University of Pittsburgh scientists developed new technology to stop hospital outbreaks before they start.
Hospital-acquired infections (HAIs), infections that patients get when receiving treatment in the hospital for another condition, are a serious threat to patient safety and a leading cause of increased costs and patient mortality in hospitals, according to the Centers for Disease Control (CDC).
Now, a new technology that can detect outbreaks before they spread may help physicians better address HAIs.
The Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT) system, an infectious diseases detection platform, developed by University of Pittsburgh scientists working with UPMC infection preventionists, proved over a two-year trial that it stops outbreaks, saves lives and cuts costs.
“We saved lives while saving money. This isn’t theoretical – this happened in a real hospital with real patients,” said lead author Alexander Sundermann, Dr.P.H., assistant professor of infectious diseases in Pitt’s School of Medicine. “This technology could easily be scaled. The more hospitals implement this practice, the more everyone benefits, not just by stopping previously undetected outbreaks within the walls of the hospital, but by finding medical device or medication-linked outbreaks sweeping the nation.”
The study was conducted from November 2021 through October 2023 at UPMC Presbyterian Hospital. The results are published in the journal Clinical Infectious Diseases, making the case for adoption in hospitals nationwide and the development of a national early outbreak detection database.
The power of genomic sequencing
The EDS-HAT transmission system uses genomic sequencing to analyze infectious disease samples from patients. If two or more patients have near-identical strains of an infection, the platform flags the results for the infection prevention team to find the commonality and halt transmission.
Patients with the same type of infection who don’t have an obvious link – such as staying in the same hospital unit – may unknowingly spread the infection, leading to an outbreak growing significantly before it is detected.
“Addressing outbreaks in hospitals was the main purpose of the EDS-HAT, as this technology is much more effective compared to the current method of disease detection in hospitals, where a nurse or clinician is needed to detect disease in each patient,” said Dr. Sundermann. “Then, when more than one patient has a certain type of infection, the infection control department is called in to investigate. Oftentimes, through that lengthy process of reactive sequencing, what we find is that it’s usually not an outbreak like the clinician initially thought it was.”
Without genomic sequencing, hospital infection preventionists have no way of knowing if two hospitalized patients coincidentally have the same infection, or if one of them was infected by another.
“Instead of waiting to find an outbreak to sequence when a patient has symptoms, the basis of the Pitt program is to start doing genetic sequencing on everything moving forward,” said Dr. Sundermann. “In this case study specifically, our research lab would work with our clinical lab every week to collect patient infections that were potentially acquired at the hospital and sequence them, review the data, and find if outbreaks were occurring in the hospital.”
“We would then figure out where in the hospital the outbreak was occurring and then we would work to stop it through further investigation, staff education, and cleaning and sterilization,” said Dr. Sundermann. “This program showed that EDS-HAT was effective at preventing outbreaks that go undetected at hospitals without this program.”
Geonomic analysis
Algorithms used in the EDS-HAT technology included bioinformatics, also known as genomics analysis, which works by analyzing patient DNA using publicly available bioinformatics tools, a well-established methodology that helps researchers build an analysis pipeline and determine if one patient’s infection is the same as another’s, said Dr. Sundermann.
“For this study we looked at common bacterial pathogens that are seen in hospitals and prioritized the ones where patients that had been in the hospital for more than two days or had recently been discharged from the hospital within the prior 30 days, to prioritize infections that were more likely to be acquired in the hospital and therefore more likely to cause an outbreak,” said Dr. Sundermann. “We have found that through genomic sequencing, we can address these infections faster with earlier intervention.”
Saving hospitals money
During the time of the study, analysis showed that EDS-HAT prevented 62 infections and five deaths, compared to if the system had not been running. The project, through UPMC’s academic partnership with Pitt, netted savings of nearly $700,000 in infection treatment costs, which is a 3.2-fold return on investment.
“A hospital acquired infection increases a patient’s length of stay by nearly eight hospital days. The main metrics that we were looking for in this study were infections prevented, deaths prevented, and cost savings,” said Dr. Sundermann. “It costs about $90 to sequence a patient infection using our methodology. A typical infection, on average, can be about $20,000 to treat, so if one patient’s infection is prevented, you’re freeing up a lot of money.”
Without tools like the EDS-HAT, infection preventionists may spend time and resources trying to avert a nonexistent outbreak when patients happen to have the same type of infection, but the transmission is found to be from unrelated sources.
“It is very clear that hospitals will save money, reduce length of stay in hospitals and improve patient outcomes with this technology. Our hope is that the more that we share this with hospital leadership at other facilities, the more people are going to want to sign off,” said Dr. Sundermann. “It’s a true win-win for the hospital and patients, and so we are hoping that this will scale, and more people will adopt it.”
Expanding genomic sequencing to scale
The healthcare field is in general agreement that this technology works at preventing infections, said Dr. Sundermann. The next question, then, is how to expand the technology to scale.
“The evidence on cost savings for genomic sequencing technology is there and everything is moving in the right direction,” said Dr. Sundermann. “We must have discussions with hospital leadership about this, and when other hospitals realize that this is a new approach works, I believe they’ll make investments in it.”
Dr. Sundermann and his research team hope to implement EDS-HAT at more healthcare facilities nationwide and wants the findings to contribute to ongoing conversations among U.S. health care leadership, payors and policymakers about the benefits of genomic surveillance as standard practice in health care.
If health care facilities across the U.S. adopt EDS-HAT, a nationwide outbreak system could be developed, similar to PulseNet, the U.S. CDC’s network for detecting multistate outbreaks of foodborne illness, said Dr. Sundermann.
“We intentionally use publicly available bioinformatics tools to build our analysis pipeline, as we call it, and we publish it extensively, so that other healthcare facilities can download the exact same tools we’re using and follow the exact same process we’re using, and it’s pretty well established,” he said.
Dr. Sundermann and colleagues previously found that, had such a system existed, a 2023 outbreak of deadly bacteria linked to contaminated eye drops could have been stopped far earlier.
“This was a great example that shows that when more hospitals are taking advantage of this approach to infection prevention, and that we can share that data, the more benefit we’re going to get,” said Dr. Sundermann. “We must encourage public health involvement, because in order to share this data across institutions, it will require public health or federal involvement.”