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Chapter 32 : Population Genetics

Authors: Sebastian Suerbaum1, Mark Achtman2
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Affiliations: 1: Institute of Hygiene and Microbiology, University of Wuerzburg, Josef-Schneider-Strasse 2, 97080 Wuerzburg, Germany; 2: Max-Planck Institut fur Infektionsbiologie, Berlin, Germany
Content Type: Monograph
Publication Year: 2001

Category: Bacterial Pathogenesis

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Population Genetics, Page 1 of 2

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Abstract:

The first part of this chapter contains a general introduction to bacterial population genetics, and the second part reviews the available data on the genetic diversity within and the mechanisms that have generated this diversity. Three types of population structures includes clonal, panmictic, and epidemic. Genetic diversity arises by intragenomic genetic events including point mutations, deletions, insertions, and rearrangements. As early as 1986, it was recognized that exhibits an unusual degree of genetic heterogeneity. Compatibility matrices yielded results that were consistent with frequent recombination in . The frequency of both recombination and purification remains to be quantitated. Biogeographical diversity of three virulence-associated genes such as , , and could arise by various mechanisms, ranging from founder effects associated with vertical transmission to selection for antigenic or functional variants with differential fitness for certain host populations. Subsequent analyses of the same housekeeping genes from additional isolates from Indonesia and South Africa have confirmed the original conclusions, but further analyses are needed to test whether virulence genes such as also fall into three populations. An initial study failed to detect genomic changes in paired isolates obtained 2 years apart from 20 patients, but two subsequent studies have shown that strains can indeed change during chronic colonization.

Citation: Suerbaum S, Achtman M. 2001. Population Genetics, p 355-361. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch32

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Population Genetics
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Citation: Suerbaum S, Achtman M. 2001. Population Genetics, p 355-361. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch32
/content/10.1128/9781555818005.chap32.fig32-1
Figure 1

Comparison of the mean homoplasy ratio (H) and mean genetic distance at synonymous sites (D) among different bacterial species. The sources of the data for these analyses are given in reference 1. Modified from reference with permission.

10.1128/9781555818005/fig32-1_thmb.gif
10.1128/9781555818005/fig32-1.gif
Image of Figure 1
Figure 1

Comparison of the mean homoplasy ratio (H) and mean genetic distance at synonymous sites (D) among different bacterial species. The sources of the data for these analyses are given in reference 1. Modified from reference with permission.

Citation: Suerbaum S, Achtman M. 2001. Population Genetics, p 355-361. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch32
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References

