Skip to main content
SpringerLink
Log in
Book cover

Bacterial Genomes and Infectious Diseases pp 255–264Cite as

Future Directions of Infectious Disease Research

  • Chapter

  • 1176 Accesses

Abstract

Sequencing of bacterial genomes and comparative genomics provide novel approaches for the identification of previously unrecognized microbial pathogens that likely cause a variety of infectious diseases in humans and animals. In addition, the genetic approaches probably will discover new virulence determinants that can be used as targets in the development of novel intervention strategies for both the prevention and treatment of infectious diseases. This chapter cites specific examples in support of these contentions, with particular reference to recent advances of selected infectious and chronic inflammatory diseases involving the gastrointestinal tract.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Doolittle, R. F. (1998) Microbial genomes opened up. Nature 392, 339–342.

    Article  PubMed  CAS  Google Scholar 

  2. Jenks, P. J. (1998) Sequencing microbial genomes—what will it do for microbiology? J. Med. Microbiol. 47, 375–382.

    Article  PubMed  CAS  Google Scholar 

  3. Chan, V. L. (2003) Bacterial genomes and infectious diseases. Pediatr. Res. 54, 1–7.

    Article  PubMed  Google Scholar 

  4. Ussery, D. W. (2004) Genome update: 161 prokaryotic genomes sequenced, and counting. Microbiology 150, 261–263.

    Article  PubMed  CAS  Google Scholar 

  5. Moran, N. A. (2002) Microbial minimalism: genome reduction in bacterial pathogens. Cell 108, 583–586.

    Article  PubMed  CAS  Google Scholar 

  6. Rappe, M. S. and Giovannoni, S. J. (2003) The uncultured microbial majority. Annu. Rev. Microbiol. 57, 369–394.

    Article  PubMed  CAS  Google Scholar 

  7. Raoult, D., Birg M. L., La Scola, B., et al. (2000) Cultivation of the bacillus of Whipple’s disease. N. Engl. J. Med. 342, 620–625.

    Article  PubMed  CAS  Google Scholar 

  8. Bentley, S. D., Malwald, M., Murphy, L. D., et al. (2003) Sequencing and analysis of the genome of the Whipple’s disease bacterium Tropheryma whipplei. Lancet 361, 637–644.

    Article  PubMed  CAS  Google Scholar 

  9. Maiwald, M., Von Herbay, A., Lepp, P. W., and Relman, D. A. (2000) Organization, structure, and variability of the rRNA operon of the Whipple’s disease bacterium (Tropheryma whipplei). J. Bacteriol. 182, 3293–3297.

    Article  Google Scholar 

  10. Allan, P. (2001) What’s the story H pylori? Lancet 357, 694.

    Article  Google Scholar 

  11. Peek, R. M. Jr. and Blaser, M. J. (2002) Helicobacter pylori and gastrointestinal tract adenocarcinoma. Nature Rev. Cancer 2, 28–37.

    Article  CAS  Google Scholar 

  12. Houghton, J. M., Stoicov, C., Nomura S., et al. (2004) Gastric cancer originating from bone marrow-derived cells. Science 306, 1568–1571.

    Article  PubMed  CAS  Google Scholar 

  13. Lecuit, M., Abachin, E., Martin, A., et al. (2004) Immunoproliferative small intestinal disease associated with Campylobacter jejuni. N. Engl. J. Med. 350, 239–248.

    Article  PubMed  CAS  Google Scholar 

  14. Linskens, R. K., Huijsdens, X. W., Savelkoul, P. H. M., Vandenbroucke-Grauls, J. E., and Meuwissen, S. G. M. (2001) The bacterial flora in inflammatory bowel disease: current insight in pathogenesis and the influence of antibiotics and probiotics. Scand. J. Gastroenterol. 36(Suppl 234), 29–40.

    Article  Google Scholar 

  15. Selby, W. S. (2004) Mycobacterium avium subspecies paratuberculosis bacteraemia in patients with inflammatory bowel disease. Lancet 364, 1013–1014.

    Article  PubMed  Google Scholar 

  16. Saunders, K. E., Shen, Z., Dewhirst, F. E., Paster, B. J., Dangler, C. A., and Fox, J. G (1999) Novel intestinal Helicobacter species isolated from cotton-top tamarins (Sanguinus oedipus) with chronic colitis. J. Clin. Microbiol. 37, 146–151.

    PubMed  CAS  Google Scholar 

  17. Jiang, H.-Q., Kushnir, N., Thurnheer, M. C., Bos, N. A., and Cebra, J. J. (2002) Monoassociation of SCID mice with Helicobacter muridarum, but not four other enterics, provokes IBD upon receipt of T cells. Gastroenterology 122, 1346–1354.

