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

Senior Investigator

Bacterial Pathogenesis and Antimicrobial Resistance Unit


Building 29B, Room 5NN08
9000 Rockville Pike
Bethesda, MD 20814


Research Topics

The emergence of antimicrobial resistance (AMR) in bacteria has been recognized as a critical threat to public health. Many important classes of bacterial AMR undergo selection and evolution in the natural context of antibiotic treatment in a human host, though important features of host context are not commonly included in studies of AMR. One of the main areas of focus within the Bacterial Pathogenesis and Antimicrobial Resistance Unit is the application of systems biology approaches to understand the evolutionary mechanisms by which resistance emerges in this natural context. The approaches applied include genomic sequencing of current and historical clinical bacterial isolates in combination with in vitro models of adaptive evolution to characterize pathways by which present day resistance to specific antimicrobial drug classes has evolved. As many clinically important resistance genes are located within bacterial plasmids, the laboratory is also focused on the study of principles of plasmid evolution and mechanisms controlling gene expression in resistance plasmids. RNA-seq and proteomics approaches are applied to these problems.

Another important area of focus within the unit is the study of bacterial pathoadaptation in the immunocompromised host. Population genomics approaches are applied in combination with molecular genetic analysis to understand selection dynamics and host-pathogen interactions in the context of defined genetic immunodeficiency diseases.

Recent progress in characterizing molecular mechanisms of antimicrobial resistance has also made possible the development of new approaches to the detection of AMR based on proteomics and sequencing. The Bacterial Pathogenesis and Antimicrobial Resistance Unit has developed novel approaches to rapid AMR diagnostics based on mass spectrometry and nanopore sequencing, and work in this area is another focus of the laboratory.


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 Clinical Center as a Senior Staff member of the Microbiology Service in the Department of Laboratory Medicine. In this role, he co-directed the Bacteriology, Specimen Processing, Parasitology, and Molecular Epidemiology sections of the laboratory, and established the Genomics Section before serving as acting chief of the Microbiology Service in 2018. In 2018, Dr. Dekker was named a Lasker Clinical Research Scholar and recruited as a tenure-track investigator within the NIAID intramural research program, where he established the Bacterial Pathogenesis and Antimicrobial Resistance Unit within the Laboratory for Clinical Immunology and Microbiology. In addition, he continues to oversee the Genomics Section within the Microbiology Service, which focuses on the development of next-generation sequencing-based approaches with applications in epidemiology and infectious diseases. He received tenure in 2024.

Dr. Dekker has served on FDA anti-infective drug advisory committees and is an editor for the Journal of Clinical Microbiology. He received the Beckman-Coulter Young Investigator award from the American Society for Microbiology in 2016, an NIH Clinical Center CEO Award in 2017, and the American Society for Clinical Investigation Young Physician-Scientist Award in 2020. He is a fellow of the College of American Pathologists and an elected member of the American Society for Clinical Investigation.

Selected Publications

  1. Tisza MJ, Smith DDN, Clark AE, Youn JH, NISC Comparative Sequencing Program, Khil PP, Dekker JP. Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group. Nat Commun. 2023;14(1):4082.
  2. Dulanto Chiang A, Patil PP, Beka L, Youn JH, Launay A, Bonomo RA, Khil PP, Dekker JP. Hypermutator strains of Pseudomonas aeruginosa reveal novel pathways of resistance to combinations of cephalosporin antibiotics and beta-lactamase inhibitors. PLoS Biol. 2022;20(11):e3001878.
  3. Launay A, Wu CJ, Dulanto Chiang A, Youn JH, Khil PP, Dekker JP. In vivo evolution of an emerging zoonotic bacterial pathogen in an immunocompromised human host. Nat Commun. 2021;12(1):4495.
  4. Wang H, Cissé OH, Bolig T, Drake SK, Chen Y, Strich JR, Youn JH, Okoro U, Rosenberg AZ, Sun J, LiPuma JJ, Suffredini AF, Dekker JP. A Phylogeny-Informed Proteomics Approach for Species Identification within the Burkholderia cepacia Complex. J Clin Microbiol. 2020;58(11).
  5. Khil PP, Dulanto Chiang A, Ho J, Youn JH, Lemon JK, Gea-Banacloche J, Frank KM, Parta M, Bonomo RA, Dekker JP. Dynamic Emergence of Mismatch Repair Deficiency Facilitates Rapid Evolution of Ceftazidime-Avibactam Resistance in Pseudomonas aeruginosa Acute Infection. mBio. 2019;10(5).

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This page was last updated on Thursday, March 21, 2024