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CSI: Microbiology

CSI: Microbiology
Reported by
Marcia Stone

Posted March 13, 2010

Presented By


Until recently, nature has been the most effective bioterrorist; however the ability to create genetically engineered microbes is enabling man to catch up. Recognizing the dangers inherent in microbes both natural and maliciously designed, the Academy's Genomic Medicine and Emerging Infectious Diseases Discussion Groups convened a joint session to encourage scientific discourse on the subject. Three leading microbial detectives talked about the new DNA-based tools that help identify disease-causing bacteria, trace their heritage and, most importantly, distinguish natural from nefarious.

Paul Keim described how he has applied genomics in investigations of anthrax, plague, and tularemia. Barry Kreiswirth discussed current genotyping techniques, particularly the mapping of insertion sequence IS6110, which scientists monitor as it moves around on a mycobacterial genome, and the polymerase chain reaction (PCR)-based techniques of strain-specific mycobacterial interspersed repeat unit (MIRU) analysis and spacer oligonucleotide typing (spoligotyping). David Stenger outlined recent developments in sequence-based microbial surveillance.

Use the tabs above to view the meeting report and multimedia presentations.

Web Sites

Affymetrix Microarray Bulletin
Highlights microarray research and diagnostic developments around the world. AMB features interviews by and for scientists, statisticians and software engineers.

American Society for Microbiology (ASM)
A wealth of information on all things microbial, including information on the ASM's yearly biodefense meeting.

The Centers for Disease and Control and Prevention (CDC)
Web site of the CDC, including pages for the Division of Tuberculosis Elimination and information on infectious agents recognized by the CDC as potential bioterrorism agents/diseases.

The Center for Bio/Molecular Science and Engineering
Part of the U.S. Naval Research Laboratory, the Center researches biomimetic materials, bioengineered systems, biosensors, responsive materials, tissue engineering, proteogenomics, microfluidics, and liquid crystals for and in collaboration with the U.S. Navy, U.S. Department of Defense, and corporate and academic partners.

Infectious Diseases Society of America (IDSA)
A professional society for infectious disease specialists. The bioterrorism section of the Web site is a collaboration between IDSA and the Center for Infectious Disease Research and Policy at the University of Minnesota with funding from the CDC.

The Institute for Genomic Research (TIGR)
A nonprofit center dedicated to deciphering and analyzing genomes, TIGR allows researchers access all bacterial genome sequences completed to date, and much more.

National Center for Biotechnology Information (NCBI)
NCBI offers one of the most heavily used sequence analysis tools in the public domain: the Basic Local Alignment Search Tool (BLAST), which compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. The genome sequence of and comparative genomic information on Bacillus anthracis are available at the NCBI web site.

The New York City Department of Health and Mental Hygiene
The web site includes the Bureau of Tuberculosis Control.

The Public Health Research Institute at the International Center for Public Health
The Public Health Research Institute (PHRI) is an independent, nonprofit research organization founded in 1941 to study infectious diseases. The aim of the Institute is to help eliminate worldwide infectious disease threats through research and leadership in public health support programs.

Translational Genomics Research Institute (TGen)
TGen is a nonprofit biomedical research institute whose mission is to make and translate genomic discoveries into advances in human health.

U.S. Army Medical Research Institute of Infectious Diseases
Home of the National Interagency Biodefense Campus.

The World Health Organization
The World Health Organization (WHO) is the United Nations specialized agency for health. WHO's Stop TB Department offers global tuberculosis control, surveillance, planning and financing.

Journal Articles

Genomics in the Time of Anthrax: Powering Microbial Forensics

Achtman, M., G. Morelli, P. Zhu, et al. 2004. Microevolution and history of the plague bacillus, Yersinia pestis. Proc. Natl. Acad. Sci. USA 101: 17837-17842. Full Text (PDF, 422 KB)

Girard, J. M., D. M. Wagner, A. J. Vogler, et al. 2004. Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales. Proc. Natl. Acad. Sci. USA 101: 8408-8413. Full Text (PDF, 1049 KB)

Hacker, J., U. Hentschel & U. Dobrindt. 2003. Prokaryotic chromosomes and disease. Science 301: 790-792.

Hoffmaster, A. R., J. Ravel, D. A. Rasko, et al. 2004. Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proc. Natl. Acad. Sci. USA 101: 8449-8459. Full Text (PDF, 487 KB)

Jackson, P. J., E. A. Walthers, A. Kalif, et al. 1997. Characterization of the variable-number tandem repeats in vrra from different Bacillus anthracis isolates. Appl. Environ. Microbiol. 63: 1400-1405. Full Text (PDF, 448 KB)

Jeffreys, A. J. 2005. Genetic fingerprinting. Nat. Med. 11: 1035-1039.

Johansson, A., J. Farlow, P. Larsson, et al. 2004. World-wide genetic relationships among Franciella tularensis isolates using multiple-locus variable-number tandem repeat analysis (MLVA). J. Bacteriol. 186: 5808-5818. Full Text (PDF, 429KB)

Lok, C. 2005. A defensive strategy. Nature 437: 1392-1393.

