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Bacterial Genomes and Infectious Diseases pp 31–39Cite as

Genomic Approach to Understanding Infectious Disease Mechanisms

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Abstract

Close to 100 genomes of bacterial pathogens have been sequenced, and yet most of the genomes sequenced have approx 25% of their open reading frames annotated as proteins with no known function. When genomic sequences of virulent and nonvirulent strains of a particular species are available, comparative genomic analysis is a powerful tool to identify putative virulence genes. Variation in virulence between strains of the same species is a common phenomenon. Availability of the genome sequence of a pathogen permits the application of DNA microarrays to investigate the genetic basis of this variation. DNA microarray technology has facilitated the identification of putative virulence determinants, host specificity genes, and bacterial and host genes that are activated or repressed during an infection. Isogenic mutants and suitable virulence assays are critical in verifying the role of the putative virulence genes identified.

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References

  1. Parkhill, J., Wren, B. W., Thomson, N. R., et al. (2001) Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413, 523–527.

    Article  PubMed  CAS  Google Scholar 

  2. Deng, W., Burland, V., Plunkett, G. III., et al. (2002) Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184, 4601–4611.

    Article  PubMed  CAS  Google Scholar 

  3. Song, Y., Tong, Z., Wang, J., et al. (2004) Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res. 11, 179–197.

    Article  PubMed  CAS  Google Scholar 

  4. Lan, R., Alles, M. C., Donohoe, K., Martinez, M. B., and Reeves, P. R. (2004) Molecular evolutionary relationships of enteroinvasive Escherichia coli and Shigella spp. Infect. Immun. 72, 5080–5088.

    Article  PubMed  CAS  Google Scholar 

  5. Wei, J., Goldberg, M. B., Burland, V., et al. (2003) Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71, 2775–2786.

    Article  PubMed  CAS  Google Scholar 

  6. Jin, Q., Yuan, Z., Xu, J., et al. (2002) Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30, 4432–4441.

    Article  PubMed  CAS  Google Scholar 

  7. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470.

    Article  PubMed  CAS  Google Scholar 

  8. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P. O., and Davis, R. W. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA 93, 10,614–10,619.

    Article  PubMed  CAS  Google Scholar 

  9. Joyce, E. A., Chan, K., Salama, N. R., and Falkow, S. (2002) Redefining bacterial populations: a post-genomic reformation. Nat. Rev. Genet. 3, 462–473.

    PubMed  CAS  Google Scholar 

  10. Conway, T. and Schoolnik, G. K. (2003) Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Mol. Microbiol. 47, 879–889.

    Article  PubMed  CAS  Google Scholar 

  11. Rajashekara, G., Glasner, J. D., Glover, D. A., and Splitter, G. A. (2004) Comparative whole-genome hybridization reveals genomic islands in Brucella species. J. Bacteriol. 186, 5040–5051.

    Article  PubMed  CAS  Google Scholar 

  12. Gandara, B., Merino, A. L., Rogel, M. A., and Martinez-Romero, E. (2001) Limited genetic diversity of Brucella spp. J. Clin. Microbiol. 39, 235–240.

    Article  PubMed  CAS  Google Scholar 

  13. Nelson, K. E., Fleischmann, R. D., DeBoy, R. T., et al. (2003) Complete genome sequence of the oral pathogenic Bacterium Porphyromonas gingivalis strain W83. J. Bacteriol. 185, 5591–5601.

    Article  PubMed  CAS  Google Scholar 

  14. Schachter, J. (1978) Chlamydial infections (first of three parts). N. Engl. J. Med. 298, 428–435.

    Article  PubMed  CAS  Google Scholar 

  15. Stephens, R. S., Kalman, S., Lammel, C., et al. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282, 754–759.

    Article  PubMed  CAS  Google Scholar 

  16. Read, T. D., Brunham, R. C., Shen, C., et al. (2000) Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 28, 1397–1406.

    Article  PubMed  CAS  Google Scholar 

  17. Shirai, M., Hirakawa, H., Kimoto, M., et al. (2000) Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA. Nucleic Acids Res. 28, 2311–2314.

    Article  PubMed  CAS  Google Scholar 

  18. Salama, N., Guillemin, K., McDaniel, T. K., Sherlock, G., Tompkins, L., and Falkow, S. (2000) A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc. Natl. Acad. Sci. USA 97, 14,668–14,673.

