Abstract
Bacterial genome sequencing has revolutionized the research landscape and promises to deliver important changes to the clinical microbiology laboratory, through the identification of novel diagnostic targets and through the birth of a new discipline or “genomic epidemiology.” Current progress and future prospects for exploitation of genome sequences in clinical bacteriology are reviewed.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512.
Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270, 397–403.
Moxon, E. R. (1995) Whole genome sequencing of pathogens: a new era in microbiology. Trends Microbiol. 3, 335–337.
Moxon, E. R., Hood, D. W., Saunders, N. J., Schweda, E. K., and Richards, J. C. (2002) Functional genomics of pathogenic bacteria. Philos. Trans. R Soc. Lond. B Biol. Sci. 357, 109–116.
Schoolnik, G. K. (2002) Functional and comparative genomics of pathogenic bacteria. Curr. Opin. Microbiol. 5, 20–26.
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Veronneau, S., et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391.
Winzeler, E. A., Liang, H., Shoemaker, D. D., and Davis, R. W. (2000) Functional analysis of the yeast genome by precise deletion and parallel phenotypic characterization. Novartis Found. Symp. 229, 105–111.
Kim, S. H. (2000) Structural genomics of microbes: an objective. Curr. Opin. Struct. Biol. 10, 380–383.
Rain, J. C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., et al. (2001) The protein-protein interaction map of Helicobacter pylori. Nature 409, 211–215.
Dieckman, L., Gu, M., Stols, L., Donnelly, M. I., and Collart, F. R. (2002) High throughput methods for gene cloning and expression. Protein Expr. Purif. 25, 1–7.
Schoolnik, G. K. (2002) Microarray analysis of bacterial pathogenicity. Adv. Microb. Physiol. 46, 1–45.
Hinton, J. C. (1997) The Escherichia coli genome sequence: the end of an era or the start of the FUN? Mol. Microbiol. 26, 417–422.
Eiglmeier, K., Parkhill, J., Honore, N., Garnier, T., Tekaia, F., Telenti, A., et al. (2001) The decaying genome of Mycobacterium leprae. Lepr. Rev. 72, 387–398.
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.
Fraser, C. M., Norris, S. J., Weinstock, G. M., White, O., Sutton, G. G., Dodson, R., et al. (1998) Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281, 375–388.
Norris, S. J., Fraser, C. M., and Weinstock, G. M. (1998) Illuminating the agent of syphilis: the Treponema pallidum genome project. Electrophoresis 19, 551–553.
Norris, S. J., Cox, D. L., and Weinstock, G. M. (2001) Biology of Treponema pallidum: correlation of functional activities with genome sequence data. J. Mol. Microbiol. Biotechnol. 3, 37–62.
Weinstock, G. M., Hardham, J. M., McLeod, M. P., Sodergren, E. J., and Norris, S. J. (1998) The genome of Treponema pallidum: new light on the agent of syphilis. FEMS Microbiol. Rev. 22, 323–332.
Weinstock, G. M., Smajs, D., Hardham, J., and Norris, S. J. (2000) From microbial genome sequence to applications. Res. Microbiol. 151, 151–158.
Ye, R. W., Tao, W., Bedzyk, L., Young, T., Chen, M., and Li, L. (2000) Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J. Bacteriol. 182, 4458–4465.
Helmann, J. D., Wu, M. F., Kobel, P. A., Gamo, F. J., Wilson, M., Morshedi, M. M., et al. (2001) Global transcriptional response of Bacillus subtilis to heat shock. J. Bacteriol. 183, 7318–7328.
Okinaka, Y., Yang, C. H., Perna, N. T., and Keen, N. T. (2002) Microarray profiling of Erwinia chrysanthemi 3937 genes that are regulated during plant infection. Mol. Plant Microbe Interact. 15, 619–629.
Khil, P. P. and Camerini-Otero, R. D. (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 44, 89–105.
Hood, D. W., Deadman, M. E., Allen, T., Masoud, H., Martin, A., Brisson, J. R., et al. (1996) Use of the complete genome sequence information of Haemophilus influenzae strain Rd to investigate lipopolysaccharide biosynthesis. Mol. Microbiol. 22, 951–965.
McDevitt, D. and Rosenberg, M. (2001) Exploiting genomics to discover new antibiotics. Trends Microbiol. 9, 611–617.
Raczniak, G., Ibba, M., and Soll, D. (2001) Genomics-based identification of targets in pathogenic bacteria for potential therapeutic and diagnostic use. Toxicology 160, 181–189.
Fairlamb, A. H. (2002) Metabolic pathway analysis in trypanosomes and malaria parasites. Philos. Trans. R. Soc. Lond. B Biol. Sci. 357, 101–107.
