A genomics-based approach to biodefence preparedness

Nature Reviews Genetics

Volumn 5, Issue 1, 2004, Pages 23-33

  Fraser, Claire M ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTHRAX; BACTERIAL INFECTION; BACTERIAL VIRULENCE; BIOLOGICAL WARFARE; DNA MICROARRAY; FORENSIC MEDICINE; GENOME; GENOMICS; GRAM POSITIVE BACTERIUM; IMMUNE RESPONSE; INFECTION; INFECTION CONTROL; MEDICAL RESEARCH; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; REVIEW; SEVERE ACUTE RESPIRATORY SYNDROME; SPIROCHETE; TERRORISM; VACCINATION; VARIABLE NUMBER OF TANDEM REPEAT; VIRUS INFECTION;

ANTHRAX; ANTI-INFECTIVE AGENTS; BACILLUS ANTHRACIS; BIOLOGICAL WARFARE; BIOTERRORISM; GENOMICS; HUMANS; PROTEOMICS; SARS VIRUS; SEVERE ACUTE RESPIRATORY SYNDROME; UNITED STATES; VACCINES;

ANTHRAX; BACTERIA (MICROORGANISMS); POSIBACTERIA; SPIROCHAETALES;

EID: 0346097887     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrg1245     Document Type: Review

References (68)

