Meet a genomic epidemiologist
Dr. Alex Sundermann, applying genomic epi for infection prevention & control
I’m excited to introduce you to Dr. Alex Sundermann, Assistant Professor of Epidemiology at the University of Pittsburgh. I first learned about Alex’s work several years ago through Twitter, and he was kind enough to meet me for coffee when he was in the Seattle area attending the SHEA 2023 conference. We’ve kept in touch ever since, and he provided an excellent recommendation for a Pittsburgh restaurant and joined us for the genomic epi dinner at the CSTE conference. Alex is a pioneer in using genomic epidemiology for infection control in a hospital setting, and has published extensively on that topic.
One of the key aspects of Alex’s success has been his eagerness to collaborate across disciplines. He has a strong foundation in epidemiology and infection prevention, and leans on laboratory and bioinformatics colleagues to learn from their expertise. This interdisciplinary work has been critical to successful implementation of genomics into a hospital infection prevention program. Lets jump right in so you can hear directly from Alex about his journey into genomic epidemiology and applying it to hospital infection prevention and control.
Academic pathway
B.S., Microbiology, University of Rochester, 2013
M.P.H., Infectious Diseases & Microbiology, University of Pittsburgh, 2014
Dr.P.H., Epidemiology, University of Pittsburgh, 2022
What first sparked your interest in genomic epidemiology? Tell the story of your career journey that brought you to where you are today.
It started in college when I took a course on emerging pathogens and got interested in how microbes spread and cause outbreaks. After graduation, I wasn’t sure which path to take, so I went on to study public health and infectious diseases to get my MPH. This led me to a job in healthcare infection prevention and control (IP&C), where I tracked infections in hospitals.
One of the first major projects I worked on was a fatal outbreak of mold infections. The outbreak garnered some national attention and even had the CDC EIS involved. Through our investigations, we eventually traced it back to contaminated linen12. After the outbreak, retrospectively, we were able to use some sequencing capacity which was super interesting to see3.
Around that time, I met Dr. Lee Harrison, who had just secured a grant for a project focused on genomic surveillance. His lab had also provided ‘reactive’ sequencing for our IP&C efforts, or sequencing to confirm/refute our department’s suspicion of an ongoing outbreak. He proposed that I work on the project as part of my DrPH dissertation, and I took the opportunity. I continued working full-time in IP&C while pursuing my doctorate which was a great learning pathway as we were applying genomic surveillance to the hospital/department where I worked full-time.
During that project, I was more on the applied side, and Dr. Harrison had built a strong team of lab and bioinformatics experts. Working with this team, we built a real-time genomic surveillance system at our hospital. We used it to sequence every healthcare-associated infection, not just the suspected outbreaks, which helped us detect hidden transmission events that would have otherwise been missed. One of the most interesting outbreaks I investigated to date, was an outbreak of vancomycin-resistant Enterococcus that, because of genomic surveillance, we detected and traced back to non-sterile contrast injections4. More interestingly, our hospital was following manufacturer recommendations of the procedure!
After I finished my DrPH, I stayed on as a faculty member to continue developing this approach. Now, our Center for Genomic Epidemiology routinely performs weekly genomic surveillance for outbreak detection, investigation, and prevention5. This approach has proven more effective than traditional methods and has demonstrated real impact on patient safety.
What are you most excited about in the next year or two in the field?
We recently published a pre-print of our formal analysis based on two years of prospective genomic surveillance at our hospital6. The paper details the outbreaks we detected, the interventions we implemented, the infections we prevented, and the cost savings we achieved. Unlike our retrospective analysis, this time we performed real-time IP&C interventions, which gave us some great, promising results (to be peer-reviewed). Our hope is that this paper will serve as a catalyst for other institutions to begin their own genomic surveillance programs. This approach has enormous potential for improving patient safety by detecting transmission events within and between facilities.
What advice would you give to a student or professional that's interested in pursuing genomic epidemiology?
It takes a diverse, multidisciplinary team to leverage the full potential of genomic epidemiology. You don’t need to be an expert in laboratory methods or bioinformatics—having a foundational knowledge and a willingness to collaborate are key. By building on your expertise and working alongside others with complementary skills, you can significantly enhance your work and make meaningful contributions to the field. Moreover, if you work in, or adjacent to healthcare for genomic epidemiology, I definitely recommend chatting to your local infection preventionists! These folks have a wealth of knowledge and the interworking of the hospital which can significantly enhance interpretation of results.
Open ended words of wisdom!