    Article  PubMed  Google Scholar 

  18. Whary, M. T. and Fox, J. G. (2004) Natural and experimental Helicobacter infections. Comp. Med. 54, 128–158.

    PubMed  CAS  Google Scholar 

  19. Sestak, K., Merritt, C. K., Borda, J., et al. (2003) Infectious agent and immune response characteristics of chronic enterocolitis in captive rhesus macaques. Infect. Immun. 71, 4079–4086.

    Article  PubMed  CAS  Google Scholar 

  20. Campieri, M. and Gionchetti, P. (2001) Bacteria as a cause of ulcerative colitis. Gut 48, 132–135.

    Article  PubMed  CAS  Google Scholar 

  21. Kroes, I., Lepp, P. W., and Relman, D. A. (1999) Bacterial diversity within the human subgingival crevice. Proc. Natl. Acad. Sci. USA 96, 14,547–14,552.

    Article  PubMed  CAS  Google Scholar 

  22. Lepp, P. W., Brinig, M. M., Ouverney, C. C., Palm, K., Armitage, G. C., and Relman, D. A. (2004) Methanogenic Archaea and human periodontal disease. Proc. Natl. Acad. Sci. USA 101, 6176–6181.

    Article  PubMed  CAS  Google Scholar 

  23. Pizarro, T. T., Arseneau, K. O., and Cominelli, F. (2000) Lessons from genetically engineered animal models XI. Novel mouse models to study pathogenic mechanisms of Crohn’s disease. Am. J. Physiol. 278, G665–G669.

    CAS  Google Scholar 

  24. Zareie, M., Singh, P., Irvine, E., Sherman, P., McKay, D., and Perdue, M. (2001) Monocyte/macrophage activation by normal bacteria and bacterial products: implications for epithelial function in Crohn’s disease. Am. J. Pathol. 158, 1101–1109.

    PubMed  CAS  Google Scholar 

  25. Nazli, A., Yang. P.-C, Jury, J., et al. (2004) Epithelia under metabolic stress perceive commensal bacteria as a threat. Am. J. Pathol. 164, 947–957.

    PubMed  Google Scholar 

  26. Soderholm, J., Yang, P.-C, Ceponis, P., et al. (2002) Chronic stress induces mast cell dependent bacterial adherence and initiates mucosal inflammation in rat intestine. Gastroenterology 123, 1099–1108.

    Article  PubMed  Google Scholar 

  27. Lodes, M. J., Cong, Y., Elson, C. O., et al. (2004) Bacterial flagellin is a dominant antigen in Crohn’s disease. J. Clin. Invest. 113, 1296–1306.

    Article  PubMed  CAS  Google Scholar 

  28. Waldner, H., Collins, M., and Kuchroo, V. K. (2004) Activation of antigen-presenting cells by microbial products breaks self tolerance and induces autoimmune disease. J. Clin. Invest. 113, 990–997.

    Article  PubMed  CAS  Google Scholar 

  29. Agostoni, C., Axelsson, I., Braegger, C., et al. (2004) Probiotic bacteria in dietetic products for infants: a commentary by the ESPGHAN committee on nutrition. J. Pediatr. Gastroenterol. Nutr. 38, 365–374.

    Article  PubMed  Google Scholar 

  30. Agostoni, C., Axelsson, I., Goulet, O., et al. (2004) Prebiotic oligosaccharides in dieteticproducts for infants: a commentary by the ESPGHAN committee on nutrition. J. Pediatr. Gastroenterol. Nutr. 39, 465–473.

    Article  PubMed  Google Scholar 

  31. Schell, M. A., Karmirantzou, M., Snel, B., et al. (2002) The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. USA 99, 14,422–14,227.

    Article  PubMed  CAS  Google Scholar 

  32. Boekhorst, J., Siezen, R. J., Zwahlen, M.-C, et al. (2004) The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content. Microbiology 150, 3601–3611.

    Article  PubMed  CAS  Google Scholar 

  33. Servin, A. L. (2004) Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens. FEMS Microbiol. Rev. 28, 40–440.

    Article  CAS  Google Scholar 

  34. Hamilton-Miller, J. M. (2003) The role of probiotics in the treatment and prevention of Helicobacter pylori infection. Int. J. Antimicrob. Agents 22, 360–366.

    Article  PubMed  CAS  Google Scholar 

  35. Johnson-Henry, K., Mitchell, D. J., Avitzur, Y., Galindo-Mata, E., Jones, N. L., and Sherman, P. M. (2004) Probiotics reduce bacterial colonization and gastric inflammation in H. pylori-infected mice. Dig. Dis. Sci. 49, 1095–1102.

    Article  PubMed  Google Scholar 

  36. Van Niel, C. W., Feudtner, C., Garrison, M. M., and Chritakis, D. A. (2002) Lactobacillus therapy for acute infectious diarrhea in children: a meta-analysis. Pediatrics 109, 678–684.

