Dekker Research Group

Bacterial pathogens may undergo dramatic evolution in the context of chronic infection, facilitating host adaptation and the development of antibiotic resistance. In some cases, elevated mutation rates due to evolved mismatch repair and proofreading deficiencies have been shown to contribute to accelerate this evolution. An important insight from studies of within-host adaptation has been that genetic modifications that occur during chronic infection may parallel those that underlie the emergence of human-restricted pathogens from broad-host range generalists over longer evolutionary periods. In the BPARU, we apply a systems biology approach to understand selection dynamics and host-pathogen interactions in the context of defined genetic immunodeficiency diseases. This approach integrates genomics, transcriptomics (RNA-seq), and metabolomic methods to identify and characterize specializations that occur during within-host adaptation. In these studies, we seek to address (1) the role of bacterial hypermutation and other forms of genome plasticity in within-host evolution, (2) the roles that host immune deficiencies can play in shaping the within-host evolution in persistent infections, and (3) the evolution of antimicrobial resistance in the context of acute and chronic infection.

Another linked area of focus within the BPARU are the evolutionary mechanisms by which antibiotic resistance emerges in Gram-negative bacterial pathogens in the context of acute and chronic infection. The approaches applied include genomic sequencing of current and historical clinical bacterial isolates, transcriptome analysis with RNA-seq, proteomics, metabolomics, and in vitro adaptive evolution. This work aims to reveal novel mechanisms of resistance to broad spectrum antibiotics, with implications for clinical treatment of Gram-negative infections.

John P. Dekker, M.D., Ph.D., FCAP

Lasker Clinical Research Scholar
Chief, Bacterial Pathogenesis and Antimicrobial Resistance Unit
Director, Genomics Section, Microbiology Service, Department of Laboratory Medicine, NIH Clinical Center

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Specialty(s): Pathology, Clinical, Pathology, Medical Microbiology

Education:

M.D., Harvard Medical School

Ph.D., Harvard University

Dr. Dekker received his M.D. from Harvard Medical School and Ph.D. from Harvard University through the NIH Medical Scientist Training Program. He completed pathology residency and fellowship training in medical microbiology at Massachusetts General Hospital and is board-certified in clinical pathology and medical microbiology through the American Board of Pathology. In 2013, he joined the NIH...

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John P. Dekker, M.D., Ph.D., FCAP

Augusto Dulanto Chiang, M.D. (He/Him/His)

Assistant Research Physician

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Specialty(s): Infectious Disease, Internal Medicine
Provides direct clinical care to patients at NIH Clinical Center

Education:

Infectious Diseases Fellowship and Advanced Infectious Diseases and Genomics Fellowship, 2019, NIAID

Internal Medicine Residency, Washington Hospital Center

M.D., 2011, Cayetano Heredia University, Lima

Languages Spoken: Spanish

Dr. Dulanto Chiang obtained his M.D. in 2011 from the Cayetano Heredia University in Lima, Peru, after which he completed an internal medicine residency at Washington Hospital Center followed by an Infectious Diseases Fellowship and Advanced Infectious Diseases and Genomics Fellowship at NIAID.

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Jessie Ellis, Ph.D. (She/Her/Hers)

Post-Doctoral Fellow

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Education:

Ph.D., Tufts University

Dr Ellis’s research in the BPARU explores metabolic reprogramming in zoonotic pathogens during genetic adaptation to the human host. Current work focuses on adaptation in the emerging pathogen Bordetella hinzii, and approaches include high-throughput metabolic screening, metabolic pathway analysis, and competition experiments to understand fitness values of identified metabolic changes that occur...

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Soma Ghosh, Ph.D. (She/Her/Hers)

Staff Scientist, Laboratory of Clinical Immunology and Microbiology

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Education:

Ph.D., 2015, Indian Institute of Science, Bangalore, India

Languages Spoken: Hindi, Bengali

Dr. Ghosh received her Ph.D. in 2015 from the Indian Institute of Science, Bangalore, India, where she used Systems Biology approaches to study host-pathogen interactions in the context of iron acquisition by M. tuberculosis. She joined Johns Hopkins University, Baltimore in 2015 as a post-doctoral research fellow with Dr. Tamara O’Connor in the department of Biological Chemistry. There, she...

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Abraham (Jon) Moller, Ph.D. (He/Him/His)

Post-Doctoral Fellow

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Education:

Ph.D., Microbiology and Molecular Genetics (MMG), 2021, Emory University
M.S., Cell, Molecular, and Structural Biology (CMSB); B.A., Chemistry; B.S., Microbiology, 2016, Miami University (Ohio)

Dr. Moller’s research in the BPARU focuses on understanding within-host evolution of Gram-negative opportunistic pathogens through population genomic and evolutionary biological approaches.

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Prashant Prabhakar Patil, Ph.D. (He/Him/His)

Post-Doctoral Fellow

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Languages Spoken: Hindi

Dr. Patil’s research in the BPARU focuses on novel mechanisms of resistance to advanced generation cephalosporins and cephalosporin beta-lactam inhibitor combination antibiotics in P. aeruginosa. These questions are investigated with a combination of in vitro adaptive evolution, genetic engineering, genomic sequencing, gene expression analysis with RNA-seq, and analysis of clinical isolates.

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Former Research Group Members

Jung-Ho Youn, Ph.D.
Genomics Scientist
Department of Laboratory Medicine
NIH Clinical Center  

Jonathan Ho, M.D.
Internal Medicine Resident
Brown University, RI

Jamie Lemon, Ph.D.
Director of Infectious Disease Diagnostics
Northwell Health Laboratories
New York, NY

Andrew Clark, Ph.D.
Assistant Professor
UT Southwestern Medical Center
Dallas, TX

Derek N. Smith, Ph.D.
Genomics Biologist
Environment and Climate Change Canada
Government of Canada

Lidia Beka, Ph.D.
Technology Transfer Center
National Cancer Institute

Chao-Jung Wu, Ph.D.
Assistant Professor
Taipei Medical University
Taiwan

Mike Tisza, Ph.D.
Bioinformatics Scientist
Baylor College of Medicine
Houston, TX

Adrien Launay, Ph.D.
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