Center for Genomic Epidemiology
The mission of the Center for Genomic Epidemiology (CGE) is to apply cutting-edge microbial genomic and data mining and machine learning tools to study the epidemiology and evolution of serious pathogens. Examples include research on pathogen transmission; strain emergence; and methods for detection, investigation, and interruption of outbreaks in healthcare and in the community. The Center uses novel genomic methods and machine learning to accomplish its goals. CGE prioritizes the training of the next generation of researchers.
People
Lee Harrison, MD
Director
Dr. Harrison is the Associate Chief of Epidemiology and education, Professor of Medicine and Epidemiology, Head of the Infectious Diseases Epidemiology Research Unit and Chair of the Allegheny County Board of Health. Dr. Harrison is the Director of the Center for Genomic Epidemiology “CGE.”
James Bina, PhD
Dr. Bina’s laboratory investigates antimicrobial resistance and bacterial pathogenesis in Gram-negative pathogens, including Vibrio cholerae and Klebsiella pneumoniae. The long-term goal of his research is to define the fundamental processes that enable bacteria to cause disease and resist antibiotics.
Jieshi Chen
Ms. Chen is a Senior Research Analyst in the Auton Lab at Carnegie Mellon University’s Robotics Institute. She specializes in applying machine learning techniques to detect and characterize anomalous patterns in large-scale temporal transactional data, with applications in healthcare informatics, finance, and other domains.
Vaughn S. Cooper, PhD
Dr. Cooper’s laboratory applies evolutionary biology to improve human health, enhance K–12 science education, and investigate biodiversity. His team studies the evolution, ecology, and genome dynamics of both experimental and clinical microbial populations.
Yohei Doi, MD, PhD
Dr. Doi is Director of the Center for Innovative Antimicrobial Therapy at the University of Pittsburgh. His laboratory focuses on antimicrobial resistance in Gram-negative pathogens, examining the genetic and molecular basis of resistance, developing rapid diagnostic methods, and pursuing inhibitor-based drug discovery. Current projects include studies of colistin resistance in Acinetobacter baumannii and fosfomycin resistance in Escherichia coli.
Artur Dubrawski, PhD
Dr. Dubrawski is a Research Professor at Carnegie Mellon University’s Robotics Institute, where he directs the Auton Lab, a research group of more than 80 scientists focused on fundamental and applied machine learning. With three decades of R&D experience, he has held executive roles in industry and served as principal investigator on numerous AI projects for government and industrial partners.
Elise Martin, MD, MS
Dr. Martin is Medical Director of Infection Prevention and Hospital Epidemiology at the VA Pittsburgh Healthcare System (VAPHS). Her research focuses on improving infection prevention practices, particularly around personal protective equipment, isolation strategies, and contact precautions, while maintaining high-quality patient care. She also studies infection prevention in dialysis, central line-associated bloodstream infections (CLABSI), and medical education.
Barbara Methé, PhD
Dr. Methé is Director of the Center for Medicine and the Microbiome and Visiting Professor of Medicine. She has extensive expertise in genomics, metagenomics, microbial ecology, and physiology, and has led numerous large-scale comparative genome analyses. As a leader in the NIH Human Microbiome Project, she has advanced systems biology approaches to study the human microbiome in health and disease, including psoriasis and lung disease.
James Kyle Miller, MS
Mr. Miller is a Senior Project Scientist in the Auton Lab at Carnegie Mellon University’s Robotics Institute. His expertise includes mathematical modeling and machine learning, with applications in human health, nuclear safety, and predictive maintenance
Tung Phan, MD, PhD, D(ABMM)
Dr. Phan is a board-certified medical microbiologist with expertise in virology and molecular diagnostics. His research focuses on novel virus discovery using next-generation sequencing, molecular epidemiology and evolution of viruses, and the development of diagnostic assays for both known and emerging pathogens.
Lora Pless, PhD
Dr. Pless is Director of the Microbial Genomic Epidemiology Laboratory (MiGEL). Her work combines whole genome sequencing and epidemiology to track the transmission of important human pathogens and support Infection Prevention efforts at UPMC.
