promise and limitations of AI,” said Alexander Ding, MD (above), AMA Trustee and Associate Vice President for Physician Strategy and Medical Affairs at Humana, in a press release. “There is a lot of uncertainty about the direction and regulatory framework for this use of AI that has found its way into the day-to-day practice of medicine.” Clinical laboratory professionals following advances in AI may want to remain informed on the use of generative AI solutions in healthcare. (Photo copyright: American Medical Association.)

Preventing Spread of Mis/Disinformation

GPTs are “a family of neural network models that uses the transformer architecture and is a key advancement in artificial intelligence (AI) powering generative AI applications such as ChatGPT,” according to Amazon Web Services.

In addition to creating human-like text and content, GPTs have the ability to answer questions in a conversational manner. They can analyze language queries and then predict high-quality responses based on their understanding of the language. GPTs can perform this task after being trained with billions of parameters on massive language datasets and then generate long responses, not just the next word in a sequence. 

“AI holds the promise of transforming medicine,” said diagnostic and interventional radiologist Alexander Ding, MD, AMA Trustee and Associate Vice President for Physician Strategy and Medical Affairs at Humana, in an AMA press release.

“We don’t want to be chasing technology. Rather, as scientists, we want to use our expertise to structure guidelines, and guardrails to prevent unintended consequences, such as baking in bias and widening disparities, dissemination of incorrect medical advice, or spread of misinformation or disinformation,” he added.

The AMA plans to work with the federal government and other appropriate organizations to advise policymakers on the optimal ways to use AI in healthcare to protect patients from misleading AI-generated data that may or may not be validated, accurate, or relevant.

Advantages and Risks of AI in Medicine

The AMA’s proposal was prompted by AMA-affiliated organizations that stressed concerns about the lack of regulatory oversight for GPTs. They are encouraging healthcare professionals to educate patients about the advantages and risks of AI in medicine. 

“AI took a huge leap with large language model tool and generative models, so all of the work that has been done up to this point in terms of regulatory and governance frameworks will have to be treated or at least reviewed with this new lens,” Sha Edathumparampil, Corporate Vice President, Digital and Data, Baptist Health South Florida, told Healthcare Brew.

According to the AMA press release, “the current limitations create potential risks for physicians and patients and should be used with appropriate caution at this time. AI-generated fabrications, errors, or inaccuracies can harm patients, and physicians need to be acutely aware of these risks and added liability before they rely on unregulated machine-learning algorithms and tools.”

According to the AMA press release, the organization will propose state and federal regulations for AI tools at next year’s annual meeting in Chicago.

In a July AMA podcast, AMA’s President, Jesse Ehrenfeld, MD, stressed that more must be done through regulation and development to bolster trust in these new technologies.

“There’s a lot of discomfort around the use of these tools among Americans with the idea of AI being used in their own healthcare,” Ehrenfeld said. “There was a 2023 Pew Research Center poll [that said] 60% of Americans would feel uncomfortable if their own healthcare provider relied on AI to do things like diagnose disease or recommend a treatment.”

WHO Issues Cautions about Use of AI in Healthcare

In May, the World Health Organization (WHO) issued a statement advocating for caution when implementing AI-generated large language GPT models into healthcare.

A current example of such a GPT is ChatGPT, a large language-based model (LLM) that enables users to refine and lead conversations towards a desired length, format, style, level of detail and language. Organizations across industries are now utilizing GPT models for Question and Answer bots for customers, text summarization, and content generation and search features. 

“Precipitous adoption of untested systems could lead to errors by healthcare workers, cause harm to patients, erode trust in AI, and thereby undermine (or delay) the potential long-term benefits and uses of such technologies around the world,” commented WHO in the statement.

WHO’s concerns regarding the need for prudence and oversight in the use of AI technologies include:

  • Data used to train AI may be biased, which could pose risks to health, equity, and inclusiveness.
  • LLMs generate responses that can appear authoritative and plausible, but which may be completely incorrect or contain serious errors.
  • LLMs may be trained on data for which consent may not have been given.
  • LLMs may not be able to protect sensitive data that is provided to an application to generate a response.
  • LLMs can be misused to generate and disseminate highly convincing disinformation in the form of text, audio, or video that may be difficult for people to differentiate from reliable health content.

Tech Experts Recommended Caution

Generative AI will continue to evolve. Therefore, clinical laboratory professionals may want to keep a keen eye on advances in AI technology and GPTs in healthcare diagnosis.

“While generative AI holds tremendous potential to transform various industries, it also presents significant challenges and risks that should not be ignored,” wrote Edathumparampil in an article he penned for CXOTECH Magazine. “With the right strategy and approach, generative AI can be a powerful tool for innovation and differentiation, helping businesses to stay ahead of the competition and better serve their customers.”

GPT’s may eventually be a boon to healthcare providers, including clinical laboratories, and pathology groups. But for the moment, caution is recommended.

JP Schlingman

Related Information:

AMA Adopts Proposal to Protect Patients from False and Misleading AI-generated Medical Advice

Regulating Misleading AI Generated Advice to Patients

AMA to Develop Recommendations for Augmented Intelligence

What is GPT?

60% of Americans Would Be Uncomfortable with Provider Relying on AI in Their Own Health Care

Navigating the Risks of Generative AI: A Guide for Businesses

Contributed: Top 10 Use Cases for AI in Healthcare

Anatomic Pathology at the Tipping Point? The Economic Case for Adopting Digital Technology and AI Applications Now

ChatGPT, AI in Healthcare and the future of Medicine with AMA President Jesse Ehrenfeld, MD, MPH

What is Generative AI? Everything You Need to Know

WHO Calls for Safe and Ethical AI for Health

GPT-3

Researchers Use Whole Genome Sequencing to Make Surprising Discovery about Hospital-Acquired C. Diff Infections

By analyzing strains of the bacterium from a hospital ICU, the scientists learned that most infections were triggered within patients, not from cross-transmission

Tracking the source of Hospital-acquired infections (HAI) has long been centered around the assumption that most HAIs originate from cross-transmission within the hospital or healthcare setting. And prevention measures are costly for hospitals and medical laboratories. However, new research puts a surprising new angle on a different source for some proportion of these infections.

The study suggests that most infections caused by Clostridioides difficile (C. Diff), the bacterium most responsible for HAIs, arise not from cross-transmission in the hospital, but within patients who already carry the bacterium.

The research team, led by immunologist Evan Snitkin, PhD, and microbiologist Vincent Young, MD, PhD, both from the University of Michigan (UM), and epidemiologist Mary Hayden, MD, of Rush University Medical Center in Chicago, analyzed fecal samples from more than 1,100 patients in Rush Medical Center’s intensive care unit over a nine-month period.

A researcher performed whole genome sequencing on 425 strains of the bacterium isolated from the samples and found “very little evidence that the strains of C. diff from one patient to the next were the same, which would imply in-hospital acquisition,” according to a UM news story.

“In fact, there were only six genomically supported transmissions over the study period. Instead, people who were already colonized were at greater risk of transitioning to infection,” UM stated.

Arianna Miles-Jay, PhD, a postdoctoral fellow in The Snitkin Lab at the University of Michigan and Manager of the Genomic Analysis Unit at the Michigan Department of Health and Human Services, performed the genomic sequencing. “By systematically culturing every patient, we thought we could understand how transmission was happening. The surprise was that, based on the genomics, there was very little transmission,” she said in the UM news story.

The researchers published their findings in the journal Nature Medicine titled, “Longitudinal Genomic Surveillance of Carriage and Transmission of Clostridioides Difficile in an Intensive Care Unit.”

Evan Snitkin, PhD

“Something happened to these patients that we still don’t understand to trigger the transition from C. diff hanging out in the gut to the organism causing diarrhea and the other complications resulting from infection,” said Evan Snitkin, PhD (above), Associate Professor of Microbiology and Immunology, and Associate Professor of Internal Medicine, Division of Infectious Diseases at University of Michigan, in a UM news story. Medical laboratories involved in hospital-acquired infection prevention understand the importance of this research and its effect on patient safety. (Photo copyright: University of Michigan.)

Only a Fraction of HAIs Are Through Cross-Transmission

In the study abstract, the researchers wrote that “despite enhanced infection prevention efforts, Clostridioides difficile remains the leading cause of healthcare-associated infections in the United States.”

Citing data from the US Centers for Disease Control and Prevention (CDC), HealthDay reported that “nearly half a million C. diff infections occur in the United States each year. Between 13,000 and 16,000 people die from the bacterium, which causes watery diarrhea and inflammation of the colon. Many of these infections and deaths have been blamed on transmission between hospitalized patients.”

The new study, however, notes that 9.3% of the patients admitted to the ICU carried toxigenic (produces toxins) C. diff, but only 1% acquired it via cross-transmission. The carriers, the study authors wrote, “posed minimal risk to others,” but were 24 times more likely to develop a C. diff infection than non-carriers.

“Our findings suggest that measures in place in the ICU at the time of the study—high rates of compliance with hand hygiene among healthcare personnel, routine environmental disinfection with an agent active against C. diff, and single patient rooms —were effective in preventing C. diff transmission,” Snitkin told HealthDay. “This indicates that to make further progress in protecting patients from developing C. diff infections will require improving our understanding of the triggers that lead patients asymptomatically carrying C. diff to transition to having infections.”

Recognizing Risk Factors

Despite the finding that infections were largely triggered within the patients, the researchers still emphasized the importance of taking measures to prevent hospital-acquired infections.

“In fact, the measures in place in the Rush ICU at the time of the study—high rates of compliance with hand hygiene among healthcare personnel, routine environmental disinfection with an agent active against C. diff, and single patient rooms—were likely responsible for the low transmission rate,” the UM news story noted.

One expert not involved with the study suggested that hospitals’ use of antibiotics may be a factor in causing C. diff carriers to develop infections.

“These findings suggest that while we should continue our current infection prevention strategies, attention should also be given to identifying the individuals who are asymptomatic carriers and finding ways to reduce their risk of developing an infection, like carefully optimizing antibiotic usage and recognizing other risk factors,” Hannah Newman, Senior Director of Infection Prevention at Lenox Hill Hospital in New York City, told HealthDay.

Snitkin, however, told HealthDay that other factors are likely at play. “There is support for antibiotic disruption of the microbiota being one type of trigger event, but there is certainly more to it than that, as not every patient who carries C. diff and receives antibiotics will develop an infection.”

Another expert not involved with the study told HealthDay that “many patients are already colonized,” especially older ones or those who have been previously hospitalized.

“A lot of their normal flora in their GI tract can be altered either through surgery or antibiotics or some other mechanism, and then symptoms occur, and that’s when they are treated with antibiotics,” said Donna Armellino, RN, Senior VP of Infection Prevention at Northwell Health in Manhasset, New York.

Whatever is taking place, hospital-acquired infections kill thousands of people every years. It’s on the federal Centers for Medicare and Medicaid Services’ (CMS) “never event” list of hospital-acquired conditions (HOC) that should never happen to hospital patients. This affects reimbursement to hospitals for treatment of infections under Medicare’s Hospital-Acquired Condition Reduction Program

This research also demonstrates the value of faster, cheaper, more accurate gene sequencing for researching life-threatening conditions. Microbiologists, Clinical laboratory scientists, and pathologists will want monitor further developments involving these findings as researchers from University of Michigan and Rush University Medical Center continue to learn more about the source of C. diff infections.

—Stephen Beale

Related Information:

The Surprising Origin of a Deadly Hospital Infection

Patient-to-Patient Transmission Not to Blame for Most C. Difficile Infections in Hospitals

Longitudinal Genomic Surveillance of Carriage and Transmission of Clostridioides difficile in an Intensive Care Unit

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