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University of Edinburgh Study Finds Antimicrobial Bacteria in Hospital Wastewater in Research That Has Implications for Microbiologists

The highly infectious bacteria can survive treatment at local sewage plants and enter the food chain of surrounding populations, the study revealed

Researchers at the University of Edinburgh (UE) in Scotland found large amounts of antimicrobial-resistance (AMR) genes in hospital wastewater. These findings will be of interest to microbiologists and clinical laboratory managers, as the scientists used metagenomics to learn “how abundances of AMR genes in hospital wastewater are related to clinical activity.”

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.

Using Metagenomics to Surveille Hospital Patients

Antimicrobial resistance is creating super bacteria that are linked to increases in hospital-acquired infections (HAIs) nationwide. Dark Daily has reported many times on the growing danger of deadly antimicrobial resistant “super bugs,” which also have been found in hospital ICUs (see “Potentially Fatal Fungus Invades Hospitals and Public Is Not Informed,” August 26, 2019.)

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.”

AMR bacteria also are being spread by human touch throughout city subways, bus terminals, and mass transportation, making it difficult for the Centers for Disease Control and Prevention (CDC) to identify the source of the outbreak and track and contain it. This has led microbiologists to conduct similar studies using genetic sequencing to identify ways to track pathogens through city infrastructures and transportation systems. (See, “Microbiologists at Weill Cornell Use Next-Generation Gene Sequencing to Map the Microbiome of New York City Subways,” December 13, 2013.)

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;
  • Finally, they complete the genetic sequencing on an Illumina HiSeq4000 System.

The researchers reported these findings:

  • 181 clinical isolates were identified in the samples of wastewater;
  • 1,047 unique bacterial genes were detected across all samples;
  • 19 genes made up more than 60% of bacteria in samples;
  • Overriding bacteria identified as Pseudomonas and Acinetobacter environmental samples (Pseudomonas fluorescens and Acinetobacter johnsonii) were most likely from hospital pipes;
  • Gut-related bacteria—Faecalibacterium, Bacteroides, Bifidobacterium, and Escherichia, were more prevalent in the hospital samples than in those from the community;
  • 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.  

—Donna Marie Pocius

Related Information:

Secrets of the Hospital Underbelly: Abundance of Antimicrobial-Resistance Genes in Hospital Wastewater Reflects Hospital Microbial Use and Inpatient Length of Stay

Antibiotic-Resistance Genes Trouble Hospital Water; Study Emphasizes Importance of Antibiotic Stewardship Programs, Expert Says

Fact Sheet: Antibiotic Resistance

United States Gathers 350 Commitments to Combat Antibiotic Resistance, Action Must Continue

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

Dark Daily E-briefings: Hospital-Acquired Infections

NIH Study Reveals Surprising New Source of Antibiotic Resistance that Will Interest Microbiologists and Medical Laboratory Scientists

Leapfrog Group Report Shows Hospitals Failing to Eliminate Hospital-Acquired Infections; Medical Laboratories Can Help Providers’ Antimicrobial Stewardship Programs

Contrary to CMS and Joint Commission programs implemented in 2017 to reduce them, incidents of hospital-acquired infections have risen for the past few years

Clinical laboratories and anatomic pathologists know that hospital-acquired infections (HAIs) can be deadly, not just for patients, but for their caregivers and families as well. Even one HAI is too many. Thus, the federal Centers for Medicare and Medicaid Services (CMS) required healthcare organizations to upgrade their antimicrobial stewardship (AMS) programs to meet CMS requirements and Joint Commission accreditation starting in 2017.

Nevertheless, a recent Leapfrog Group report indicates hospitals are finding it increasingly difficult to remove infections all together. This has many healthcare leaders concerned.

The report, which was analyzed by Castlight Health, states that the number of hospitals reporting zero infections has declined significantly since 2015, according to a news release. According to the Leapfrog Group’s report:

  • Two million people acquire HAIs every year;
  • 90,000 people die annually from HAIs;
  • HAI costs range from $1,000 to $50,000 depending on the infection.

Hospitals spend $28 to $45 billion annually on HAI costs, Healthcare Finance reported.

“I think it’s far too easy to let something slip, so it’s clear that there really needs to be a renewed focus on getting back to zero. We do still see some hospitals that are getting to zero, so it’s clearly possible,” Erica Mobley (above), Leapfrog Group’s Director of Operations, told Fierce Healthcare. (Photo copyright: LinkedIn.)