    Article  PubMed  Google Scholar 

  37. Huang, J. S., Bousvaros, A., Lee, J. W., Diaz, A., and Davidson, E. J. (2002) Efficacy of probiotic use in acute diarrhea in children: a meta-analysis. Dig. Dis. Sci. 47, 2625–2634.

    Article  PubMed  CAS  Google Scholar 

  38. Cremonini, F., Di Caro, S., Nista, E. C., et al. (2002) Meta-analysis: the effect of probiotic administration on antibiotic-associated diarrhoea. Aliment. Pharmacol. Therap. 16, 1461–1467.

    Article  CAS  Google Scholar 

  39. Grozdanov, L., Raasch, C., Schulze, J., et al. (2004) Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917. J. Bacteriol. 186, 5432–5441.

    Article  PubMed  CAS  Google Scholar 

  40. Kruis, W., Fric, P., Pokrotnieks, J., et al. (2004) Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine. Gut 53, 1617–1623.

    Article  PubMed  CAS  Google Scholar 

  41. Dahan, S., Dalmasso, G., Imbert, V., Peyron, J. F., Rampal, P., and Czerucka, D. (2003) Saccharomyces boulardii interferes with enterohemorrhagic Escherichia coli-induced signaling pathways in T84 cells. Infect. Immun. 71, 766–733.

    Article  PubMed  CAS  Google Scholar 

  42. Stevens, D. A. (2001) Saccharomyces and enteropathogenic Escherichia coli. Infect. Immun. 69, 4192.

    Article  Google Scholar 

  43. Cassone, M., Serra, P., Mondello, F., et al. (2003) Outbreak of Saccharomyces cervisiae subtype boulardii fungemia in patients neighboring those treated with a probiotic preparation of the organism. J. Clin. Microbiol. 41, 5340–5343.

    Article  PubMed  Google Scholar 

  44. Gionchetti, P., Rizzello, F., Venturi, A., et al. (2000) Oral bacteriotherapy as maintenance treatment in patients with chronic pouchitis: a double-blind, placebo-controlled trial. Gastroenterology 119, 305–309.

    Article  PubMed  CAS  Google Scholar 

  45. Gionchetti, P., Rizello, F., Helwig, U., et al. (2003) Prophylaxis of pouchitis onset with probiotic therapy: a double-blind, placebo-controlled trial. Gastroenterology 124, 1202–1209.

    Article  PubMed  Google Scholar 

  46. Madsen, K. L., Doyle, J. S., Jewell, L. D., Tavernini, M. M., and Fedorak, R. N. (1999) Lactobacillus species prevents colitis in interleukin-10 gene-deficient mice. Gastroenterology 116, 1107–1114.

    Article  PubMed  CAS  Google Scholar 

  47. Madsen, K., Cornish, A., Soper, P., et al. (2001) Probiotic bacteria enhance murine and human intestinal epithelial barrier function. Gastroenterology 121, 580–591.

    Article  PubMed  CAS  Google Scholar 

  48. Abbott, A. (2004) Gut reaction. Nature 427, 284–286.

    Article  PubMed  CAS  Google Scholar 

  49. Mack, D. R., Michail, S., Wei, S., McDougall, L., and Hollingsworth, M. A. (1999) Probiotics inhibit enteropathogenic Escherichia coli adherence in vitro by inducing intestinal mucin gene expression. Am. J. Physiol. 276, G941–G950.

    PubMed  CAS  Google Scholar 

  50. Petrof, E. O., Kojima, K., Ropeleski, M. J., et al. (2004) Probiotics inhibit nuclear factorkB and induce heat shock proteins in colonic epithelial cells through proteasome inhibition. Gastroenterology 127, 1474–1487.

    Article  PubMed  CAS  Google Scholar 

  51. Rachmilewitz, D., Katakura, K., Karmeli, F., et al. (2004) Toll-like receptor 9 signaling mediates the anti-inflammatory effects of probiotics in murine experimental colitis. Gastroenterology 126, 520–528.

    Article  PubMed  CAS  Google Scholar 

  52. Jijon, H., Backer, J., Diaz, H., et al. (2004) DNA from probiotic bacteria modulates murine and human epithelial and immune function. Gastroenterology 126, 1358–1373.

    Article  PubMed  CAS  Google Scholar 

  53. Steidler, L., Hans, W., Schotte, L., et al. (2000) Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. Science 289, 1352–1355.

    Article  PubMed  CAS  Google Scholar 

  54. Vandenbroucke, K., Hans, W., Van Huysse, J., et al. (2004) Active delivery of trefoil factors by genetically modified Lactococcus lactis prevents and heals acute colitis in mice. Gastroenterology 127, 502–513.