Mark Roberts, MD, MPP
Dr. Roberts is Professor and Chair of Health Policy and Management, and Director of the Public Health Dynamics Lab. His research spans decision analysis, mathematical modeling, and health policy applications in infectious diseases.
Melissa Saul, MS
Ms. Saul is a Clinical Data Scientist in the Department of Medicine with expertise in extracting and validating clinical data from electronic health records. She has developed software tools to improve data accuracy and retrieval, supporting infectious diseases research collaborations for over two decades.
Graham Snyder, MD, MS
Dr. Snyder is Medical Director of Infection Prevention and Hospital Epidemiology for UPMC Presbyterian and the UPMC system. He works closely with the Center for Genomic Epidemiology to identify and investigate pathogen transmission and develop strategies to prevent infections across the health system.
Alexander Sundermann, DrPH
Dr. Sundermann studies the epidemiology and transmission dynamics of hospital-acquired pathogens, with a focus on genomic approaches to detect and prevent healthcare-associated infections.
Daria Van Tyne, PhD
Dr. Van Tyne’s laboratory investigates how bacteria evolve during human infection to resist antibiotics and evade the host immune system, using comparative genomics and functional analyses.
Kady Waggle, BS
Ms. Waggle manages the Microbial Genomic Epidemiology Laboratory (MiGEL) at the University of Pittsburgh. She has expertise in genomics and microbiology, with research interests in the transmission of hospital-acquired pathogens.
Publications
Torso LM, Voorhees RE, Forest SA, Gordon AZ, Silvestri SA, Kissler B, Schlackman J, Sandt CH, Toma P, Bachert J, Mertz KJ, Harrison LH. Escherichia coli O157:H7 outbreak associated with restaurant beef grinding. J Food Prot 2015;78:1272-1279.
Mustapha MM, Marsh JW, Krauland MG, Fernandez JO, de Lemos AP, Dunning Hotopp JC, Wang X, Mayer LW, Lawrence JG, Hiller NL, Harrison LH. Genomic epidemiology of hypervirulent serogroup W, ST-11 Neisseria meningitidis. EBioMedicine 2015;2:1447-55. doi: 10.1016/j.ebiom.2015.09.007. PMCID: PMC4634745
Marsh JW, Krauland KG, Nelson JS, Schlackman JL, Brooks AM, Pasculle AW, Shutt, KA, Doi Y, Querry AM, Muto CA, Harrison LH. Genomic epidemiology of an endoscope-associated outbreak of KPC carbapenemase-producing Klebsiella pneumoniae. PLoS One 2015 Dec 4;10(12):e0144310. doi: 10.1371/journal.pone.0144310.
Mustapha MM, Marsh JW, Krauland MG, Fernandez JO, de Lemos AP, Dunning Hotopp JC, Wang X, Mayer LW, Lawrence JG, Hiller NL, Harrison LH. Genomic investigation reveals highly conserved, mosaic, recombination events associated with capsular switching among invasive Neisseria meningitidis serogroup W sequence type (ST)-11 strains. Genome Biol Evol. 2016 Jul 3;8(6):2065-75. doi: 10.1093/gbe/evw122.
Mustapha MM, Marsh JW, Ezeonwuka CD, Pasculle AW, Pacey MP, Querry AM, Muto CA, Harrison LH. Draft Genome Sequences of Four Hospital-Associated Pseudomonas putida Genome Announc. 2016 Sep 29;4(5). pii: e01039-16. doi: 10.1128/genomeA.01039-16.
