Genomic Surveillance A New Frontier in Health Care Outbreak Detection

Health care–associated infections (HAIs) are a persistent challenge in hospitals, leading to significant patient morbidity, mortality, and financial burden on health care systems. Traditionally, infection prevention and control (IPC) departments rely on clinical observation, manual outbreak investigations, and retrospective data analysis to detect and manage outbreaks. However, with advancements in genomic epidemiology, a new approach called genomic surveillance transforms how health care outbreaks are detected and controlled.

Alexander Sundermann, DrPH, CIC, FAPIC, an assistant professor in the Division of Infectious Diseases at the University of Pittsburgh Center for Genomic Epidemiology and a member of Infection Control Today’s Editorial Advisory Board, discussed a study recently published in medRxiv¹ that explored the use of genomic surveillance for enhanced health care outbreak detection. This research aims to shift the paradigm from reactive to proactive outbreak management, leveraging real-time genomic data to identify and mitigate outbreaks before they escalate.

“With our prior publication,² real-time bacterial genomic surveillance can detect multiple health care outbreaks that go otherwise undetected, guide interventions, stop outbreaks, reduce infections, and save net costs. We think this will soon become routine in hospitals,” Sundermann said.

Traditional Outbreak Detection: Limitations

“Typically, for infection control…an infection preventionist [IP] might suspect that there could be an outbreak…by reviewing the monthly HAIs and seeing an increase,” Sundermann said. “When that happens, a hospital and the [IPC] department will start an outbreak investigation. You make your line list, try to find additional cases, look at charts, and do interventions.”

He also explained that genomic testing is not always available. “Some hospitals [can] do some type of genomic sequencing or DNA fingerprinting to determine whether what we’re looking into is truly an outbreak or unrelated, meaning they’re not part of an outbreak or a point source. Our prior research² has found that when this happens, genomic sequencing typically indicates [that] this isn’t an outbreak, which means that the time and investment we’ve made trying to investigate and intervene might have been misallocated to stopping what we thought was an outbreak.”

Key Findings of the Second Study⁷

However, Sundermann points out that this approach has limitations. Many suspected outbreaks are unrelated infections, wasting time and resources on unnecessary investigations. Meanwhile, other outbreaks may go undetected until they have already affected numerous patients. These delays can lead to higher infection rates, increased patient morbidity, and extended hospital stays. Genomics should then be considered. “Because we’re going above and beyond the standard practice…we are providing the best and safest care for our patients. Through that perspective, through safer patient care, through transparency, through cost savings, [and] through preventing these outbreaks is [how] we can succeed.”

The Power of Genomic Surveillance

Genomic surveillance offers a more precise and timely method of identifying health care outbreaks. Instead of waiting for clinical patterns to emerge, hospitals can sequence the genomes of health care–associated pathogens in real time, providing detailed insights into the relationships between infections. This technology allows health care professionals to determine whether infections are part of an actual outbreak (ie, caused by the same strain) or are unrelated.

In the second study2 conducted at the University of Pittsburgh Medical Center (UPMC), Sundermann and his team sequenced nearly 3000 HAIs over 2 years. They discovered 99 outbreaks affecting 297 patients—far more than the 15 outbreaks identified by the traditional infection control methods. Significantly, many of these outbreaks would have gone undetected without genomic surveillance, demonstrating its potential to revolutionize health care outbreak detection. Sundermann says this means that “genomic surveillance could vastly find these outbreaks that go undetected, and our current methods of infection control missed outbreaks and were misguided to different outbreaks.”

Building on these findings, the UPMC team launched a prospective study in 2021.¹ This new research involved weekly genomic surveillance of HAIs, allowing the infection control team to detect outbreaks early (ideally after only 2 cases) rather than waiting until an outbreak had already spread to multiple patients.

The Future of Infection Control

Sundermann’s research demonstrates that genomic surveillance can be a game changer in IPC. However, implementing this technology across health care facilities will require significant investment and collaboration. Not every hospital has the resources to conduct in-house genomic sequencing, especially smaller community hospitals. However, Sundermann suggests that partnerships with commercial laboratories or larger health care systems could provide a scalable solution.

