1887

Abstract

The most widely used DNA-based method for bacterial strain typing, multi-locus sequence typing (MLST), lacks sufficient resolution to distinguish among many bacterial strains within a species. Here, we show that strain typing based on the presence or absence of distributed genes is able to resolve all completely sequenced genomes of six bacterial species. This was accomplished by the development of a clustering method, neighbour grouping, which is completely consistent with the lower-resolution MLST method, but provides far greater resolving power. Because the presence/absence of distributed genes can be determined by low-cost microarray analyses, it offers a practical, high-resolution alternative to MLST that could provide valuable diagnostic and prognostic information for pathogenic bacterial species.

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/content/journal/micro/10.1099/mic.0.035188-0
2010-04-01
2024-03-29
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References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410
    [Google Scholar]
  2. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
    [Google Scholar]
  3. Didelot X., Falush D. 2007; Inference of bacterial microevolution using multilocus sequence data. Genetics 175:1251–1266
    [Google Scholar]
  4. Ehrlich G. D., Hu F. Z., Shen K., Stoodley P., Post J. C. 2005; Bacterial plurality as a general mechanism driving persistence in chronic infections. Clin Orthop Relat Res20–24
    [Google Scholar]
  5. Feil E. J., Spratt B. G. 2001; Recombination and the population structures of bacterial pathogens. Annu Rev Microbiol 55:561–590
    [Google Scholar]
  6. Feil E. J., Smith J. M., Enright M. C., Spratt B. G. 2000; Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154:1439–1450
    [Google Scholar]
  7. Feil E. J., Holmes E. C., Bessen D. E., Chan M. S., Day N. P., Enright M. C., Goldstein R., Hood D. W., Kalia A. other authors 2001; Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci U S A 98:182–187
    [Google Scholar]
  8. Feil E. J., Cooper J. E., Grundmann H., Robinson D. A., Enright M. C., Berendt T., Peacock S. J., Smith J. M., Murphy M. other authors 2003; How clonal is Staphylococcus aureus?. J Bacteriol 185:3307–3316
    [Google Scholar]
  9. Feil E. J., Li B. C., Aanensen D. M., Hanage W. P., Spratt B. G. 2004; eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 186:1518–1530
    [Google Scholar]
  10. Go M. F., Kapur V., Graham D. Y., Musser J. M. 1996; Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure. J Bacteriol 178:3934–3938
    [Google Scholar]
  11. Guttman D. S., Dykhuizen D. E. 1994; Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 266:1380–1383
    [Google Scholar]
  12. Hall B. G., Barlow M. 2006; Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases. Ann Epidemiol 16:157–169
    [Google Scholar]
  13. Hiller N. L., Janto B., Hogg J. S., Boissy R., Yu S., Powell E., Keefe R., Ehrlich N. E., Shen K. other authors 2007; Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol 189:8186–8195
    [Google Scholar]
  14. Hogg J. S., Hu F. Z., Janto B., Boissy R., Hayes J., Keefe R., Post J. C., Ehrlich G. D. 2007; Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol 8:R103
    [Google Scholar]
  15. Hughes A. L., Friedman R. 2005; Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus. J Bacteriol 187:2698–2704
    [Google Scholar]
  16. Lapierre P., Gogarten J. P. 2009; Estimating the size of the bacterial pan-genome. Trends Genet 25:107–110
    [Google Scholar]
  17. Lefebure T., Stanhope M. J. 2007; Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 8:R71
    [Google Scholar]
  18. Lindsay J. A., Moore C. E., Day N. P., Peacock S. J., Witney A. A., Stabler R. A., Husain S. E., Butcher P. D., Hinds J. 2006; Microarrays reveal that each of the ten dominant lineages of Staphylococcus aureus has a unique combination of surface-associated and regulatory genes. J Bacteriol 188:669–676
    [Google Scholar]
  19. Meats E., Feil E. J., Stringer S., Cody A. J., Goldstein R., Kroll J. S., Popovic T., Spratt B. G. 2003; Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing. J Clin Microbiol 41:1623–1636
    [Google Scholar]
  20. Olive D. M., Bean P. 1999; Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37:1661–1669
    [Google Scholar]
  21. O'Rourke M., Spratt B. G. 1994; Further evidence for the non-clonal population structure of Neisseria gonorrhoeae: extensive genetic diversity within isolates of the same electrophoretic type. Microbiology 140:1285–1290
    [Google Scholar]
  22. Perez-Losada M., Browne E. B., Madsen A., Wirth T., Viscidi R. P., Crandall K. A. 2006; Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data. Infect Genet Evol 6:97–112
    [Google Scholar]
  23. Snel B., Huynen M. A., Dutilh B. E. 2005; Genome trees and the nature of genome evolution. Annu Rev Microbiol 59:191–209
    [Google Scholar]
  24. Sorensen T. I., Nielsen G. G., Andersen P. K., Teasdale T. W. 1988; Genetic and environmental influences on premature death in adult adoptees. N Engl J Med 318:727–732
    [Google Scholar]
  25. Tettelin H., Masignani V., Cieslewicz M. J., Donati C., Medini D., Ward N. L., Angiuoli S. V., Crabtree J., Jones A. L. other authors 2005; Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A 102:13950–13955
    [Google Scholar]
  26. van Belkum A., Struelens M., de Visser A., Verbrugh H., Tibayrenc M. 2001; Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clin Microbiol Rev 14:547–560
    [Google Scholar]
  27. Willenbrock H., Hallin P. F., Wassenaar T. M., Ussery D. W. 2007; Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol 8:R267
    [Google Scholar]
  28. Wirth T., Falush D., Lan R., Colles F., Mensa P., Wieler L. H., Karch H., Reeves P. R., Maiden M. C. other authors 2006; Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 60:1136–1151
    [Google Scholar]
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