Potts CC, Joseph SJ, Chang HY, Chen A, Vuong J, Hu F, Jenkins LT, Schmink S, Blain A, MacNeil JR, Harrison LH, Wang X. Population structure of invasive Neisseria meningitidis in the United States, 2011-15. J Infect. 2018 Jun 28. pii: S0163-4453(18)30186-5. doi: 10.1016/j.jinf.2018.06.008. [Epub ahead of print]
Marsh JW, Pacey MP, Ezeonwuka C, Ohm SL, Snyder D, Cooper VS, Harrison LH, Doi Y, Mustapha MM. J Clostridioides difficile: a potential source of NpmA in the clinical environment. Antimicrob Chemother. 2018 Oct 5. doi: 10.1093/jac/dky420. [Epub ahead of print]
Guo Q, Mustapha MM, Chen M, Chen M, Qu D, Marsh JW, Zhang X, Doi Y, Wang M, Harrison LH. Evolution of sequence type 4821 clonal complex meningococcal strains in China from pre-quinolone to quinolone era 1972-2013. Emerg Infect Dis 2018;24:683-690.
Galdys AL, Marsh JW, Delgado E, Pasculle AW, Pacey M, Ayres AM, Metzger A, Harrison LH, Muto CAM. Bronchoscope-associated clusters of multidrug-resistant Pseudomonas aeruginosa and carbapenem-resistant Klebsiella pneumoniae. Infect Control Hosp Epidemiol 2018 Nov 19:1-7. doi: 10.1017/ice.2018.263. [Epub ahead of print].
Miller JK, Chen J, Sundermann A, Marsh JW, Saul MI, Shutt KA, Pacey M, Mustapha MM, Harrison LH, Dubrawski A. Statistical outbreak detection by joining medical records and pathogen similarity. J Biomed Inform. 2019 Mar;91:103126. doi: 10.1016/j.jbi.2019.103126. Epub 2019 Feb 13.
Sundermann AJ, Miller JK, Marsh JW, Saul MI, Shutt KA, Pacey M, Mustapha MM, Ayres A, Pasculle AW, Chen J, Snyder GM, Dubrawski AW, Harrison LH. Automated data mining of the electronic health record for investigation of healthcare-associated outbreaks. Infect Control Hosp Epidemiol. 2019 Mar;40(3):314-319.
Babiker A, Mustapha MM, Pacey MP, Shutt KA, Ezeonwuka CD, Ohm SL, Cooper VS, Marsh JW, Doi Y, Harrison LH. The use of online tools for antimicrobial resistance prediction by whole genome sequencing in MRSA and VRE. J Glob Antimicrob Resist. 2019 Apr 18. pii: S2213-7165(19)30095-5. doi: 10.1016/j.jgar.2019.04.006. [Epub ahead of print]
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;70:2336-2343.
Marsh JW, Mustapha MM, Griffith MP, Evans DR, Ezeonwuka C, Pasculle AW, Shutt KA, Sundermann A, Ayres AM, Shields RK, Babiker A, Cooper VS, Van Tyne D, Harrison LH. Evolution of outbreak-causing carbapenem-resistant Klebsiella pneumoniae ST258 at a tertiary care hospital over eight years. MBio. 2019 Sep 3;10(5). pii: e01945-19. doi: 10.1128/mBio.01945-19.
Mustapha MM, Lemos APS, Griffith MP, Evans DR, Marx R, Coltro ESF, Siebra CA, Timm L, Ribeiro H, Monteiro A, Pasculle AW, Marsh JW, Van Tyne D, Harrison LH, Sacchi CT. Two cases of a newly-characterized Neisseria Emerg Infect Dis 2020;26:366-369.
Namburete EI, Dippenaar A, Conceição EC, Feliciano C, Passeri do Nascimento MM, Peronni K, Silva WA, Ferro JJ, Harrison LH, Warren RM, Bollela VR. Phylogenomic assessment of drug-resistant Mycobacterium tuberculosis strains from Beira, Mozambique. Tuberculosis 2020 Jan 29[Online ahead of print]. DOI: 10.1016/j.tube.2020.101905.
Evans DR, Griffith MP, Sundermann AJ, Shutt KA, Saul MI, Mustapha MM, Marsh JW, Cooper VS, Harrison LH, Van Tyne D. Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital. Elife 2020;9. PMCID: PMC7156236
Kumar P, Sundermann AJ, Martin EM, Snyder GM, Marsh JW, Harrison LH, Roberts MS. Method for economic evaluation of bacterial whole genome sequencing surveillance compared to standard of care in detecting hospital outbreaks. Clin Infect Dis. 2020 May 5:ciaa512. doi: 10.1093/cid/ciaa512. Online ahead of print.