1. Bloom, B. R. Genome sequences. A microbial minimalist. Nature 378, 236 (1995).
2. Inglesby, T. V. et al. Anthrax as a biological weapon: medical and public health management. Working Group on Civilian Biodefense. JAMA 281, 1735-1745 (1999).
3. Dennis, D. T. et al. Tularemia as a biological weapon: medical and public health management. JAMA 285, 2763-2773 (2001).
4. Inglesby, T. V. et al. Plague as a biological weapon: medical and public health management. Working Group on Civilian Biodefense. JAMA 283, 2281-2290 (2000).
5. Sullivan, P. Cardiac cases trigger advisory about smallpox vaccination. CMAJ 168, 1167 (2003).
6. Bartlett, J. et al. Smallpox vaccination in 2003: key information for clinicians. Clin. Infect. Dis. 36, 883-902 (2003).
7. Hayes, S. C. & World, M. J. Adverse reactions to anthrax immunization in a military field hospital. J. R. Med. Corps 146, 191-195 (2000).
8. Hotopf, M. et al. Role of vaccinations as risk factors for ill health in veterans of the Gulf War: cross sectional study. Br. Med. J. 320, 1363-1367 (2000).
9. Swanson-Biearman, B. & Krenzelok, E. P. Delayed life-threatening reaction to anthrax vaccine. J. Toxicol. Clin. Toxicol. 39, 81-84 (2001).
10. Asa, P. B., Wilson, R. B., & Garry, R. F. Antibodies to squalene in recipients of anthrax vaccine. Exp. Mol. Pathol. 73, 19-27 (2002).
11. Boucher, Y., Nesbo, C. L. & Doolittle, W. F. Microbial genomes: dealing with diversity. Curr. Opin. Microbiol. 4, 285-289, Comparison of the genome sequences of several pairs of closely related pathogens has revealed tremendous diversity, with some strains of the same species differing by more than 20% in their gene content. This review summarizes these findings and suggests new conceptual and methodological approaches for further analysis of microbial genome diversity.
12. Shannon, J. G., Ross, C. L., Koehler, T. M. & Rest, R. F. Characterization of anthrolysin O, the Bacillus anthracis cholersterol-dependent cytolysin. Infect. Immun. 71, 3183-3189 (2003).
13. Brousseau, R. & Masson, L. Bacillus thuringiensis insecticidal crystal toxins: gene structure and mode of action. Biotechnol. Adv. 6, 697-724 (1988).
14. Paulsen, I. T. et al. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc. Natl Acad. Sci. USA 99, 13148-13153 (2002). This paper reports on the sequence of the bioterror pathogen Brucella suis, with a discussion of the similarities between this organism and other animal and plant pathogens.
15. Del Vecchio, V. G. et al. The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc. Natl Acad. Sci. USA 99, 443-448 (2002).
16. Kaneko, T. et al. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7, 331-338 (2000).
17. Diehn, M. & Relman, D. A. Comparing functional genomic datasets: lessons from DNA microarray analyses of host-pathogen interactions. Curr. Opin. Microbiol. 4, 95-101 (2001).
18. Grifanti et al. Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nature Biotechnol. 20, 914-921 (2002).
19. Dietrich, G. et al. Transcdptome analysis of Neisseria meningitidis during infection. J. Bacteriol. 185, 155-164 (2003). Analysis of the global changes in gene expression that are induced in Neisseria meningitidis after two key steps in meningococcal infection. These data provide new insights into pathogenicity mechanisms of N. meningitidis and reveal differences in gene expression that could possibly be exploited in the development of new therapeutics to treat this infection.
20. He, X. Y., Zhuang, Y. H., Zhang, X. G. & Li. G. L. Comparative proteome analysis of culture supernatant proteins of Mycobacterium tuberculosis H37Rv and H37Ra. Microbes Infect. 5, 851-856 (2003).
21. Lei, B., Mackie, S., Lukomski, S. & Musser, J. M. Identification and immunogenicity of Group A Streptococcus culture supernatant proteins. Infect. Immun. 68, 6807-6818 (2000).
22. Lai, E.-M. et al. Proteomic analysis of the spore coats of Bacillus subtilis and Bacillus anthracis. J. Bacteriol. 185, 1443-1454 (2003).
23. Sonenshein, A. L. in Prokaryotic Development (eds Brun, Y. V. & Shimkets, L. J.) 133-150 (ASM Press, Washington DC, 2000).
24. Dixon, T. C., Meselson, M., Guillemin, J., & Hanna, P. C. Anthrax. N. Engl. J. Med. 341, 815-826 (1999).
25. Cox, J. M. et al. cDNA array analysis of cag pathogenicity island-associated Helicobacter pylori epithelial cell response genes. Infect. Immun. 69, 6970-6980 (2001).
26. Cover T. L. & Blaser, M. J. Helicobacter pylori infections, a paradigm for chronic mucosal inflammation: pathogenesis and implications for eradication and therapy. Adv. Intern. Med. 41, 85-117 (1996).
27. Webb, P. M., Crabtree, J. E. & Forman, D. Gastric cancer, cytotoxin-associated gene A positive Helicobacter pylori, and serum pepsinogens: an international study. The Eurogst Study Group. Gastroenterology 116, 269-276 (1999).
28. Crabtree, J. E. et al. Mucosal IgA recognition of Helicobacter pylori 120 kDa protein, peptic ulceration, and gastric pathology. Lancet 328, 332-225 (1991).
29. Parsonnet, J., Friedman, G. D., Orentreich, N. & Vogelman, H. Risk for gastric cancer in people with CagA positive or CagA negative Helicobacter pylori infection. Gut 40, 297-301 (1997).
30. Ng, L. C., Forslund, O., Koh, S., Kuoppa, K. & Sjostedt, A. The response of murine macrophages to infection with Yersinia pestis as revealed by DNA microarray analysis. Adv. Exp. Med. Biol. 529, 155-160 (2003).
31. Boldnck, J. C. et al. Stereotyped and specific gene expression programs in human innate immune responses to bactena. Proc. Natl Acad. Sci. USA 99, 972-977 (2002). This work uses DNA microarray technology to investigate the gene expression programme that is triggered in human PBMCs after exposure to bacteria and bacterial products. It revealed a remarkable conserved set of changes in gene expression under different conditions and that cell communication within the immune system was an important component of this response.
