Bacterial population genetics, evolution and epidemiology

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 354, Issue 1384, 1999, Pages 701-710

  Spratt, Brian G ^a   Maiden, Martin C J ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Horizontal gene transfer; Linkage disequilibrium; Non clonal; Nucleotide sequencing; Phylogenetics; Population structure

Indexed keywords

BACTERIUM; EPIDEMIOLOGY; EVOLUTION; POPULATION GENETICS;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 0033614336     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.1999.0423     Document Type: Article

References (53)

1. Achtman, M. 1996 A surfeit of YATMs? J. Clin. Microbiol. 34, 18-70.
2. Achtman, M. 1997 Microevolution and epidemic spread of serogroup A Neisseria meningitidis - a review. Gene 192, 135-140.
3. Altwegg, M., Hickman-Brenner, F. W. & Farmer, J. J. D. 1989 Ribosomal RNA gene restriction patterns provide increased sensitivity for typing Salmonella typhi strains. J. Infect. Dis. 160, 145-149.
4. Atwood, K. C., Schneider, L. K. & Ryan, F. J. 1951 Periodic selection in Escherichia coli. Proc. Natl Acad. Sci. USA 37, 146-155.
5. Bandelt, H. J. & Dress, A. W. 1992 Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol. Phylogenet. Evol. 1, 242-252.
6. Bowler, L. D., Zhang, Q. Y., Riou, J. Y. & Spratt, B. G. 1994 Interspecies recombination between the penA genes of Neisseria meningitidis and commensal Neisseria species during the emergence of penicillin resistance in N. meningitidis: natural events and laboratory simulation. J. Bacteriol. 176, 333-337.
7. Boyd, E. F., Nelson, K., Wang, F. S., Whittam, T. S. & Selander, R. K. 1994 Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica. Proc. Natl Acad. Sci. USA 91, 1280-1284.
8. Boyd, E. F., Wang, F. S., Whittam, T. S. & Selander, R. K. 1996 Molecular genetic relationships of the salmonellae. Appl. Environ. Microbiol. 62, 804-808.
9. Brown, A. H. D., Feldman, M. W. & Nevo, E. 1980 Multilocus structure of natural populations of Hordeum spontaneum. Genetics 98, 523-536.
10. Caugant, D. A., Froholm, L. O., Bovre, K., Holten, E., Frasch, C. E., Mocca, L. F., Zollinger, W. D. & Selander, R. K. 1986 Intercontinental spread of a genetically distinctive complex of clones of Neisseria meningitidis causing epidemic disease. Proc. Natl Acad. Sci. USA 83, 4927-4931.
11. Caugant, D. A., Froholm, L. O., Bovre, K., Holten, E., Frasch, C. E., Mocca, L. F., Zollinger, W. D. & Selander, R. K. 1987a Intercontinental spread of Neisseria meningitidis clones of the ET-5 complex. Antonie van Leewwenhoek J. Microbiol. 53, 389-394.
12. Caugant, D. A., Mocca, L. F., Frasch, C. E., Froholm, L. O., Zollinger, W. D. & Selander, R. K. 1987b Genetic structure of Neisseria meningitidis populations in relation to serogroup, serotype, and outer membrane protein pattern. J. Bacteriol. 169, 2781-2792.
13. Crook, D. W. & Spratt, B. G. 1998 Multidrug resistance in Streptococcus pneumoniae. Br. Med. Bull. 54, 593-608.
14. Dopazo, J., Dress, A. & Von Haeseler, A. 1993 Split decomposition: a technique to analyze viral evolution. Proc. Natl Acad. Sci. USA 90, 10320-10324.
15. Enright, M. & Spratt, B. G. 1998 A multilocus sequence typing scheme for Streptococcus pneumoniae identification of clones associated with serious invasive disease. Microbiology 144, 3049-3060.
