Pilot project aims to create a new pipeline for microbial research
Tessa Andermann is building a pathway that could help researchers access a wide range of clinical samples from the hospital.
Tessa M. Andermann, MD, MPH
There are plenty of benefits that come with major academic health systems like UNC Health. Doctors and nurses get to work alongside researchers studying new advances in medical science, researchers get a first-hand look at the fundamentals of medical practice, and patients get access to a wealth of resources and specialists. And as the science of medicine expands, researchers and clinicians can even forge new connections to help the healthcare system evolve.
Tessa Andermann, an infectious disease researcher at the Institute for Global Health and Infectious Diseases at the UNC School of Medicine, is now working on forging one of those connections. Andermann studies interactions between the gut microbiome and infections in people with immune system deficienciesand to do some of her research, she needs bacterial samples isolated from immunocompromised patients. So now, Andermann and her colleagues, David van Duin and Kevin Alby, are creating a process to acquire those samples directly from the UNC hospital system through a Clinical and Translational Science (CTS) Pilot Program grant from the North Carolina Translational and Clinical Sciences (NC TraCS) Institute and help from two different units of the TraCS Informatics and Data Sciences group.
Eventually, Andermann hopes to use this new process to create a biobank of microbial isolates that could help clinicians and researchers further understand North Carolina's infectious disease landscape. But by demonstrating a new way to connect researchers to the hospital labs, this kind of pipeline could also support scientists across UNCproviding them with access to many different kinds of clinical samples and opening up countless new research initiatives.
Currently, UNC researchers who need to study bacterial isolates from patients don't have a formal way to obtain those isolates from the hospital system. Sometimes, Andermann points out, that means these researchers end up purchasing those isolates from an outside source, which can be expensive.
This new pipeline would keep the whole process in-house. When the hospital's microbiology lab tests a sample from a patient, information on that sample will end up in the Carolina Data Warehouse for Health (CDW-H), the centralized system for clinical data at UNC Health. This project would create a way to transfer relevant information about those samples between the CDW-H and a new database in REDCap, a secure data storage application used for research.
The goal is to have a supported core available for researchers, clinicians, and collaborators to draw from.
Researchers could prompt the CDW-H to scan for any new samples in the lab that match a set of criteria they're interested in. For this pilot project, and in line with Andermann's research needs, the team is focusing on bacterial cultures from blood, respiratory, urine and skin samples that contain multidrug-resistant bacteria from several patient groups, including those undergoing blood and marrow transplantation or who have hematologic malignancies. On a regular, ongoing basis, the CDW-H will upload information on those samples to the new REDCap database, where the pilot project team will be able to mark off which samples they're interested in. This, in turn, will cue a lab technician to save the bacteria from those samples and place the isolates in the lab freezer for pick-up.
Currently, the pilot project is going through a series of trial periods to finesse the details of this pipeline. But if implemented permanently, and with further support from UNC and researchers, this system could help researchers across the university access microbial isolates from patients in the hospital. In addition, this kind of pipeline could be replicated to help researchers access samples from various other hospital labs, such as those from the chemistry or hematology labs.
"The whole point of this project is to ensure that this can be more widely used as a tool, where a REDCap-Carolina Data Warehouse pipeline can be set up for other researchers as well," Andermann says.
To help make that happen, the pilot project team hopes to set up a fee-for-service payment system to support the pipeline's infrastructure long-term. In addition, multiple researchers at UNC have already indicated their interest in ensuring this pipeline's long-term sustainability via letters of support for the pilot project, noting the broad potential of having an easy way for researchers to access these clinical samples.
Some E. coli bacteria on a dish
photo courtesy of Tessa Andermann
Andermann notes that support from NC TraCS has been critical in making this project possible. The CTS Pilot Program at NC TraCS is designed to help researchers study part of the pathway between research and patient care. The grant covers one year of funding, after which the investigator could have a new lead or proof of concept toward improving that pathway. In addition, TraCS staff have provided vital support on the CDW-H and REDCap work for this project.
This project will also serve as a jumping-off point for one of Andermann's more ambitious goals. By capturing these microbial isolates, Andermann and her colleagues would have the ability to build a collective biorepository of bacteria isolated from patients in the health system. These bacteria could all be genetically sequenced, studied for drug resistance, and cataloguedhelping researchers understand the evolving ecosystem of bacterial infections and antimicrobial resistance in North Carolina.
"The goal is to have a supported core available for researchers, clinicians, and collaborators to draw from," Andermann says.
And that could have a more immediate impact on patient health. By understanding the nuances and patterns of antibiotic resistance in the community, clinicians could make more informed decisions on how to treat patients with infections. "We see a lot of patients who are not getting the right antibiotic initially because we don't have information about the resistance in the community," Andermann says.
Creating a pipeline between the hospital labs and the research community at UNC is just the first step toward rectifying that problem. But through this pilot project, Andermann and her colleagues are making the hospital system a little more effective in supporting patients, researchers andultimatelythe whole state of North Carolina.
NC TraCS is the integrated hub of the NIH Clinical and Translational Science Awards (CTSA) Program at the University of North Carolina at Chapel Hill that combines the research strengths, resources, and opportunities of the UNC-Chapel Hill campus with partner institutions North Carolina State University in Raleigh and North Carolina Agricultural and Technical State University in Greensboro.