/content/book/10.1128/9781555818005.chap32
1. Achtman, M., 2001 Population structure of Helicobacter pylori and other pathogenic bacterial species, p. 311– 321. In M. Achtman, and S. Suerbaum (ed.), Helicobacter pylori: Molecular and Cellular Biology. Horizon Scientific Press, Wymondham, United Kingdom.
2. Achtman, M.,, T. Azuma,, D. E. Berg,, Y. Ito,, G. Morelli,, Z. J. Pan,, S. Suerbaum,, S. A. Thompson,, A. van der Ende,, and L. J. van Doom. 1999. Recombination and clonal groupings within Helicobacter pylori from different geographic regions. Mol. Microbiol. 32: 459– 470.
3. Achtman, M.,, and S. Suerbaum. 2000. Sequence variation in Helicobacter pylori. Trends Microbiol. 8: 57– 58.
4. Achtman, M.,, K. Zurth,, G. Morelli,, G. Torrea,, and E. Carniel. 1999. Yersinia pestis, the cause of pandemic plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 96: 14043– 14048.
5. Agostini, H. T.,, R. Yanagihara,, V. Davis,, C. F. Ryschkewitsch,, and G. L. Stoner. 1997. Asian genotypes of JC virus in Native Americans and in a Pacific Island population: markers of viral evolution and human migration. Proc. Natl. Acad. Sci. USA 94: 14542– 14546.
6. Akopyanz, N.,, N. O. Bukanov,, T. U. Westblom,, and D. E. Berg. 1992. PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nucleic Acids Res. 20: 6221– 6225.
7. Akopyanz, N.,, N. O. Bukanov,, T. U. Westblom,, S. Kresovich,, and D. E. Berg. 1992. DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Res. 20: 5137– 5142.
8. Atherton, J. C.,, P. Cao,, R. M. Peek,, M. K. R. Tummuru,, M. J. Blaser,, and T. L. Cover. 1995. Mosaicism in vacuolating cytotoxin alleles of Helicobacter pylori. J. Biol. Chem. 270: 17771– 17777.
9. Bamford, K. B.,, J. Bickley,, J. S. Collins,, B. T. Johnston,, S. Potts,, V. Boston,, R. J. Owen,, and J. M. Sloan. 1993. Helicobacter pylori: comparison of DNA fingerprints provides evidence for intrafamilial infection. Gut 34: 1348– 1350.
10. Covacci, A.,, J. L. Telford,, G. Del Giudice,, J. Parsonnet,, and R. Rappuoli. 1999. Helicobacter pylori virulence and genetic geography. Science 284: 1328– 1333.
11. Duim, B.,, L. Vogel,, W. Puijk,, H. M. Jansen,, R. H. Meloen,, J. Dankert,, and L. van Alphen. 1996. Fine mapping of outer membrane protein P2 antigenic sites which vary during persistent infection by Haemophilus influenzae. Infect. Immun. 64: 4673– 4679.
12. Enright, M. C.,, N. P. Day,, C. E. Davies,, S. J. Peacock,, and B. G. Spratt. 2000. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J. Clin. Microbiol. 38: 1008– 1015.
13. Enright, M. C.,, and B. G. Spratt. 1998. A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144: 3049– 3060.
14. Go, M. F.,, V. Kapur,, D. Y. Graham,, and J. M. Musser. 1996. Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure. J. Bacteriol. 178: 3934– 3938.
15. Hudson, R. R. 1990. Gene geneologies and the coalescent process. Oxford Sum. Evol. Biol. 7: 1– 44.
16. Jakobsen, I.B., andS. Easteal. 1996. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput. Appl. Biosci. 12: 291– 295.
17. Kansau, I.,, J. Raymond,, E. Bingen,, P. Courcoux,, N. Kalach,, M. Bergeret,, N. Braimi,, C. Dupont,, and A. Labigne. 1996. Genotyping of Helicobacter pylori isolates by sequencing of PCR products and comparison with the RAPD technique. Res. Microbiol. 147: 661– 669.
18. Keim, P.,, A. Kalif,, J. Schupp,, K. Hill,, S. E. Travis,, K. Richmond,, D. M. Adair,, M. Hugh-Jones,, C. R. Kuske,, and P. Jackson. 1997. Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers. J. Bacteriol. 179: 818– 824.
19. Kersulyte, D.,, H. Chalkauskas,, and D. E. Berg. 1999. Emergence of recombinant strains of Helicobacter pylori during human infection. Mol. Microbiol. 31: 31– 43.
20. Kersulyte, D.,, A. K. Mukhopadhyay,, B. Velapatino,, W. Su,, Z. Pan,, C. Garcia,, V. Hernandez,, Y. Valdez,, R. S. Mistry,, R. H. Gilman,, Y. Yuan,, H. Gao,, T. Alarcon,, M. Lopez-Brea,, N. G. Balakrish,, A. Chowdhury,, S. Datta,, M. Shirai,, T. Nakazawa,, R. Ally,, I. Segal,, B. C. Wong,, S. K. Lam,, F. O. Olfat,, T. Boren,, L. Engstrand,, O. Torres,, R. Schneider,, J. E. Thomas,, S. Czinn,, and D. E. Berg. 2000. Differences in genotypes of Helicobacter pylori from different human populations. J. Bacteriol. 182: 3210– 3218.
21. Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, United Kingdom.
22. Kuipers, E. J.,, D. A. Israel,, J. G. Kusters,, M. M. Gerrits,, J. Weel,, A. van der Ende,, R. W. van der Hulst,, H. P. Wirth,, J. Nikanne,, S. A. Thompson,, and M. J. Blaser. 2000. Quasispecies development of Helicobacter pylori observed in paired isolates obtained years apart from the same host. J. Infect. Dis. 181: 273– 282.
23. Lafay, B.,, J. C. Atherton,, and P. M. Sharp. 2000. Absence of translationally selected synonymous codon usage bias in Helicobacter pylori. Microbiology 146: 851– 860.
24. Langenberg, W.,, E. A. Rauws,, A. Widjojokusumo,, G. N. Tytgat,, and H. C. Zanen. 1986. Identification of Campylobacter pyloridis isolates by restriction endonuclease DNA analysis. J. Clin. Microbiol. 24: 414– 417.
25. LeClerc, J.E.,, B. Li,, W. L. Payne,, and T. A. Cebula. 1996. High mutation frequencies among Escherichia coli and Salmonella pathogens. Science 274: 1208– 1211.
26. Maiden, M. C.,, J. A. Bygraves,, E. Feil,, G. Morelli,, J. E. Russell,, R. Urwin,, Q. Zhang,, J. Zhou,, K. Zurth,, D. A. Caugant,, I. M. Feavers,, M. Achtman,, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95: 3140– 3145.
27. Majewski, J.,, and F. M. Cohan. 1999. Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity. Genetics 152: 1459– 1474.
28. Majewski, S. I.,, and C. S. Goodwin. 1988. Restriction endonuclease analysis of the genome of Campylobacter pylori with a rapid extraction method: evidence for considerable genomic variation. J. Infect. Dis. 157: 465– 471.
29. Maynard Smith, J. 1999. The detection and measurement of recombination from sequence data. Genetics 153: 1021– 1027.
30. Maynard Smith, J.,, N. H. Smith,, M. O'Rourke,, and B. G. Spratt. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90: 4384– 4388.
31. Maynard, S. J.,, and N. H. Smith. 1998. Detecting recombination from gene trees. Mol. Biol. Evol. 15: 590– 599.
32. Morelli, G.,, B. Malorny,, K. Muller,, A. Seiler,, J. F. Wang,, J. Del Valle,, and M. Achtman. 1997. Clonal descent and micro-evolution of Neisseria meningitidis during 30 years of epidemic spread. Mol. Microbiol. 25: 1047– 1064.
33. Mukhopadhyay, A. K.,, D. Kersulyte,, J. Y. Jeong,, S. Datta,, Y. Ito,, A. Chowdhury,, S. Chowdhury,, A. Santra,, S. K. Bhattacharya,, T. Azuma,, G. B. Nair,, and D. E. Berg. 2000. Distinctiveness of genotypes of Helicobacter pylori in Calcutta, India. J. Bacteriol. 182: 3219– 3227.
34. Musser, J. M.,, J. S. Kroll,, D. M. Granoff,, E. R. Moxon,, B. R. Brodeur,, J. Campos,, H. Dabernat,, W. Frederiksen,, J. Hamel,, G. Hammond,, E. A. Hoiby,, K. E. Jonsdottir,, M. Kabeer,, I. Railings,, W. N. Khan,, M. Kilian,, K. Knowles,, H. J. Koornhof,, B. Law,, I. Li,, J. Montgomery,, P. E. Pattison,, J.-C. Piffaretti,, A. K. Takala,, M. L. Thong,, R. A. Wall,, J. I. Ward,, and R. K. Selander. 1990. Global genetic structure and molecular epidemiology of encapsulated Haemophilus influenzae. Rev. Infect. Dis. 12: 75– 111.
35. Ng, E. K.,, S. A. Thompson,, G. I. Perez-Perez,, I. Kansau,, A. van der Ende,, A. Labigne,, J. J. Sung,, S. C. Chung,, and M. J. Blaser. 1999. Helicobacter pylori heat shock protein A: serologic responses and genetic diversity. Clin. Diagn. Lab. Immunol. 6: 377– 382.
36. Nwokolo, C. U.,, J. Bickley,, A. R. Attard,, R. J. Owen,, M. Costas,, and I. A. Fraser. 1992. Evidence of clonal variants of Helicobacter pylori in three generations of a duodenal ulcer disease family. Gut 33: 1323– 1327.
37. Ochman, H.,, and A. C. Wilson. 1987. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26: 74– 86.
38. Odenbreit, S.,, J. Pills,, B. Sedlmaier,, E. Gerland,, W. Fischer,, and R. Haas. 2000. Translocation of Helicobacter pylori CagA into gastric epithelial cells by type IV secretion. Science 287: 1497– 1500.
39. Owen, R. J.,, J. Bickley,, A. Lastovica,, J. P. Dunn,, P. Borman,, and C. Hunton. 1992. Ribosomal RNA gene patterns of Helicobacter pylori from surgical patients with healed and recurrent peptic ulcers. Epidemiol. Infect. 108: 39– 50.