Besides financial factors, implementing genomic surveillance also presents logistical challenges. Sundermann’s team included a dedicated laboratory technician, a part-time bioinformatician, and infection control professionals to analyze and act on the genomic data. Although this level of staffing may not be feasible for every facility, the growing accessibility of genomic sequencing technology and bioinformatics tools will likely make it easier for hospitals of all sizes to adopt this approach in the future.

“This method of sequencing almost everything as they occur detects these outbreaks, makes interventions, stops them, and saves money. We hope we can take away from this study that what we’re doing at our hospital, which is not current [standard] practice [but] should be and, [and hopefully it will become] standard practice for all health care facilities,” he said.

Implications for Health Care Leaders

Health care leaders should take note of the potential benefits of genomic surveillance, both in terms of patient safety and cost savings. As the cost of genomic sequencing continues to decline, the return on investment for hospitals will increase. IPs and epidemiologists can use Sundermann’s research to advocate for genomic surveillance programs within their institutions, highlighting the potential to prevent costly outbreaks and improve patient outcomes.

In the coming years, genomic surveillance may become a standard practice in IPC, much like hand hygiene and environmental cleaning are today. Patients, too, may begin to consider genomic

surveillance as a factor in choosing where to receive care, particularly for high-risk procedures such as transplants or surgeries. Hospitals that adopt genomic surveillance will be able to demonstrate their commitment to providing the safest and highest quality care for their patients.

Unusual Findings of the Second Study

“Typically, we would find endoscope outbreaks from a single contaminated scope, building patient upon patient. We were one of the first facilities in the US to discover the [endoscopic retrograde cholangiopancreatography] issue back in 2012, when we had 17 infections and 5 deaths over many months, as it took us that long to identify the problem. So, we had these outbreaks of endoscopes that used to be very large, and now we find 2 cases associated with a single endoscope, which directs us to it right then and there. We [then] pull that scope from service. Sometimes we find issues with that scope because of this, and we no longer see any endoscope-associated outbreak exceeding 2 patients, whereas they used to be much larger.”

What IPs Should Take From the Studies

Genomic surveillance represents a new frontier in health care outbreak detection and control. Sundermann’s research has shown that this approach can detect outbreaks earlier, guide targeted interventions, and prevent costly infections.

“We hope hospitals will see this, recognize it, and use [these] data we’ve produced to take to their hospital leadership to advocate for…genomic capabilities,” Sundermann said. “At least to have a reactive capability to help them confirm or refute the presence of these outbreaks…take [these] data and say, ‘Maybe we can start investing or reaching out to see [whether there are] partners we can work with to make this program at our own facility.’ ”

Sundermann explained that is why he and his coauthors put in the cost analysis in the study. “[T]he main driver is that we know [IPC], and [infectious disease] in general, is not a cost-generating department. We don’t make money for the hospital; we prevent and save infections. By having [these] data, I hope to empower IPs and their departments to say, ‘Look at this paper from UPMC…and some of the other papers, [and] let’s go to our hospital leadership and say we should be doing this, too.’ ”

References

1. Johnson E. Enhancing infection prevention in medical devices through quality systems. Infection Control Today. July 24, 2024. Accessed October 31, 2024. https://www.infectioncontroltoday.com/view/enhancing-infection-prevention-in-medical-devices-through-quality-systems
2. Part 820—quality system regulation. Code of Federal Regulations. Updated October 30, 2024. Accessed August 29, 2024. https://www.ecfr.gov/current/title-21/chapter-I/subchapter-H/part-820
3. ISO 13485: medical devices. International Organization for Standardization. Accessed October 31, 2024. https://www.iso.org/iso-13485-medical-devices.html
4. About ISO. International Organization for Standardization. Accessed August 29, 2024. https://www.iso.org/about
5. Medical devices; quality system regulation amendments. Federal Register. February 2, 2024. Accessed August 29, 2024. https://www.federalregister.gov/d/2024-01709
6. ISO 13485: frequently asked questions. BSI. Accessed August 29, 2024. https://www.bsigroup.com/siteassets/pdf/en/insights-and-media/insights/brochures/bsi-md-iso-13485-faqs-en-gb.pdf