Move fast and learn from mistakes. In genomic epidemiology, nothing is ever perfect, and that’s okay. The field of genomic surveillance for healthcare outbreak detection is moving so fast that there’s still no universal agreement on how to do things—how to sequence, which analysis pipelines to use, how to interpret results, what transmission thresholds to set, or even the best way to intervene. But that doesn’t mean we should hold back progress or wait for everything to align. Instead, we need to keep applying genomic surveillance and adapt as we learn more. Hesitation shouldn’t stop us from advancing the field—progress comes from trying, failing, and figuring out how to do it better next time.
Wrapping up
I hope you’ve enjoyed getting to know Alex and learning more about his perspective and career journey. As genomic epidemiology gains more of a foothold in public health agencies, it’s critical for hospitals to come on board as well. Robust genomic surveillance requires strong collaborations not only across disciplines, but between public health institutions, academic institutions, and private sector organizations. The work that Alex and others are doing in academic medical centers to provide the evidence base for the effectiveness of incorporating genomics for improving patient safety and preventing infections is critical to garnering the financial and other support needed to expand these programs.
If you’d like to keep up with Alex, you can follow him on Twitter/X at https://x.com/SundermannAJ or find additional contact information on his faculty page here (https://www.publichealth.pitt.edu/directory/alexander-sundermann). Thanks Alex for taking the time to share with Applied and Genomic Epi readers!
References
Sundermann AJ, Clancy CJ, Pasculle AW, Liu G, Cumbie RB, Driscoll E, Ayres A, Donahue L, Pergam SA, Abbo L, Andes DR, Chandrasekar P, Galdys AL, Hanson KE, Marr KA, Mayer J, Mehta S, Morris MI, Perfect J, Revankar SG, Smith B, Swaminathan S, Thompson GR, Varghese M, Vazquez J, Whimbey E, Wingard JR, Nguyen MH. How Clean Is the Linen at My Hospital? The Mucorales on Unclean Linen Discovery Study of Large United States Transplant and Cancer Centers. Clin Infect Dis. 2019 Feb 15;68(5):850-853. doi: 10.1093/cid/ciy669. PMID: 30299481; PMCID: PMC6765054.
Sundermann AJ, Clancy CJ, Pasculle AW, Liu G, Cheng S, Cumbie RB, Driscoll E, Ayres A, Donahue L, Buck M, Streifel A, Muto CA, Nguyen MH. Remediation of Mucorales-contaminated Healthcare Linens at a Laundry Facility Following an Investigation of a Case Cluster of Hospital-acquired Mucormycosis. Clin Infect Dis. 2022 Apr 28;74(8):1401-1407. doi: 10.1093/cid/ciab638. PMID: 34282829.
Nguyen MH, Kaul D, Muto C, Cheng SJ, Richter RA, Bruno VM, Liu G, Beyhan S, Sundermann AJ, Mounaud S, Pasculle AW, Nierman WC, Driscoll E, Cumbie R, Clancy CJ, Dupont CL. Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients. Microb Genom. 2020 Dec;6(12):mgen000473. doi: 10.1099/mgen.0.000473. Epub 2020 Nov 27. PMID: 33245689; PMCID: PMC8116672.
Sundermann AJ, Babiker A, Marsh JW, Shutt KA, Mustapha MM, Pasculle AW, Ezeonwuka C, Saul MI, Pacey MP, Van Tyne D, Ayres AM, Cooper VS, Snyder GM, Harrison LH. Outbreak of Vancomycin-resistant Enterococcus faecium in Interventional Radiology: Detection Through Whole-genome Sequencing-based Surveillance. Clin Infect Dis. 2020 May 23;70(11):2336-2343. doi: 10.1093/cid/ciz666. PMID: 31312842; PMCID: PMC7456351.
Sundermann AJ, Chen J, Kumar P, Ayres AM, Cho ST, Ezeonwuka C, Griffith MP, Miller JK, Mustapha MM, Pasculle AW, Saul MI, Shutt KA, Srinivasa V, Waggle K, Snyder DJ, Cooper VS, Van Tyne D, Snyder GM, Marsh JW, Dubrawski A, Roberts MS, Harrison LH. Whole-Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection. Clin Infect Dis. 2022 Aug 31;75(3):476-482. doi: 10.1093/cid/ciab946. PMID: 34791136; PMCID: PMC9427134.
Sundermann AJ, Kumar P, Griffith MP, Waggle KD, Srinivasa VR, Raabe N, Mills EG, Coyle H, Ereifej D, Creager HM, Ayres A, Tyne DV, Pless LL, Snyder GM, Roberts M, Harrison LH. Genomic Surveillance for Enhanced Healthcare Outbreak Detection and Control. medRxiv [Preprint]. 2024 Sep 22:2024.09.19.24313985. doi: 10.1101/2024.09.19.24313985. PMID: 39371154; PMCID: PMC11451765.
Fantastic interview! Great job, Krisandra. You always surprise me with the quality content for all the thing you do!