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 Bacterial Pathogenesis and Antimicrobial Resistance Section (BPARS), 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 BPARS 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.

Senior Investigator
Lasker Clinical Research Scholar
Chief, Bacterial Pathogenesis and Antimicrobial Resistance Section

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

Jessie Ellis, Ph.D.

Postdoctoral Fellow

Education:

Ph.D., Tufts University

Dr Ellis’s research in the BPARS 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.

Staff Scientist

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 postdoctoral research fellow with Dr. Tamara O’Connor in the department of biological chemistry. There, she...

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Grace Morales, Ph.D.

Postdoctoral IRTA Fellow

Education:

Ph.D., 2024, Vanderbilt University, Nashville, TN

Dr. Morales received her Ph.D. in 2024 from Vanderbilt University. Her work was largely focused on connecting microbial genotypes to clinical phenotypes, with an emphasis on uropathogenic E. coli and the development of UTI and asymptomatic bacteriuria. This work employed a combination of genomics and host-pathogen interaction work in the context of UTIs. Dr. Morales joined BPARS in October 2024...

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Prashant Prabhakar Patil, Ph.D.

Postdoctoral Fellow

Languages Spoken: Hindi

Dr. Patil’s research in the BPARS 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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Arthi Ramkumar, B.S.

Postbaccalaureate IRTA Fellow

Education:

B.S., 2023, University of Maryland College Park, College Park, MD

Arthi Ramkumar joined the BPARS as a Postbaccalaureate IRTA Fellow in July 2023. In the BPARS, she is using genetic engineering to study the molecular biology of RND transporters involved in antibiotic resistance in Pseudomonas aeruginosa. She also has interests in public health and medicine.

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Nick Vereecke, Ph.D., ir.

Postdoctoral Visiting Fellow

Education:

Ph.D., 2023, Ghent University, Ghent, Belgium

Languages Spoken: Dutch, French

Dr. Vereecke received his Ph.D. in 2023 from Ghent University, Ghent, Belgium, where he studied the use of long-read sequencing for viral and bacterial diagnostics in veterinary medicine. While his work focused on sequencing-driven diagnostics, it also shed new light on the use of genomics in the context of antimicrobial resistance in Mycoplasmopsis bovis, Brachyspira hyodysenteriae, and...

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Tommy Yoon, B.A.

Postbaccalaureate IRTA Fellow

Education:

B.A., 2024, Reed College, Portland, OR

Tommy Yoon joined the BPARS as a Postbaccalaureate IRTA Fellow in July 2024. He is using genomic approaches including nanopore sequencing to study DNA methylation in clinical  Bacteroides fragilis group 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, Rhode Island
  • Jamie Lemon, Ph.D., Director of Infectious Disease Diagnostics, Northwell Health Laboratories, New York, New York
  • Andrew Clark, Ph.D., Assistant Professor, UT Southwestern Medical Center, Dallas, Texas
  • Derek N. Smith, Ph.D., Genomics Biologist
  • 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., Assistant Professor, Baylor College of Medicine, Houston, Texas
  • Adrien Launay, Ph.D., Chief, Bioinformatics, Endogenomiks, Mexico
  • Augusto Dulanto Chiang, M.D., Assistant Professor, Vanderbilt University Medical Center, Vanderbilt, Tennessee
  • Abraham (Jon) Moller, Ph.D., Bioinformatics System Analyst, CARD, NIA, NIH
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