    Article  PubMed  CAS  Google Scholar 

  19. Fitzgerald, J. R., Sturdevant, D. E., Mackie, S. M., Gill, S. R., and Musser, J. M. (2001) Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. USA 98, 8821–8826.

    Article  PubMed  CAS  Google Scholar 

  20. Carlson, J. H., Hughes, S., Hogan, D., et al. (2004) Polymorphisms in the Chlamydia trachomatis cytotoxin locus associated with ocular and genital isolates. Infect. Immun. 72, 7063–7072.

    Article  PubMed  CAS  Google Scholar 

  21. Leonard, E. E. II, Tompkins, L. S., Falkow, S., and Nachamkin, I. (2004) Comparison of Campylobacter jejuni isolates implicated in Guillain-Barre syndrome and strains that cause enteritis by a DNA microarray. Infect. Immun. 72, 1199–1203.

    Article  PubMed  CAS  Google Scholar 

  22. Taboada, E. N., Acedillo, R. R., Carrillo, C. D., et al. (2004) Large-scale comparative genomics meta-analysis of Campylobacter jejuni isolates reveals low level of genome plasticity. J. Clin. Microbiol. 42, 4566–4576.

    Article  PubMed  CAS  Google Scholar 

  23. Dziejman, M., Balon, E., Boyd, D., Fraser, C. M., Heidelberg, J. F., and Mekalanos, J. J. (2002) Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc. Natl. Acad. Sci. USA 99, 1556–1561.

    Article  PubMed  CAS  Google Scholar 

  24. Hakenbeck, R., Balmelle, N., Weber, B., Gardes, C., Keck, W., and de Saizieu, A. (2001) Mosaic genes and mosaic chromosomes: intra-and interspecies genomic variation of Streptococcus pneumoniae. Infect. Immun. 69, 2477–2486.

    Article  PubMed  CAS  Google Scholar 

  25. Orihuela, C. J., Radin, J. N., Sublett, J. E., Gao, G., Kaushal, D., and Tuomanen, E. I. (2004) Microarray analysis of pneumococcal gene expression during invasive disease. Infect. Immun. 72, 5582–5596.

    Article  PubMed  CAS  Google Scholar 

  26. Tu, A. H., Fulgham, R. L., McCrory, M. A., Briles, D. E., and Szalai, A. J. (1999) Pneumococcal surface protein A inhibits complement activation by Streptococcus pneumoniae. Infect. Immun. 67, 4720–4724.

    PubMed  CAS  Google Scholar 

  27. Bethe, G., Nau, R., Wellmer, A., et al. (2001) The cell wall-associated serine protease PrtA: a highly conserved virulence factor of Streptococcus pneumoniae. FEMS Microbiol. Lett. 205, 99–104.

    Article  PubMed  CAS  Google Scholar 

  28. Snyder, J. A., Haugen, B. J., Buckles, E. L., et al. (2004) Transcriptome of uropathogenic Escherichia coli during urinary tract infection. Infect. Immun. 72, 6373–6381.

    Article  PubMed  CAS  Google Scholar 

  29. Rappuoli, R. (2000) Pushing the limits of cellular microbiology: microarrays to study bacteria-host cell intimate contacts. Proc. Natl. Acad. Sci. USA 97, 13,467–13,469.

    Article  PubMed  CAS  Google Scholar 

  30. Bryant, P. A., Venter, D., Robins-Browne, R., and Curtis, N. (2004) Chips with everything: DNA microarrays in infectious diseases. Lancet Infect. Dis. 4, 100–111.

    Article  PubMed  CAS  Google Scholar 

  31. Rosenberger, C. M., Scott, M. G., Gold, M. R., Hancock, R. E., and Finlay, B. B. (2000) Salmonella typhimurium infection and lipopolysaccharide stimulation induce similar changes in macrophage gene expression. J. Immunol. 164, 5894–5904.

    PubMed  CAS  Google Scholar 

  32. Cohen, P., Bouaboula, M., Bellis, M., et al. (2000) Monitoring cellular responses to Listeria monocytogenes with oligonucleotide arrays. J. Biol. Chem. 275, 11,181–11,190.

    Article  PubMed  CAS  Google Scholar 

  33. Belcher, C. E., Drenkow, J., Kehoe, B., et al. (2000) From the cover: the transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies. Proc. Natl. Acad. Sci. USA 97, 13,847–13,852.