16. Feil, E., Carpenter, G. & Spratt, B. G. 1996a Electrophoretic variation in adenylate kinase of Neisseria meningitidis is due to inter- and intraspecies recombination. Proc. Natl Acad. Sci. USA 92, 10535-10539.
17. Feil, E., Zhou, J., Maynard Smith, J. & Spratt, B. G. 1996b A comparison of the nucleotide sequences of the adk and recA genes of pathogenic and commensal Neisseria species: evidence for extensive interspecies recombination within adk. J. Mol. Evol. 43, 631-640.
18. 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.
19. Gutjahr, T. S., O'Rourke, M., Ison, C. A. & Spratt, B. G. 1997 Arginine-, hypoxanthine-, uracil-requiring isolates of Neisseria ganorrhoeae are a clonal lineage within a non-clonal population. Microbiology 143, 633-640.
20. Guttman, D. S. 1997 Recombination and clonality in natural populations of Escherichia coli. Trends Ecol. Evol. 12, 16-22.
21. Guttman, D. S. & Dykhuizen, D. E. 1994 Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 266, 1380-1383.
22. Kohl, P. K., Knapp, J. S., Hofmann, H., Gruender, K., Petzoldt, D., Tams, M. R. & Holmes, K. K. 1986 Epidemiological analysis of Neisseria gonorrhoeae in the Federal Republic of Germany by auxotyping and serological classification using monoclonal antibodies. Genitourin. Med. 62, 145-150.
23. Levin, B. R. 1981 Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. Genetics 99, 1-23.
24. Lorenz, M. G. & Wackernagel, W. 1994 Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58, 563-602.
25. Maiden, M. C. J. 1998 Horizontal genetic exchange, evolution, and spread of antibiotic resistance in bacteria. Clin. Infect. Dis. 27, S12-S20.
26. Maiden, M. C. J. & Feavers, I. M. 1995 Population genetics and global epidemiology of the human pathogen Neisseria meningitidis. In Population genetics of bacteria (ed. S. Baumberg, J. P. W. Young, E. M. H. Wellington & J. R. Saunders), pp. 269-293. Cambridge University Press.
27. Maiden, M. C. J. (and 12 others) 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.
28. Maynard Smith, J. 1989 Trees, bundles or nets. Trends Ecol. Evol. 4, 302-304.
29. Maynard Smith, J. 1992 Analysing the mosaic structure of genes. J. Mol. Evol. 34, 126-129.
30. Maynard Smith, J. 1995 Do bacteria have population genetics? In Population genetics of bacteria (ed. S. Baumberg, J. P. W. Young, E. M. H. Wellington & J. R. Saunders), pp. 1-12. Cambridge University Press.
31. Maynard Smith, J. & Smith, N. H. 1998 Detecting recombination from gene trees. Mol. Biol. Evol. 15, 590-599.
32. Maynard Smith, J., Dowson, C. G. & Spratt, B. G. 1991 Localized sex in bacteria. Nature 349, 29-31.
33. Maynard Smith, J., Smith, N. H., O'Rourke, M. & Spratt, B. G. 1993 How clonal are bacteria? Proc. Natl Acad. Sci. USA 90, 4384-4388.
34. Morelli, G., Malorny, B., Muller, K., Seiler, A., Wang, J. F., del Valle, J. & Achtman, M. 1997 Clonal descent and microevolution of Neisseria meningitidis during 30 years of epidemic spread. Mol. Microbiol. 25, 1047-1064.
35. Musser, J. M. 1996 Molecular population genetic analysis of emerged bacterial pathogens: selected insights. Emerg. Infect. Dis. 2, 1-17.
36. Navarro, F., Llovet, T., Echeita, M. A., Coll, P., Aladuena, A., Usera, M. A. & Prats, G. 1996 Molecular typing of Salmonella enterica scrovar typhi. J. Clin. Microbiol. 4, 2831-2834.