Fraser, C. M., Eisen, J. A., and Salzberg, S. L. (2000) Microbial genome sequencing. Nature 406, 799–803.
Saunders, N. J. and Moxon, E. R. (1998) Implications of sequencing bacterial genomes for pathogenesis and vaccine development. Curr. Opin. Biotechnol. 9, 618–623.
Pizza, M., Scarlato, V., Masignani, V., Giuliani, M. M., Arico, B., Comanducci, M., et al. (2000) Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287, 1816–1820.
Dingle, K. E., Colles, F. M., Wareing, D. R., Ure, R., Fox, A. J., Bolton, F. E., et al. (2001) Multilocus sequence typing system for Campylobacter jejuni. J. Clin. Microbiol. 39, 14–23.
Homan, W. L., Tribe, D., Poznanski, S., Li, M., Hogg, G., Spalburg, E., et al. (2002) Multilocus sequence typing scheme for Enterococcus faecium. J. Clin. Microbiol. 40, 1963–1971.
Desai, M., Logan, J. M., Frost, J. A., and Stanley, J. (2001) Genome sequencebased fluorescent amplified fragment length polymorphism of Campylobacter jejuni, its relationship to serotyping, and its implications for epidemiological analysis. J. Clin. Microbiol. 39, 3823–3829.
Parkhill, J., Wren, B. W., Mungall, K., Ketley, J. M., Churcher, C., Basham, D., et al. (2000) The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403, 665–668.
Dorrell, N., Mangan, J. A., Laing, K. G., Hinds, J., Linton, D., Al-Ghusein, H., et al. (2001) Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Res. 11, 1706–1715.
Wren, B. W., Linton, D., Dorrell, N., and Karlyshev, A. V. (2001) Post genome analysis of Campylobacter jejuni. Symp. Ser. Soc. Appl. Microbiol. 30, 36S–44S.
Linton, D., Karlyshev, A. V., and Wren, B. W. (2001) Deciphering Campylobacter jejuni cell surface interactions from the genome sequence. Curr. Opin. Microbiol. 4, 35–40.
Karlyshev, A. V. and Wren, B. W. (2001) Detection and initial characterization of novel capsular polysaccharide among diverse Campylobacter jejuni strains using alcian blue dye. J. Clin. Microbiol. 39, 279–284.
Karlyshev, A. V., McCrossan, M. V., and Wren, B. W. (2001) Demonstration of polysaccharide capsule in Campylobacter jejuni using electron microscopy. Infect. Immun. 69, 5921–5924.
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.
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.
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.
Shafi, J. (2002) Oral Presentation: Rapid Genomic and Biological Characterisation Of The Leicester School Tuberculosis Outbreak Strain, at Acid-FaSt Club Summer Meeting, Cardiff, UK.
Watson, J. M. and Moss, F. (2001) TB in Leicester: out of control, or just one of those things? BMJ 322, 1133–1134.
Alli, O. A. T., McBride, A., Wilkinson, K., Hinks, L., Day, I. N. M., and Pallen, M. J. (2002) Poster presentation: long PCR as a tool for exploring genomic diversity in Escherichia coli, at Genome-based Pathogen Biology: The First 25 Years and Beyond, Hinxton Hall Conference Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, England.
Read, T. D., Salzberg, S. L., Pop, M., Shumway, M., Umayam, L., Jiang, L., et al. (2002) Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296, 2028–2033.
Bannantine, J. P., Baechler, E., Zhang, Q., Li, L., and Kapur, V. (2002) Genome scale comparison of Mycobacterium avium subsp. paratuberculosis Mycobacterium avium subsp. avium reveals potential diagnostic sequences. J. Clin. Microbiol. 40, 1303–1310.
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.
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.
Gill, R. T., Wildt, S., Yang, Y. T., Ziesman, S., and Stephanopoulos, G. (2002) Genome-wide screening for trait conferring genes using DNA microarrays. Proc. Natl. Acad. Sci. USA 99, 7033–7038.
Monday, S. R., Whittam, T. S., and Feng, P. C. (2001) Genetic and evolutionary analysis of mutations in the gusA gene that cause the absence of beta-glucuronidase activity in Escherichia coli O157:H7. J. Infect. Dis. 184, 918–921.
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
Pallen, M.J. (2004). Bacterial Genomes for the Masses. In: Woodford, N., Johnson, A.P. (eds) Genomics, Proteomics, and Clinical Bacteriology. Methods in Molecular Biology™, vol 266. Humana Press. https://doi.org/10.1385/1-59259-763-7:003
Download citation
DOI: https://doi.org/10.1385/1-59259-763-7:003
Publisher Name: Humana Press
Print ISBN: 978-1-58829-218-6
Online ISBN: 978-1-59259-763-5
eBook Packages: Springer Protocols