McGinnis, S. & T. L. Madden. 2004. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32 (Web Server issue): W20-25. Full Text (PDF, 554 KB)

Pearson, T., J. D. Busch, J. Ravel, et al. 2004. Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc. Natl. Acad. Sci. USA 101: 13536-13541. Full Text (PDF, 515 KB)

Radnedge, L., P. G. Agron, K. K. Hill, et al. 2003. Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Appl. Environ. Microbiol. 69: 2755-2764. Full Text (PDF, 386 KB)

Read, T. D., M. Salzberg, M. Pop, et al. 2002. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296: 2028-2033.

Relman, D. A. 2006. Bioterrorism: preparing to fight the next war. N. Engl. J. Med. 354: 113-115.

Takahashi, H., P. Keim, K. L. Kaufmann, et al. 2004. Epidemiological and laboratory investigation of a Bacillus anthracis bioterrorism incident, Kameido, Tokyo, 1993. Emerg. Infect. Dis. 10: 117-120.

Tong, Z. Z., D. S. Zhou, Y. J. Song, et al. 2005. Genetic variations in the pgm locus among natural isolates of Yersinia pestis. J. Gen. Appl. Microbiol. 51: 11-19.

A Molecular Epidemiologist's View of Tuberculosis

Barnes, P. F. & M. D. Cave. 2003. Molecular epidemiology of tuberculosis. N. Engl. J. Med. 349: 1149-1156.

Centers for Disease Control. 1991. Nosocomial transmission of multidrug-resistant tuberculosis among HIV-infected persons, Florida and New York, 1988-1991. MMWR 40: 585-591.

Frieden, T. R., L. F. Sherman, K. L. Maw, et al. 1996. A multi-institutional outbreak of highly drug-resistant tuberculosis. JAMA 276: 1229-1235.

Geng, E.H., B. N. Kreiswirth, J. Burzynski & N. W. Schluger. 2005. Transmission trends for human immunodeficiency virus associated tuberculosis in New York City. Int. J. Tuberc. Lung Dis. 9: 661-666.

Kurepina, N., E. Likhoshvay, E. Shashkina, et al. 2005. Targeted hybridization of IS6110 fingerprints identifies the W-Beijing Mycobacterium tuberculosis strains among clinical isolates. J. Clin. Microbiol. 43: 2148-2154. Full Text (PDF, 165 KB)

McElroy, P. D., R. R. Sterling, C. R. Driver, et al. 2002. Use of DNA fingerprinting to investigate a multiyear, multistate tuberculosis outbreak. Emerg. Infect. Dis. 8: 1252-1256. Full Text

Munsiff, S. S., B. Nivin, G. Sacajiu, et al. 2003. Persistence of a highly resistant strain of tuberculosis in New York City during 1990-1999. J. Infect. Dis. 188: 356-363. Full Text

Post, F. A., P. A. Willcox, B. Mathema, et al. 2004. Genetic polymorphism in Mycobacterium tuberculosis isolates from patients with chronic multidrug-resistant tuberculosis. J. Infect. Dis. 190: 99-106. Full Text

Reed, M. B., P. Domenech, C. Manca, et al. 2004. A glycolipid of hyervirulent tuberculosis strains that inhibits the innate immune response. Nature 431: 84-87.

Tsenova, L., E. Ellison, R. Harbacheuski, et al. 2005. Virulence of selected Mycobacterium tuberculosis clinical isolates in the rabbit model of meningitis is dependent on phenolic glycolipid produced by the bacilli. J. Infect. Dis. 192: 98-106.

Sequence-based Pathogen Diagnostics and Surveillance

Cutler, D. J., M. E. Zwick, M. M. Carrasquillo, et al. 2001. High-throughput variation detection and genotyping using microarrays. Genome Res. 11: 1913-1925. Full Text

Davidson, A. J., M. Benko & B. Harrach. 2003. Genetic content and evolution of adenoviruses. J. Gen. Virol. 84: 2895-2908. Full Text

DeSantis, T. Z., C. E. Stone, S. R. Murray, et al. 2005. Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using microarray. FEMS Microbiol. Lett. 245: 271-278.

Gingeras, T. R., G. Ghandour, E. Wang, et al. 1998. Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genom. Res. 8: 435-448. Full Text (PDF, 401 KB)

Vora, G. J., C. E. Meador, D. A. Stenger & J. D. Andreadis. 2004. Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl. Environ. Microbiol. 70: 3047-3054. Full Text

Weinberg, S. 2004. Emergent FDA biodefense issues for microarray technology: process and analytical technology. Expert Rev. Mol. Diagn. 4: 779-781.

Wilson, W. J., C. L. Strout, T. Z. DeSantis, et al. 2002. Sequence-specifice identification of 18 pathogenic microorganisms using microarray technology. Mol. Cell Probes 16: 119-127.


Keyes, D. C., J. L. Burstein, R. B. Schwartz & R. E. Swienton, Eds. 2005. Medical Response to Terrorism: Preparedness and Clinical Practice. Lippincott Williams & Wilkins, Philadelphia.