37. Nelson, K. & Selander, R. K. 1992 Evolutionary genetics of the proline permease gene (putP) and the control region of the proline utilization operon in populations of Salmonella and Escherichia coli. J. Bacteriol. 174, 6886-6895.
38. Nelson, K., Whittam, T. S. & Selander, R. K. 1991 Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. Proc. Natl Acad. Sci. USA 88, 6667-6671.
39. O'Rourke, M., Ison, C. A., Renton, A. M. & Spratt, B. G. 1995 Opa-typing: a High resolution tool for studying the epidemiology of gonorrhoea. Mol. Microbiol. 17, 865-875.
40. Reeves, P. R. 1992 Variation in O-antigens, niche-specific selection and bacterial populations. FEMS Microbiol. Lett. 79, 509-516.
41. Salaun, L., Audibert, C., Le Lay, G., Burucoa, C., Fauchere, J. L. & Picard, B. 1998 Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. FEMS Microbiol. Lett. 161, 231-239.
42. Sawyer, S. 1989 Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6, 526-538.
43. Selander, R. K., Caugant, D. A., Ochman, H., Musser, J. M., Gilmour, M. N. & Whittam, T. S. 1986 Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51, 837-884.
44. Selander, R. K., Beltran, P., Smith, N. H., Barker, R. M., Crichton, P. B., Old, D. C., Musser, J. M. & Whittam, T. S. 1990a Genetic population structure, clonal phylogeny, and pathogenicity of Salmonella paratyphi B. Infect. Immun. 58, 1891-1901.
45. Selander, R. K., Beltran, P., Smith, N. H., Helmuth, R., Rubin, F. A., Kopecko, D. J., Ferris, K., Tall, B. D., Cravioto, A. & Musser, J. M. 1990b Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers. Infect. Immun. 58, 2262-2275.
46. Shortridge, V. D., Stone, G. G., Flamm, R. K., Beyer, J., Versalovic, J., Graham, D.W. & Tanaka, S. K. 1997 Molecular typing of Helicobacter pylori isolates from a multicenter U.S. clinical trial by ureC restriction fragment length polymorphism. J. Clin. Microbiol. 35, 471-473.
47. Spratt, B. G., Smith, N. H., Zhou, J., O'Rourke, M. & Feil, E. 1995 The population genetics of the pathogenic Neisseria. In Population genetics of bacteria (ed. S. Baumberg, J. P. W. Young, E. M. H. Wellington & J. R. Saunders), pp. 143-160. Cambridge University Press.
48. Suerbaum, S., Maynard Smith, J., Bapumia, K., Morelli, G., Smith, N. H., Kunstmann, E., Dyrek, I. & Achtman, M. 1998 Free recombination within Helicobacter pylori. Proc. Natl Acad. Sci. USA 95, 12619-12624.
49. Sved, J. A. 1968 The stability of linked systems of loci with a small population size. Genetics 59, 543-563.
50. Vazquez, J., Berron, S., O'Rourke, M., Carpenter, G., Feil, E., Smith, N. H. & Spratt, B. G. 1995 Interspecies recombination in nature: a meningococcus that has acquired a gonococcal PIB porin. Mol. Microbiol. 15, 1001-1007.
51. Whittam, T. S. 1995 Genetic population structure and pathogenicity in enteric bacteria. In Population genetics of bacteria (ed. S. Baumberg, J. P. W. Young, E. M. H. Wellington & J. R. Saunders), pp. 217-245. Cambridge University Press.
52. Whittam, T. S., Ochman, H. & Selander, R. K. 1983 Multilocus genetic structure in natural populations of Escherichia coli. Proc. Natl Acad. Sci. USA 80, 1751-1755.
53. Zhou, J., Bowler, L. D. & Spratt, B. G. 1997 Interspecies recombination, and phylogenetic distortions, within the glutamine synthetase and shikimate dehydrogenase genes of Neisseria meningitidis and commensal. Neisseria species. Mol. Microbiol. 23, 799-812.