40. Pagliaccia, C.,, M. De Bernard,, P. Lupetti,, X. Ji,, D. Burroni,, T. L. Cover,, E. Papini,, R. Rappuoli,, J. L. Telford,, and J. M. Reyrat. 1998. The m2 form of the Helicobacter pylori cytotoxin has cell type-specific vacuolating activity. Proc. Natl. Acad. Sci. USA 95: 10212– 10217.
41. Romling, U.,, K. D. Schmidt,, and B. Tiimmler. 1997. Large chromosomal inversions occur in Pseudomonas aeruginosa clone C strains isolated from cystic fibrosis patients. FEMS Microbiol. Lett. 150: 149– 156.
42. Salama, S. M.,, Q. Jiang,, N. Chang,, R. W. Sherbaniuk,, and D. E. Taylor. 1995. Characterization of chromosomal DNA profiles from Helicobacter pylori strains isolated from sequential gastric biopsy specimens. J. Clin. Microbiol. 33: 2496– 2497.
43. Salaun, L.,, C. Audibert,, G. Le Lay,, C. Burucoa,, J. L. Fauchere,, and B. Picard. 1998. Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. FEMS Microbiol. Lett. 161: 231– 239.
44. Sawyer, S. 1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6: 526– 538.
45. Segal, E. D.,, J. Cha,, J. Lo,, S. Falkow,, and L. S. Tompkins. 1999. Altered states: involvement of phosphorylated CagA in the induction of host cellular growth changes by Helicobacter pylori. Proc. Natl. Acad. Sci. USA 96: 14559– 14564.
46. Selander, R. K.,, J. Li,, and K. Nelson,. 1996. Evolutionary genetics of Salmonella enterica, p. 2691– 2707. In F. C. Neidhardt (ed.), Escherichi coli and Salmonella: Cellular and Molecular Biology, 2nd ed. ASM Press, Washington, D. C.
47. Sreevatsan, S.,, X. Pan,, K. E. Stockbauer,, N. D. Connell,, B. N. Kreiswirth,, T. S. Whittam,, and J. M. Musser. 1997. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94: 9869– 9874.
48. Stephens, J. C. 1985. Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Mol. Biol. Evol. 2: 539– 556.
49. Suerbaum, S.,, J. Maynard Smith,, K. Bapumia,, G. Morelli,, N. H. Smith,, E. Kunstmann,, I. Dyrek,, and M. Achtman. 1998. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA 95: 12619– 12624.
50. Suerbaum, S.,, J.-M. Thiberge,, I. Kansau,, R. L. Ferrero,, and A. Labigne. 1994. Helicobacter pylori hspA-hspB heat shock gene cluster: nucleotide sequence, expression, putative function and immunogenicity. Mol. Microbiol. 14: 959– 974.
51. van der Ende, A.,, Z. J. Pan,, A. Bart,, R. W. van der Hulst,, M. Feller,, S. D. Xiao,, G. N. Tytgat,, and J. Dankert. 1998. cagA-positive Helicobacter pylori populations in China and the Netherlands are distinct. Infect. Immun. 66: 1822– 1826.
52. van Doom, L. J.,, C. Figueiredo,, F. Megraud,, S. Pena,, P. Midolo,, D. M. Queiroz,, F. Cameiro,, B. Vanderborght,, M. D. Pegado,, R. Sanna,, W. de Boer,, P. M. Schneeberger,, P. Correa,, E. K. Ng,, J. Atherton,, M. J. Blaser,, and W. G. Quint. 1999. Geographic distribution of vacA allelic types of Helicobacter pylori. Gastroenterology 116: 823– 830.
53. van Doom, L. J.,, C. Figueiredo,, R. Sanna,, M. J. Blaser,, and W. G. Quint. 1999. Distinct variants of Helicobacter pylori cagA are associated with vacA subtypes. J. Clin. Microbiol. 37: 2306– 2311.
54. van Doom, L. J.,, C. Figueiredo,, R. Sanna,, S. Pena,, P. Midolo,, E. K. Ng,, J. C. Atherton,, M. J. Blaser,, and W. G. Quint. 1998. Expanding allelic diversity of Helicobacter pylori vacA. J. Clin. Microbiol. 36: 2597– 2603.
55. Vincent, P.,, F. Gottrand,, P. Pemes,, M. O. Husson,, M. Lecomte Houcke,, D. Turck,, and H. Leclerc. 1994. High prevalence of Helicobacter pylori infection in cohabiting children. Epidemiology of a cluster, with special emphasis on molecular typing. Gut 35: 313– 316.
56. Wang, G.,, M. Z. Humayun,, and D. E. Taylor. 1999. Mutation as an origin of genetic variability in Helicobacter pylori. Trends Microbiol. 7: 488– 493.
57. Wang, J. T.,, J. C. Sheu,, J. T. Lin,, T. H. Wang,, and M. S. Wu. 1993. Direct DNA amplification and restriction pattern analysis of Helicobacter pylori in patients with duodenal ulcer and their families. J. Infect. Dis. 168: 1544– 1548.
58. Whittam, T. S.,, S. D. Reid,, and R. K. Selander. 1998. Mutators and long-term molecular evolution of pathogenic Escherichia coli 0157:H7. Emerg. Infect. Dis. 4: 615– 617.

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