Kobilinsky, L., T. F. Liotti & J. Oeser-Sweat. 2005. DNA: Forensic and Legal Applications. John Wiley & Sons. Hoboken, NJ.

Lindler, L. E., F. J. Lebeda & G. W. Korch, Eds. 2005. Biological Weapons Defense: Infectious Diseases and Counterbioterrorism. Humana Press, Totowa.

Scott, S. & C. J. Duncan. 2001. Biology of Plagues: Evidence from Historical Populations. Cambridge University Press. Cambridge, UK.


Paul Keim, PhD

Northern Arizona University
Translational Genomics Research Institute
e-mail | web site | publications

Paul Keim is head of the Keim Genetics Laboratory, an Arizona Regents Professor, and the Cowden Endowed Chair in Microbiology at Northern Arizona University. He also serves as the division director of pathogen genomics at the Translational Genomics Research Institute (TGen). Bioweapon genomics, especially phylogenetic and high-resolution strain identification, is Keim's major research area. It was his laboratory's ground breaking work on hypermutable loci in Bacillus anthracis that enabled them to quickly identify the bacilli used in the October 2001 bioterrorism attacks. Since then Keim's group has developed similar genetic tools for all major bacterial biothreats.

Keim serves on the National Research Council committee that monitors biological weapons facilities in the former Soviet Union. He is a member of the U.S. scientific team that inspects abandoned bioweapons sites in Russia and Central Asia. The National Institutes of Health also appointed Keim to the National Science Advisory Board for Biosecurity, where he recently chaired the communications working group. Keim also has a longtime affiliation with the Los Alamos National Laboratory.

Keim earned his PhD in plant biochemistry from the University of Kansas in 1981. He was a postdoctoral fellow and research assistant professor with Karl G. Lark at the University of Utah, where he worked on the genomic analysis of bacteria, plants, and mammals. Keim went on to Iowa State University as a biotechnology research associate, combining molecular genetic analysis with population and quantities genetics of the soybean. This investigation yielded some of the original genetic markers used to identify quantitative biological traits. In 1988 Keim joined biological sciences faculty at Northern Arizona University and has been there ever since.

Barry Kreiswirth, PhD

Public Health Research Institute
e-mail | web site | publications

Barry Kreiswirth joined the Public Health Research Institute (PHRI) in 1978 as a graduate student working on the molecular biology of Staphylococcus aureus and fourteen years later, in response to the New York City outbreak, became the director of its first Tuberculosis Center. Initially established as a genotyping laboratory, it now has one of the largest mycobacterial strain and DNA fingerprint libraries in the world. The Center is best known for its characterization of the highly multidrug-resistant W strain of M. tuberculosis.

Scientists at PHRI's TB Center have always worked closely with both the Centers for Disease Control and the New York City Department of Health to integrate their molecular tools into tuberculosis control programs. During the last decade, the Center has extended its local collaborations to include the New Jersey Department of Health and Human Services and the Wadsworth Center in Albany, New York. Globally, the Center works with researchers and resources mycobacterial specimens from Russia, South Africa, the Czech Republic, India, and Egypt.

Despite a major investment in tuberculosis research, the Center has not abandoned work on Kreiswirth's initial interest, the molecular typing of methicillin resistant S. aureus (MRSA). A rapid DNA-sequenced-based genotyping test differentiating one S. aureus isolate from another has recently been developed. The approach has been adapted to a variety of nosocomial pathogens and is now used to construct a nosocomial surveillance database in collaboration with the New Jersey Department of Health and Hospitals.

David A. Stenger, PhD

U.S. Naval Research Laboratory
e-mail | web site | publications

David Stenger is a principal investigator and head of the Laboratory for Biosensors and Biomaterials at the Center for Bio/Molecular Science and Engineering (CBMSE). His major area of research is biological detection with a focus on microarray-based functional genomics and bioinformatics algorithm development.

Stenger was awarded a PhD in biophysics from the State University of New York at Buffalo in 1989. After graduation, Stenger continued to work in the university's membrane biophysics laboratory at Roswell Park Cancer Institute investigating the fundamental properties of artificial lipid and intact biological membranes. While there, Stenger used his experience with membrane fusion techniques to generate lymphocyte-derived antibody-producing hybridoma lines. In 1992 Stenger joined the CBMSE where he worked on the characterization and applications of self-assembled monolayer formations. He also investigated cell-based biosensor development as well as neural stem cell isolation, culture, and differentiation.

Stenger serves as an external reviewer for the Defense Threat Reduction Agency Biological Defense Program. He has also acted as a representative from the Department of Defense to the Central Intelligence Agency's Neuroscience Program. Stenger has received numerous citations including the Navy Unit Commendation Award, the Berman Research Publication Award, and a Special Intervention Award from the U.S. Navy.

Marcia Stone

web site

Marcia Stone is a science writer based in New York City and a longtime member of the Academy's Microbiology Section. More of her work can be found on