    Article  PubMed  CAS  Google Scholar 

  34. Alm, R. A., Ling, L. S., Moir, D. T., et al. (1999) Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397, 176–180.

    Article  PubMed  CAS  Google Scholar 

  35. Covacci, A., Telford, J. L., Del Giudice, G., Parsonnet, J., and Rappuoli, R. (1999) Helicobacter pylori virulence and genetic geography. Science 284, 1328–1333.

    Article  PubMed  CAS  Google Scholar 

  36. Nagasako, T., Sugiyama, T., Mizushima, T., Miura, Y., Kato, M., and Asaka, M. (2003) Up-regulated Smad5 mediates apoptosis of gastric epithelial cells induced by Helicobacter pylori infection. J. Biol. Chem. 278, 4821–4825.

    Article  PubMed  CAS  Google Scholar 

  37. Ohnishi, M., Terajima, J., Kurokawa, K., et al. (2002) Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning. Proc. Natl. Acad. Sci. USA 99, 17,043–17,048.

    Article  PubMed  CAS  Google Scholar 

  38. Beres, S. B., Sylva, G. L., Sturdevant, D. E., et al. (2004) Genome-wide molecular dissection of serotype M3 group A Streptococcus strains causing two epidemics of invasive infections. Proc. Natl. Acad. Sci. USA 101, 11,833–11,838.

    Article  PubMed  CAS  Google Scholar 

  39. Jin, S., Joe, A., Lynett, J., Hani, E. K., Sherman, P. M., and Chan, V. L. (2001). JlpA, a novel surface-exposed lipoprotein specific to Campylobacter jejuni, mediates adherence to host epithelial cells. Mol. Microbiol. 39, 1225–1236.

    Article  PubMed  CAS  Google Scholar 

  40. Chan, V. L., Hani, E. K., Joe, A., Lynett, J., Ng, D., and Steele, M. (2000). The hippuricase gene and other unique genes of Campylobacter jejuni, in Campylobacter (Blaser, M. J. and Nachamkin, I., eds.). ASM Press, Washington, DC, pp. 455–463.

    Google Scholar 

  41. Parkhill, J., Wren, B. W., Mungall, K., et al. (2000) The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403, 665–668.

    Article  PubMed  CAS  Google Scholar 

  42. Jin, S., Song, Y. C., Emili, A., Sherman, P. M., and Chan, V. L. (2003) JlpA of Campylobacter jejuni interacts with surface-exposed heat shock protein 90a and triggers signaling pathways leading to the activation of NF-KB and p38 MAP kinase in epithelial cells. Cell. Microbiol. 5, 165–174.

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada

    Voon Loong Chan PhD

  2. Department of Paediatrics Department of Laboratory Medicine and Pathobiology Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada

    Philip M. Sherman MD, FRCPC

  3. Children’s Research Center, Our Lady’s Hospital for Sick Children, School of Medicine and Medical Science, Dublin, Ireland

    Billy Bourke MD, FRCPI

  4. Conway Institute for Biomolecular and Biomedical Research, Dublin, Ireland

    Billy Bourke MD, FRCPI

Authors
  1. Voon Loong Chan PhD
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  2. Philip M. Sherman MD, FRCPC
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  3. Billy Bourke MD, FRCPI
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Editor information

Editors and Affiliations

  1. Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada

    Voon L. Chan PhD

  2. Department of Paediatrics Department of Laboratory Medicine and Pathobiology Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada

    Philip M. Sherman MD, FRCPC

  3. Children’s Research Center, Our Lady’s Hospital for Sick Children, School of Medicine and Medical Science, Dublin, Ireland

    Billy Bourke MD, FRCPI

  4. Conway Institute for Biomolecular and Biomedical Research, University College, Dublin, Ireland

    Billy Bourke MD, FRCPI

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© 2006 Humana Press Inc., Totowa, NJ

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Chan, V.L., Sherman, P.M., Bourke, B. (2006). Genomic Approach to Understanding Infectious Disease Mechanisms. In: Chan, V.L., Sherman, P.M., Bourke, B. (eds) Bacterial Genomes and Infectious Diseases. Humana Press. https://doi.org/10.1007/978-1-59745-152-9_3

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  • DOI: https://doi.org/10.1007/978-1-59745-152-9_3

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-496-8

  • Online ISBN: 978-1-59745-152-9

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