32. Perrin, A. et al. Comparative genomics identified the genetic islands that distinguish Neisseria meningitidis, the agent of cerebrospinal meningitis, from other Neisseria species. Infect. Immun. 70, 7063-7072 (2002).
33. Tettelin, H. et al. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc. Natl Acad. Sci. USA 99, 12391-12396 (2002)
34. Read T. D. et al. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423, 81-86 (2003).
35. Perna N. et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529-533 (2001).
36. Wilson, W. J. et al. Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol. Cell Probes 16, 119-127 (2002).
37. Laassri, M. et al. Detection and discrimination of orthopoxviruses using microarrays of immobilized oligonucleotides. J. Virol. Methods 112, 67-78 (2003).
38. Jones, R. N. et al. Epidemiological trends in nosocomial and community-acquired infections due to antibiotic-resistant Gram-positive bacteria. Diagn. Microbiol. Infect. Dis. 33, 101-112 (1999).
39. Archer, G. L. Staphylococcus aureus: a well armed pathogen. Clin. Infect Dis. 26, 1179-1181 (1998).
40. Pfaller, M. A. et al. Bacterial pathogens isolated from patients with blood stream infection: frequency of occurrence and antimicrobial susceptibility patterns. Antimicrob. Agents Chemother. 42, 1762-1770 (1998).
41. Wodd Health Organization. Anti-tuberculosis drug resistance in the world: the WHO/IUATLD Global Project on Anti-tuberculosis Drug Resistance Surveillance, 1994-1997. Report No. WHO/TB/97.229 (WHO Global Tuberculosis Programme Geneva, Switzerland, 1997).
42. McDevitt, D. & Rosenberg, M. Exploiting genomics to discover new antibiotics. Trends Microbiol. 9, 611-617, 2001. This review summarizes many of the new genome-enabled approaches that are being used in the discovery and validation of new antibiotic targets.
43. Hughes, D. Exploiting genomics, genetics and chemistry to combat antibiotic resistance. Nature Rev Genet. 4, 432-441 (2003).
44. Hutchison, C. A. et al. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286, 2165-2169 (1999).
45. Lamichhane, G. et al. A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 100, 7213-7218 (2003).
46. Akerley, B. J. et al. A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae. Proc. Natl Acad. Sci. USA 99, 966-971 (2002).
47. Mahan, M. J. et al. Antibiotic-based selection for bacterial genes that are specifically induced during infection of a host. Proc. Natl Acad. Sci. USA 92, 669-673 (1995).
48. Schmid, M. B. Novel approaches to the discovery of antimicrobial agents. Curr. Opin. Chem. Biol. 2, 529-234 (1998).
49. Alksne, L. et al. Identification and analysis of bacterial secretion inhibitors utilizing a SecA-LacZ reporter fusion system. Antimicrob. Agents Chemother. 44, 1418-1427 (2000).
50. Barrelt, J. F. et al. Antimicrobial agents that inhibit two component signal transduction systems. Proc. Natl Acad. Sci. USA 95, 5317-5322 (1998).
51. Payne D. J. et al. The impact of genomics on novel antibacterial targets. Curr. Opin. Drug Discov. Devel. 3, 177-190 (2000).
52. Rappuoli, R. Reverse vaccinology, a genome based approach to vaccine development. Vaccine 19, 2688-2691 (2001). This review summarizes many of the new genome-enabled approaches that are being used in the discovery of new vaccine candidates.
53. Pizza et al. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287, 1816-1820 (2000).
54. Wizemann, T. M., et al. Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection. Infect. Immun. 69, 1593-1598 (2001).
55. Etz, H. et al. Identification of in vivo expressed vaccine candidate antigens from Staphylococcus aureus. Proc. Natl Acad. Sci. USA 99, 6573-6578 (2002).
56. Cummings, C. A. & Relman, D. A. Microbial forensics - cross-examining pathogens. Science 296, 1976-1978 (2002).
57. Read, T. D. et al. Comparative genome sequencing for the discovery of novel polymorphisms in Bacillus anthracis. Science 296, 2028-2033 (2002).
58. Fauci, A. S. Biodefence on the research agenda. Nature 421, 787 (2003). This commentary summarizes the new biodefence research agenda of the NIAID at the NIH.
59. Epstein, G. L. Controlling biological warfare threats: resolving potential tensions among the research community, industry, and the national security community. Crit. Rev. Microbiol. 27, 321-354 (2001).
60. Statement on the consideration of biodefence and biosecurity. Nature 421, 771 (2003).
61. Atlas, R. M. Bioterrorism and biodefence research: changing the focus of microbiology. Nature Rev. Microbiol. 1, 70-74 (2003).
62. Committee on Research Standards and Practices to Prevent the Destructive Application of Biotechnology, Development, Security, and Cooperation, National Research Council of the National Academies of Science. Biotechnology Research in an Age of Terrorism: Confronting the "Dual Use" Dilemma, [online] 〈http://www.nap.edu/books/0309089778/html〉 (National Academies Press, Washington DC, 2003). This report summarizes the present rules and regulations that govern research on pathogens and potentially dangerous biotechnology research. It recommends changes in these practices that could further prevent misuse of dual-use research. This is a seminal report that is likely to have a profound impact on how dual-use research is conducted in the years to come.
63. Amherst, J. Letter, British Manuscript Project, Library of Congress, Washington DC (Amherst to Bouquet, 16 July 1763).
64. Meselson, M. et al. The Sverdlosk anthrax outbreak of 1979. Science 268, 1202-1208 (1994).
65. Smithson, A. E. in Ataxia: The Chemical and Biological Terrorism Threat and the US Response. (eds Smithson, A. E. & Levy, L. E.) Stimson Center Report No. 35, 71-111 (The Henry L. Stimson Center, Washington DC, 2000).
66. Keim P. et al. Molecular investigation of the Aum Shinrikyo anthrax release in Kameido, Japan. J. Clin, Microbiol, 39, 4566-4567, 2001.
67. Fraser C. et al. Microbial genome sequencing. Nature 406, 799-803 (2000).
68. Keim, P. et al. Multiple-locus vanable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J. Bacteriol. 182, 2928-2936 (2000).