    Article  PubMed  CAS  Google Scholar 

  55. Verdue, E. F., Bercik, P., Bergonzelli, G. E., et al. (2004) Lactobacillus paracasei normalizes muscle hypercontractility in a murine model of postinfective gut dysfunction. Gastroenterology 127, 826–837.

    Article  CAS  Google Scholar 

  56. Reid, G., Jass, J., Sebulsky, M. T., and McCormick, J. K. (2003) Potential uses of probiotics in clinical practice. Clin. Microbiol. Rev. 16, 658–672.

    Article  PubMed  Google Scholar 

  57. Bansal, A. K. and Meyer, T. E. (2002) Evolutionary analysis by whole-genome comparisons. J. Bacteriol. 184, 2260–2272.

    Article  PubMed  CAS  Google Scholar 

  58. Doolittle, F. R. (2002) Microbial genomes multiply. Nature 416, 697–700.

    Article  PubMed  CAS  Google Scholar 

  59. Eppinger, M., Baar, C., Raddatz, G., Huson, D. H., and Schuster, S. C. (2004) Comparative analysis of four Campylobacterales. Nature Rev. Microbiol. 2, 872–885.

    Article  CAS  Google Scholar 

  60. Read, T. D., Salzberg, S. L., Pop, M., et al. (2002) Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296, 2028–2033.

    Article  PubMed  CAS  Google Scholar 

  61. Cummings, C. A. and Relman, D. A. (2002) Microbial forensics—“cross-examining pathogens.” Science 296, 1976–1979.

    Article  PubMed  CAS  Google Scholar 

  62. Boyce, J. D., Cullen, P. A., and Adler, B. (2004) Genomic-scale analysis of bacterial gene and protein expression in the host. Emerg. Infect. Dis. 10, 1357–1362.

    PubMed  CAS  Google Scholar 

  63. Gribbin, J. (2002) Science: A History. Penguin, London, UK.

    Google Scholar 

  64. Venter, J. C., Adams, M. D., Myers, E. W., et al. (2001) The sequence of the human genome. Science 291, 1304–1351.

    Article  PubMed  CAS  Google Scholar 

  65. Sanger, F., Air, G. M., Barrell, B. G., et al. (1977) Nucliotide sequence of bacteriophage phi X174 DNA. Nature 265, 687–695.

    Article  PubMed  CAS  Google Scholar 

  66. Blattner, F. R. (1983) Biological frontiers. Science 222, 719–720.

    Article  PubMed  Google Scholar 

  67. Danchin, A. (1995) Why sequence genomes? The Escherichia coli imbroglio. Mol. Microbiol. 18, 371–376.

    Article  PubMed  CAS  Google Scholar 

  68. Nowak, R. (1995) Getting the bugs worked out. Science 267, 172–174.

    Article  PubMed  CAS  Google Scholar 

  69. Fleischmann, R. D., Adams, M. D., White, O., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512.

    Article  PubMed  CAS  Google Scholar 

  70. Fraser, C. M., Gocayne, J. D., White, O., et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270, 397–403.

    Article  PubMed  CAS  Google Scholar 

  71. Blattner, F. R., Plunkett, G., 3rd, Bloch, C. A., et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474.

    Article  PubMed  CAS  Google Scholar 

  72. Fraser, C. M., Eisen, J. A., Nelson, K. E., Paulsen, I. T., and Salzberg, S. L. (2002). The value of complete microbial genome sequencing (you get what you pay for). J. Bacteriol. 184, 6403–6405.

    Article  PubMed  CAS  Google Scholar 

  73. Anonymous. (2002) A genome fest; 25 years of pathogen genome sequencing. Wellcome News 10–11.

    Google Scholar 

  74. Hughes, D. (2003) Exploiting genomics, genetics and chemistry to combat antibiotic resistance. Nat. Rev. Genet. 4, 432–441.

    Article  PubMed  CAS  Google Scholar 

  75. Meinke, A., Henics, T., and Nagy, E. (2004) Bacterial genomes pave the way to novel vaccines. Curr. Opin. Microbiol. 7, 314–320.

    Article  PubMed  CAS  Google Scholar 

  76. De Groot, A. S. and Rappuoli, R. (2004) Genome-derived vaccines. Expert Rev. Vaccines 3, 59–76.

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

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

    Philip M. Sherman MD, FRCPC

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

    Billy Bourke MD, FRCPI

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

    Billy Bourke MD, FRCPI

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

    Voon Loong Chan PhD

Authors
  1. Philip M. Sherman MD, FRCPC
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Billy Bourke MD, FRCPI
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Voon Loong Chan PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

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

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Humana Press Inc., Totowa, NJ

About this chapter

Cite this chapter

Sherman, P.M., Bourke, B., Chan, V.L. (2006). Future Directions of Infectious Disease Research. 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_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-152-9_14

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-496-8

  • Online ISBN: 978-1-59745-152-9

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation