Abstract
Comparative genomics is a science in its infancy. It has been driven by a huge increase in freely available genome-sequence data, and the development of computer techniques to allow whole-genome sequence analyses. Other approaches, which use hybridization as a method for comparing the gene content of related organisms, are rising alongside these more bioinformatic methods. All these approaches have been pioneered using bacterial genomes because of their simplicity and the large number of complete genome sequences available. The aim of bacterial comparative genomics is to determine what genotypic differences are important for the expression of particular traits (e.g., antibiotic resistance, virulence, or host preference). The benefits of such studies will be a deeper understanding of these phenomena; the possibility of exposing novel drug targets, including those for antivirulence drugs; and the development of molecular techniques that reveal patients who are infected with virulent organisms so that health care resources can be allocated appropriately. With more and more genome sequences becoming available, the rise of comparative genomics continues apace.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Blattner, F. R., Plunkett, G., 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474.
Perna, N. T., Plunkett, G., 3rd, Burland, V., Mau, B., Glasner, J. D., Rose, D. J., et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529–533.
Reid, S. D., Herbelin, C. J., Bumbaugh, A. C., Selander, R. K., and Whittam, T. S. (2000) Parallel evolution of virulence in pathogenic Escherichia coli. Nature 406, 64–67.
Stover, C. K., Pham, X. Q., Erwin, A. L., Mizoguchi, S. D., Warrener, P., Hickey, M. J., et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406, 959–964.
Clarke, G. D., Beiko, R. G., Ragan, M. A., and Charlebois, R. L. (2002) Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184, 2072–2080.
Edwards, R. A., Olsen, G. J., and Maloy, S. R. (2002) Comparative genomics of closely related salmonellae. Trends Microbiol. 10, 94–99.
Parkhill, J., Dougan, G., James, K. D., Thomson, N. R., Pickard, D., Wain, J., et al. (2001) Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413, 848–852.
McClelland, M., Sanderson, K. E., Spieth, J., Clifton, S. W., Latreille, P., Courtney, L., et al. (2001) Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413, 852–856.
Hansen-Wester, I. and Hensel, M. (2002) Genome-based identification of chromosomal regions specific for Salmonella spp. Infect. Immun. 70, 2351–2360.
Hou, Y. M. (1999) Transfer RNAs and pathogenicity islands. Trends Biochem. Sci. 24, 295–298.
Parkhill, J., Wren, B. W., Thomson, N. R., Titball, R. W., Holden, M. T., Prentice, M. B., et al. (2001) Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413, 523–527.
Deng, W., Burland, V., Plunkett, G., 3rd, Boutin, A., Mayhew, G. F., Liss, P., et al. (2002) Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184, 4601–4611.
Kuroda, M., Ohta, T., Uchiyama, I., Baba, T., Yuzawa, H., Kobayashi, I., et al. (2001) Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357, 1225–1240.
Avison, M. B., Bennett, P. M., Howe, R. A., and Walsh, T. R. (2002) Preliminary analysis of the genetic basis for vancomycin resistance in Staphylococcus aureus strain Mu50. J. Antimicrob. Chemother. 49, 255–260.
O’Neill, A. J. and Chopra, I. (2002) Insertional inactivation of mutS in Staphylococcus aureus reveals potential for elevated mutation frequencies, although the prevalence of mutators in clinical isolates is low. J. Antimicrob. Chemother. 50, 161–169.
Baba, T., Takeuchi, F., Kuroda, M., Yuzawa, H., Aoki, K., Oguchi, A., et al. (2002) Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 359, 1819–1827.
Herron, L. L., Chakravarty, R., Dwan, C., Fitzgerald, J. R., Musser, J. M., Retzel, E., et al. (2002) Genome sequence survey identifies unique sequences and key virulence genes with unusual rates of amino acid substitution in bovine Staphylococcus aureus. Infect. Immun. 70, 3978–3981.
Cunningham, M. W. (2000) Pathogenesis of group A streptococcal infections. Clin. Microbiol. Rev. 13, 470–511.
Smoot, J. C., Barbian, K. D., Van Gompel, J. J., Smoot, L. M., Chaussee, M. S., Sylva, G. L., et al. (2002) Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Proc. Natl. Acad. Sci. USA 99, 4668–4673.