Regressing Instead of Progressing Toward Total HAI Elimination

Leapfrog Group’s report is based on 2017 hospital survey data submitted by 2,000 providers. The data indicates that in just two years the number of hospitals reporting zero HAIs dropped by up to 50%. The reported HAIs include:

The remaining infection measures studied by Leapfrog Group had less dramatic decreases over the same time period, according to Fierce Healthcare. Nevertheless, they are significant. They include:

  • Surgical site infections (SSI) following colon surgery: 19% zero infections compared to 23% previously;
  • Clostridium difficile (C. difficile) inpatient infections: 3% zero inpatient infections in 2017, compared to 5% in 2015.

Joint Commission Studies Antimicrobial Program Progress

Meanwhile, the Joint Commission acknowledged that implementation of antimicrobial stewardship programs by providers can be difficult. In “The Expanding Role of Antimicrobial Stewardship Programs in Hospitals in the United States: Lessons Learned from a Multisite Qualitative Study,” the accrediting organization released insights from interviews with 12 antimicrobial stewardship program leaders nationwide.

They published their study in “The Joint Commission Journal on Quality and Patient Safety.” Three themes emerged from the interviews:

  • Hospitals have revised their antimicrobial programs, which originally operated on a “top-down” structure, to programs that include clinicians from throughout entire provider organizations;
  • Health information technology (HIT) can enable real-time opportunities to launch antimicrobial therapy and treat patients; and,
  • Some barriers exist in getting resources to integrate technology and analyze data.

“These programs used expansion of personnel to amplify the antimicrobial stewardship programs’ impact and integrated IT resources into daily workflow to improve efficiency,” the researchers wrote. “Hospital antimicrobial stewardship programs can reduce inappropriate antimicrobial use, length of stay, C. difficile infection, rates of resistant infections, and cost.”

What Do CMS and Joint Commission Expect?

According to Contagion, while the Joint Commission program is part of medication management, CMS places its requirements for the antimicrobial stewardship program under “infection prevention.”

CMS requirements for an antimicrobial stewardship program include:

  • Developing antimicrobial stewardship program policies and procedures;
  • Implementing hospital-wide efforts;
  • Involving antimicrobial stakeholders for focus on antimicrobial use and bacterial resistance;
  • Setting evidence-based antimicrobial use goals; and,
  • Reducing effects of antimicrobial use in areas of C. difficile infections and antibiotic resistance.

Leapfrog Group’s data about fewer hospitals reporting zero infections offers opportunities for hospital laboratory microbiology professionals to get involved with hospital-wide antimicrobial program teams and processes and help their hospitals progress back to zero HAIs. Clinical laboratories, both hospital-based and independent, also have opportunities to contribute to improving the antimicrobial stewardship efforts of the physicians who refer them specimens.

—Donna Marie Pocius

Related Information:

Troubling New Report on Hospital Infections Comes While Centers Medicare and Medicaid Services Considers Discontinuing Publicly Reporting Rates

Leapfrog Group: Healthcare-Associated Infections

Antimicrobial Stewardship Standards: A Comparison of Centers for Medicare and Medicaid Services and Joint Commission Requirements

Joint Commission: New Antimicrobial Stewardship Standard

Core Elements of Hospital Antibiotic Stewardship Programs

Number of Hospitals Achieving Zero Infections Drops

Hospitals Losing Ground on Effectively Preventing Infections with Dramatic Drop in Those Reporting Zero Infections

The Expanding Role of Antimicrobial Stewardship Programs in Hospitals in the United States: Lessons Learned from a Multi-Site Qualitative Study

CMS Missed 96 Hospitals with Suspected HAI Reporting Due to Limited Use of Analytics, OIG Report Reveals

OIG suggests better use of analytics by CMS could prevent gaming of the system by providers; clinical laboratories can help through test utilization management technology

It may come as a surprise to many hospital-based pathologists and clinical laboratory managers that the Centers for Medicare and Medicaid Services (CMS) has reason to suspect that some hospitals are “gaming” the system in how they report hospital-acquired infections (HAIs).

In 2015, CMS implemented the Hospital-Acquired Condition Reduction Program (HACRP) as part of the Patient Protection and Affordable Care Act (ACA). The HACRP program incentivizes hospitals to lower their HAI rates by adjusting reimbursements according to the inpatient quality reporting (hospital IQR) data provided by the healthcare providers. Hospital IQR data is the basis on which CMS validates a hospital’s HAI rate (among other things CMS is tracking) to determine the hospital’s reimbursement rate for that year.

However, an April 2017 report by the Office of the Inspector General US Department of Health and Human Services (OIG) noted that CMS was not doing enough to identify and target hospitals with abnormal reporting of HAIs.

The OIG reported:

  • CMS, in 2016, met its regulatory requirement to validate inpatient quality reporting data;
  • It reviewed data of 400 randomly selected hospitals as well as 49 hospitals targeted for failing to report half their HAIs, or for low scores in the prior year’s validation process;

However, OIG also reported that CMS did not include hospitals that displayed abnormal data patterns in its targeted sample. Targeting those hospitals, according to the OIG, could identify inaccurate reporting.

CMS staff had identified 96 hospitals with aberrant data patterns, but did not target them for validation—even though the agency can select up to 200 targeted hospitals for review, Becker’s Hospital Review pointed out.

Dollars More Important than Deaths

According to the OIG report, Medicare excluded in its investigation dozens of hospitals with suspected HAI reporting. This is odd since the CMS and the Centers for Disease Control (CDC) apparently are aware that some healthcare providers have manipulated data to improve their quality measure scores and thus increase their reimbursement rates.

“Collecting and analyzing quality data is increasingly central to Medicare programs that link payments to quality and value. Therefore, it is important for CMS to ensure that hospitals are not gaming [manipulating data to improve scores] their reporting of quality data,” the OIG report noted.

“There are greater requirements for what a company says about a washing machine’s performance than there is for a hospital on quality of care. And this needs to change,” stated Peter Pronovost, MD, PhD, in the Kaiser Health News article. “We require auditing of financial data, but we don’t require auditing of healthcare quality data, and that implies that dollars are more important than deaths.” Pronovost is Senior Vice President for Patient Safety and Quality at Johns Hopkins University School of Medicine.

 

Peter Pronovost, MD, PhD

Peter Pronovost, MD, PhD (above) testifying on preventable deaths before the Senate Subcommittee on Primary Health and Aging in 2014. He is Senior Vice President for Patient Safety and Quality at Johns Hopkins University School of Medicine in Baltimore. Pronovost told Kaiser Health News that there are no uniform standards for reviewing data that hospitals report to Medicare. (Photo copyright: US Senate Committee on Health, Education, Labor and Pensions.)

Medicare Missed Hospitals with Suspected HAI Data

CMS should have done an in-depth review of many hospitals that submitted “aberrant data patterns” in 2013 and 2014, the OIG stated in its report. According to a Kaiser Health News article, such patterns could include:

  • A rapid change in results;
  • Improbably low infection rates; and
  • Assertions that infections nearly always struck before patients arrived at the hospital.

“There’s a certain amount of blind faith that hospitals are going to tell the truth. It’s a bit much to expect that if they had a bad record they are going to fess up to it,” noted Lisa McGiffert, Director of the Safe Patient Project at Consumers Union, in the Kaiser Health News article.

CMS Needs Better Data Analytics

So, what does the OIG advise CMS to do? The agency called for “better use of analytics to ensure the integrity of hospital-reported quality data.” Specifically, OIG suggested CMS:

  • Identify hospitals with abnormal percentages of patients who had infections on admission;
  • Apply risk scores to identify hospitals with high propensity to manipulate reporting;
  • Use experiences to create and improve models that identify hospitals most likely to game their reporting.

CMS’ Administrator Seema Verma reportedly responded, “We will continue to evaluate the use of better analytics as feasible, based on Medicare’s operational capabilities.”

Medical Laboratory Diagnostic Testing Part of Gaming the System

A 2015 CMS/CDC joint statement noted “three ways that hospitals may be deviating from CDC’s definitions for reportable HAIs,” and two involve diagnostic test ordering. According to the OIG report, they include:

  • Overculturing: Diagnostic tests may be overutilized by providers in absence of clinical symptoms. Hospitals may use positive results to game their data by claiming infections that appeared days later were present on admission and thus not reportable.
  • Underculturing: Hospitals underculture when they do not order diagnostic tests in the presence of clinical symptoms. By not ordering the test, the hospital does not learn whether the patient truly has an infection and, therefore, the hospital does not have to report it.
  • Adjudication: Hospital administrative staff may inappropriately overrule those who report infections. HAIs are, therefore, not shared.

Clinical Laboratories Can Help

One in 25 people each day receives an HAI, CDC estimates. The OIG findings should be a reminder to medical laboratories and pathology groups that quality measures and patient outcomes are often transparent to media, patients, and the public.

One way medical laboratories in hospitals and health systems can help is by investing in utilization management technology and protocols that ensure appropriate lab test utilization. Informing doctors on the availability of appropriate diagnostic tests based on patients’ existing conditions, unique physiologies, or medical histories, could help prevent hospitals from inadvertently or deliberately game the system.