Babiker A, Evans DR, Griffith MP, McElheny CL, Hassan M, Clarke LG, Mettus RT, Harrison LH, Doi Y, Shields RK, Van Tyne D. Clinical and genomic epidemiology of carbapenem-non-susceptible Citrobacter at a tertiary healthcare center over two decades. J Clin Microbiol 2020;58:e00275-20.
Mustapha MM, Marsh JW, Shutt KA, Schlackman J, Ezeonwuka C, Farley MM, Stephens DS, Wang X, van Tyne D, Harrison LH. Transmission dynamics and microevolution of Neisseria meningitidis during carriage and invasive disease in high school students, Maryland and Georgia, USA, 2006-2007. J Infect Dis. 2020 Oct 27:jiaa674. doi: 10.1093/infdis/jiaa674. Online ahead of print.
Sundermann AJ, Chen J, Miller JK, Saul MI, Shutt KA, Griffith MP, Mustapha MM, Ezeonwuka C, Waggle K, Srinivasa V, Kumar P, Pasculle AW, Ayres AM, Snyder GM, Cooper VS, Van Tyne D, Marsh JW, Dubrawski AW, Harrison LH. Outbreak of Pseudomonas aeruginosa Infections from a Contaminated Gastroscope Detected by Whole Genome Sequencing Surveillance. Clin Infect Dis. 2020 Dec 25;ciaa1887
Funding
Enhanced Detection System for Healthcare-Associated Transmission of Infection (EDS-HAT)
R01AI127472
09/26/2016 – 08/31/2021
To establish the Enhanced Detection System for Healthcare Association Transmission (EDS-HAT), which uses routine WGS of bacterial pathogens and machine learning and data mining of the EMR to dramatically increase capacity to detect healthcare-associated outbreaks.
University of Pittsburgh Training Program in Antimicrobial Resistance (T32)
T32AI138954
05/16/2019 – 04/30/2024
To establish the University of Pittsburgh Training Program in Antimicrobial Resistance, a multidisciplinary training program for pre-doctoral and post-doctoral trainees. The program will focus on translational science with the goal of having our trainees transition to postdoctoral fellowships or independent research careers. We plan to use this T32 to produce the next generation of scientists with the training, creativity, and resources to be future leaders in the critical field of antimicrobial resistance.
ABCs Component of the Maryland EIP Site
U50 CK000487
01/01/2020 – 12/31/2020
This project, based at Johns Hopkins University in Baltimore, is a collaborative effort between Johns Hopkins, University of Maryland, and Maryland department of Health and Mental Hygiene. The Maryland Emerging Infections Programs (EIP) site is part of national a network that is funded and coordinated by the Centers for Disease Control and Prevention. The main mission of the EIP Network is to conduct surveillance for studies of emerging infectious disease and to evaluate methods for their prevention and control. (ongoing since 2005)
Analyzing Adult Pneumococcal Vaccination Implementation in the Underserved (Sub to Smith R01)
R01 AI116575
06/01/2020 – 05/31/2024
Pneumococcal disease continues to be an important public health problem, particularly in underserved minorities. This project will evaluate vaccination strategies to improve vaccination protection in this group
South Africa-Pittsburgh Public Health Genomic Epidemiology Research Training Program (SAPPHGenE)
D43TW011255
03/26/2019 – 12/31/2023
A public health genomic epidemiology research training program in South Africa in the areas of bacterial pneumonia, invasive bacterial diseases, and fungal infections. This will be accomplished by an expert, multidisciplinary team of research mentors at the University of Pittsburgh, the Centers for Disease Control and Prevention in Atlanta, and the National Institute for Communicable Diseases in Johannesburg, South Africa. The ultimate goal of the program is to prevent and control these diseases, some of which are vaccine preventable and all which are major causes of morbidity and mortality in South Africa and globally