Ferretti, J. J., McShan, W. M., Ajdic, D., Savic, D. J., Savic, G., Lyon, K., et al. (2001) Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc. Natl. Acad. Sci. USA 98, 4658–4663.
Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537–544.
Cole, S. T. (2002) Comparative and functional genomics of the Mycobacterium tuberculosis complex. Microbiology 148, 2919–2928.
Cole, S. T., Eiglmeier, K., Parkhill, J., James, K. D., Thomson, N. R., Wheeler, P. R., et al. (2001) Massive gene decay in the leprosy bacillus. Nature 409, 1007–1011.
Janssen, P. J., Audit, B., and Ouzounis, C. A. (2001) Strain-specific genes of Helicobacter pylori: distribution, function and dynamics. Nucleic Acids Res. 29, 4395–4404.
Garcia-Vallve, S., Janssen, P. J., and Ouzounis, C. A. (2002) Genetic variation between Helicobacter pylori strains: gene acquisition or loss? Trends Microbiol. 10, 445–447.
Thompson, L. J. and de Reuse, H. (2002) Genomics of Helicobacter pylori. Helicobacter 7, 1–7.
Ochman, H. and Jones, I. B. (2000) Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19, 6637–6643.
Richmond, C. S., Glasner, J. D., Mau, R., Jin, H., and Blattner, F. R. (1999) Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res. 27, 3821–3835.
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.
Heidelberg, J. F., Eisen, J. A., Nelson, W. C., Clayton, R. A., Gwinn, M. L., Dodson, R. J., et al. (2000) DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406, 477–483.
Behr, M. A., Wilson, M. A., Gill, W. P., Salamon, H., Schoolnik, G. K., Rane, S., et al. (1999) Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284, 1520–1523.
Malloff, C. A., Fernandez, R. C., and Lam, W. L. (2001) Bacterial comparative genomic hybridization: a method for directly identifying lateral gene transfer. J. Mol. Biol. 312, 1–5.
Brown, P. K. and Curtiss, R., 3rd (1996) Unique chromosomal regions associated with virulence of an avian pathogenic Escherichia coli strain. Proc. Natl. Acad. Sci. USA 93, 11,149–11,154.
Pradel, N., Leroy-Setrin, S., Joly, B., and Livrelli, V. (2002) Genomic subtraction to identify and characterize sequences of Shiga toxin-producing Escherichia coli O91:H21. Appl. Environ. Microbiol. 68, 2316–2325.
Ahmed, I. H., Manning, G., Wassenaar, T. M., Cawthraw, S., and Newell, D. G. (2002) Identification of genetic differences between two Campylobacter jejuni strains with different colonization potentials. Microbiology 148, 1203–1212.
Bahrani-Mougeot, F. K., Pancholi, S., Daoust, M., and Donnenberg, M. S. (2001) Identification of putative urovirulence genes by subtractive cloning. J. Infect. Dis. 183(Suppl 1), S21–S23.
Zhang, L., Foxman, B., Manning, S. D., Tallman, P., and Marrs, C. F. (2000) Molecular epidemiologic approaches to urinary tract infection gene discovery in uropathogenic Escherichia coli. Infect. Immun. 68, 2009–2015.
Jungblut, P. R. (2001) Proteome analysis of bacterial pathogens. Microbes Infect. 3, 831–840.
Betts, J. C., Dodson, P., Quan, S., Lewis, A. P., Thomas, P. J., Duncan, K. et al. (2000) Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551. Microbiology 146, 3205–3216.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Humana Press Inc.
About this protocol
Cite this protocol
Avison, M.B. (2004). Comparative Genomics. In: Woodford, N., Johnson, A.P. (eds) Genomics, Proteomics, and Clinical Bacteriology. Methods in Molecular Biology™, vol 266. Humana Press. https://doi.org/10.1385/1-59259-763-7:047
Download citation
DOI: https://doi.org/10.1385/1-59259-763-7:047
Publisher Name: Humana Press
Print ISBN: 978-1-58829-218-6
Online ISBN: 978-1-59259-763-5
eBook Packages: Springer Protocols