Clearly, transparency in healthcare is increasing. That means there will be more news stories revealing federal agencies’ failures to respond to healthcare data in ways that could have protected patients and the public. Clinical laboratories don’t want to be included in negative reporting.

—Donna Marie Pocius

Related Content:

CMS Validated Hospital Inpatient Quality Reporting Program Data, But Should Use Additional Tools to Identify Gaming

Medicare Failed to Investigate Suspicious Infection Cases from 96 Hospitals

CMS Can Do More to Validate Hospital-Reported Infection Data, OIG Report Finds

Study Suggests Medical Errors Now Third Leading Cause of Death in the US

Research Study at Johns Hopkins University Reveals CDC Does Not Record Medical Errors in Annual Mortality Report, Yet Such Errors Are Third Leading Cause of Death

Biggest Opportunity for Clinical Laboratory Industry is Utilization Management of Lab Tests, But Only If It Is Done Well

Lessons from the Pioneers: Reporting Healthcare-Associated Infections

Webinar: Simple, Swift Approaches to Lab Test Utilization Management: Proven Ways for Your Clinical Laboratory to Use Data and Collaborations to Add Value 

New Fast, Inexpensive, Mobile Device Accurately Identifies Healthcare-Acquired Infections and Communicates Findings to Doctors’ Smartphones and Portable Computers

Use of these new technologies creates opportunities for clinical laboratories and pathologists to add more value when collaborating with physicians to advance patient care

Ongoing improvements in point-of-care testing are encouraging one major academic medical center to apply this mode of testing to the diagnosis of hospital-acquired infections (HAIs). This development should be of interest to clinical laboratory professionals and pathologists, since it has the potential to create a different way to identify patients with HAIs than medical lab tests done in the central laboratory.

Massachusetts General Hospital (MGH), Harvard Medical School’s (HMS’) largest teaching hospital, has developed a prototype diagnostic system that works with doctors’ smartphones or mobile computers. The hand-held system can identify pathogens responsible for specific healthcare-acquired infections (HAIs) at the point of care within two hours, according to an MGH statement.

The researchers noted that 600,000 patients develop HAIs each year, 10% of which die, and that costs related to HAIs can reach $100 to $150 billion per year. However, as Dark Daily reported, the Centers for Medicare and Medicaid Services (CMS) does not reimburse hospitals for certain HAIs. (See Dark Daily, Consumer Reports Ranks Smaller and Non-Teaching Hospitals Highest in Infection Prevention,” October, 30, 2015.) Thus, the critical need to identify from where the infection originated, which generates a significant proportion of samples tested at the clinical laboratories of the nation’s hospitals and health systems.

Therefore, pathologists and medical laboratory scientists will understand that shifting some of that specimen volume to point-of-care testing will change the overall economics of hospital laboratories.

Smartphone-based Genetic Test for HIAs

The MGH research team created a way to do accurate genetic testing in a simple device powered by a system they call Polarization Anisotropy Diagnostics (PAD). The system measures changes in fluorescence anisotropy through a detection probe’s recognition of bacterial nucleic acid, reported Medscape Medical News. More than 35 probes for detecting bacterial species and virulence factors are available.

Optical test cubes are placed on an electronic base station that transmits data to a smartphone or computer, where results are displayed. “In a pilot clinical test, PAD accuracy was comparable to that of bacterial culture. In contrast to the culture, the PAD assay was fast (under two hours), multiplexed, and cost effective (under $2 per assay), wrote the MGH researchers in the journal Science Advances. (more…)

Consumer Reports Says Thousands of Doctors Facing Medical Probation Continue to See Patients; Calls for More Patient Access to Physician Disciplinary Records

Latest calls for easier public access to information on physician performance and quality is a reminder to clinical laboratories and pathology groups of the trend to greater transparency on provider outcomes

If any clinical laboratory executive or pathologist still doubts that more transparency of provider outcomes is a topic of interest to patients, they have only to look at Consumer Reports, well-respected for its advocacy on behalf of consumers. Consumer Reports is using multiple ways to educate their readers about medical errors and how the medical community makes it difficult for consumers to learn about physicians who have been involved in state medical board investigations.

One example is the Consumers Union, which is the policy and advocacy arm of Consumer Reports. Through its Safe Patient Project, the Consumers Union seeks to eliminate medical harm in healthcare.

Consumers Union advocates for increased public disclosure of information about such issues as: (more…)

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