Paul Keim

Paul Keim Ph.D.

Professor and Co-Director
Pathogen and Microbiome Division

Regents Prof. of Biology
Northern Arizona University

Cowden Endowed Chair in Microbiology
Northern Arizona University

Paul Keim Ph.D.

My research focuses on the advancement of forensics and genomics analysis of bacterial pathogens. The Pathogen Genomics Program will focus on three core missions:

  • Bolstering of biodefense through improved forensic analysis
  • Understanding interactions between man and microbe to develop new therapeutics and diagnostics that will alleviate the human ailments caused by dangerous pathogens
  • Developing an improved understanding of disease movement to reduce and control the incidence of disease

The Pathogen Genomics Program is a joint program between the Translational Genomics Research Institute (TGen) and the Northern Arizona University (NAU), which results in a unified approach to protecting America against dangerous pathogens, in particular Bacillus anthracis (anthrax).

While infectious agents have a long history as biological weapons, these agents pose significant danger to the United States, now more than ever. Generally, the biothreat agents themselves do not threaten our country's overall public health, however these agents do have unique attributes that facilitate their weaponization. Forensic analysis is particularly valuable as evidenced by the 1993 anthrax attack in Japan that was successfully linked to Aum Shinrikyo, the Japanese doomsday cult, by my laboratory at NAU. During the 2001 anthrax investigations, my lab was called upon to play a critical role in providing the US military and intelligence community with cutting edge assays for biological weapons. We successfully delivered assays that were far superior to the assays used previously and available through the military labs. This was critical to both the investigations and the clean-up efforts on the east coast.

Building on the existing work at NAU and the genomics tools at TGen, the Pathogen Genomics Program will provide high-resolution genomic forensic analysis of biothreat pathogenic agents such as Bacillus anthracis (anthrax), Yersinia pestis (plague), Francisella tularensis (tularemia), Burkholderia mallei (glanders), Brucella melitensis (brucellosis), and Coxiella burnett (Q fever). These are considered the most dangerous of the bacterial bioterrorism and bioweapons agents.

The Program also will build upon our collaborations with state and federal agencies in developing molecular identification tools for public health related pathogens like E. coli, Salmonella, Listeria, and tuberculosis, which cause illness in billions of individuals worldwide. We will continue to create the scientific base to launch responses for acts of bioterrorism and to develop strategies to optimize public health management.

In addition to development of advanced assays for dangerous pathogens, the Program focuses on understanding the interaction between the pathogen and its environment (ecology), the movement of the pathogen and the associated ailments though a population (epidemiology), and the changes associated with the propagation of the pathogen over time (evolution).

  • Engelthaler DM, Chiller T, Schupp JA, Colvin J, Beckstrom-Sternberg SM, Driebe EM, Moses T, Tembe W, Sinari S, Beckstrom-Sternberg JS, Christoforides A, Pearson JV, Carpten J, Keim P, Peterson A, Terashita D, Balajee SA , Next-generation sequencing of Coccidioides immitis isolated during cluster investigation Emerg Infect Dis, 17(2):227-32 2011
  • Achtman, M, G Morelli, P. Zhu, T. Wirth, I. Diehl, A.Vogler, D. Wagner, C. Allender, R. Easterday, V. Chenal-Francisque, P. Worsham, N.R. Thomsom, J. Parkhill, L.E. Lindler, E. Carniel and P. Keim. , Microevolution and history of the plague bacillus,Yersinia pestis. Proceedings of the National Academy of Sciences USA 101:17837­17842 2004
  • Pearson, Talima, Joseph Busch, Jacques Ravel, Tim Read, Shane Rhoton, Jana U¹Ren, Tatum Simonson, Sergey Kachur, Rebecca Leadem, Michelle Cardon, Matthew VanErt, Lynn Huynh, Claire Fraser and Paul Keim., Phylogenetic discovery bias in Bacillus anthracis using single nucleotide polymorphisms from whole genome sequencing Proceedings of the National Academy of Sciences (USA) 101: 13536-13541 2004
  • Johansson*, Anders, Jason Farlow*, Pär Larsson, Meghan Dukarich, Elias Chambers, Mona Byström, James Fox, May Chu, Mats Forsman, Anders Sjöstedt, Paul Keim., World-Wide Genetic Relationships Among Francisella tularensis Isolates Using Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA) J. Bacteriology 186:5808-5818 2004
  • Girard*, Jessica M., David M. Wagner*, Amy J. Vogler, Christine Keys, Christopher J. Allender, Lee C. Drickamer, Paul Keim. , Plague Population Genetic Structure is Determined by Transmission Dynamics Proceedings of the National Academy of Sciences (USA) 101:8409-8413 2004
  • Paul Keim, Matthew Van Ert, Talima Pearson, Amy Vogler, Lynn Hyunh, and David Wagner., Anthrax Molecular Epidemiology and Forensics: Using Different Markers for the Appropriate Evolutionary Scales Infection, Genetics and Evolution 4:205-213 2004
  • Takahashi, H., P. Keim, A.F. Kaufmann, K.L. Smith, C. Keys, K. Taniguchi, S. Inouye, and T. Kurata. , Epidemiological and Laboratory Investigation of a Bacillus anthracis Bioterrorism Incident, Kameido, Tokyo, 1993. Emerging Infectious Disease 10:117-120 2004
  • Read, TD, S.L. Salzberg, M. Pop, M. Shumway, L. Umayam, L. Jiang, E. Holtzapple, J. Busch, K.L. Smith, J.M. Schupp, D. Solomon, P. Keim, C.M. Fraser. , Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis Science 296:2028-2033 2002
  • Price LB, Liu CM, Melendez JH, Frankel YM, Engelthaler D, Aziz M, Bowers J, Rattray R, Ravel J, Kingsley C, Keim PS, Lazarus GS, Zenilman JM. , Community analysis of chronic wound bacteria using a 16S rRNA gene-based pyrosequencing approach: impact of diabetes and antibiotics on chronic wound microbiota PLoS One ul 31;4(7):e6462 2009
  • Beckstrom-Sternberg SM, Auerbach RK, Godbole S, Pearson JV, Beckstrom-Sternberg JS, Deng Z, Munk C, Kubota K, Zhou Y, Bruce D, Noronha J, Scheuermann RH, Wang A, Wei X, Wang J, Hao J, Wagner DM, Brettin TS, Brown N, Gilna P, Keim PS. , Complete genomic characterization of a pathogenic A.II strain of francisella tularensis subspecies tularensis. PLoS ONE 2(9): e947 2007
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