Population structure of pathogenic bacteria revisited

International Journal of Medical Microbiology

Volumn 294, Issue 2-3, 2004, Pages 67-73

  Achtman, Mark ^a  

^a MAX PLANCK INSTITUTE FOR INFECTION BIOLOGY   (Germany)

Author keywords

Bacterial population genetics; Neisseria meningitides; Yersinia pestis

Indexed keywords

ANALYTIC METHOD; BACTERIAL GENETICS; EPIDEMIC; GENETIC VARIABILITY; HERD IMMUNITY; MULTILOCUS ENZYME ELECTROPHORESIS; MULTILOCUS SEQUENCE TYPING; NEISSERIA MENINGITIDIS; NONHUMAN; POPULATION STRUCTURE; SEQUENCE ANALYSIS; SHORT SURVEY; SYSTEMATIC REVIEW; YERSINIA PESTIS;

NEISSERIA MENINGITIDIS; YERSINIA PESTIS;

EID: 4644354714     PISSN: 14384221     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijmm.2004.06.028     Document Type: Review

References (49)

1. Achtman, M., 2004. Age, descent and genetic diversity within Yersinia pestis. In: Carniel, E., Hinnebusch, B. J. (Eds.), Molecular and Cellular Biology of Yersinia. Horizon Scientific Press, Wymondham, UK, in press.
2. Achtman, M., Mercer, A., Kusecek, B., Pohl, A., Heuzenroeder, M., Aaronson, W., Sutton, A., Silver, R.P., 1983. Six widespread bacterial clones among Escherichia coli K1 isolates. Infect. Immun. 39, 315-335.
3. Achtman, M., Pluschke, G., 1986. Clonal analysis of descent and virulence among selected Escherichia coli. Annu. Rev. Microbiol. 40, 185-210.
4. Achtman, M., van der Ende, A., Zhu, P., Koroleva, I.S., Kusecek, B., Morelli, G., Schuurman, I.G.A., Brieske, N., Zurth, K., Kostyukova, N.N., Platonov, A.E., 2001. Molecular epidemiology of four successive waves of serogroup A meningitis in Moscow, Russia between 1969 and 1997. Emerg. Infect. Dis. 7, 420-427.
5. Achtman, M., Zurth, K., Morelli, G., Torrea, G., Guiyoule, A., Carniel, E., 1999. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 96, 14043-14048.
6. Adair, D.M., Worsham, P.L., Hill, K.K., Klevytska, A.M., Jackson, P.J., Friedlander, A.M., Keim, P., 2000. Diversity in a variable-number tandem repeat from Yersinia pestis. J. Clin. Microbiol. 38, 1516-1519.
7. Anisimov, A.P., Lindler, L.E., Pier, G.B., 2004. Intraspecific diversity of Yersinia pestis. Clin. Microbiol. Rev. 17, 434-464.
8. Bart, A., Barnabé, C., Achtman, M., Dankert, J., van der Ende, A., Tibayrenc, M., 2001. Strong linkage disequilibrium between different genetic markers challenges the epidemic clonality model in Neisseria meningitidis serogroup A isolates. Infect. Genet. Evol. 1, 117-122.
9. Bart, A., Schuurman, I.G.A., Achtman, M., Caugant, D.A., Dankert, J., van der Ende, A., 1998. Random amplified polymorphic DNA (RAPD) genotyping of serogroup A meningococci yields similar results to multilocus enzyme electrophoresis (MEE) and reveals new genotypes. J. Clin. Microbiol. 36, 1746-1749.
10. Bercovier, H., Mollaret, H.H., Alonso, J.M., Brault, J., Fanning, G.R., Steigerwalt, A.G., Brenner, D.J., 1980. Intra- and interspecies relatedness of Yersinia pestis by DNA hybridization and its relationship to Yersinia pseudotuberculosis. Curr. Microbiol. 4, 225-229.
11. Brown, E.W., Mammel, M.K., LeClerc, J.E., Cebula, T.A., 2003. Limited boundaries for extensive horizontal gene transfer among Salmonella pathogens. Proc. Natl. Acad. Sci. USA 100, 15676-15681.
12. Conway, D.J., Fanello, C., Lloyd, J.M., Al Joubori, B.M., Baloch, A.H., Somanath, S.D., Roper, C., Oduola, A.M., Mulder, B., Povoa, M.M., Singh, B., Thomas, A.W., 2000. Origin of Plasmodium falciparum malaria is traced by mitochondrial DNA. Mol. Biochem. Parasitol. 111, 163-171.
13. Crowe, B.A., Wall, R.A., Kusecek, B., Neumann, B., Olyhoek, T., Abdillahi, H., Hassan-King, M., Greenwood, B.M., Poolman, J.T., Achtman, M., 1989. Clonal and variable properties of Neisseria meningitidis isolated from cases and carriers during and after an epidemic in the Gambia, West Africa. J. Infect. Dis. 159, 686-700.
14. Deng, W., Burland, V., Plunkett III, G., Boutin, A., Mayhew, G.F., Liss, P., Perna, N.T., Rose, D.J., Mau, B., Zhou, S., Schwartz, D.C., Fetherston, J.D., Lindner, B., Brubaker, R.R., Plano, G.V., Straley, S.C., McDonough, K.A., Nilles, M.L., Matson, J.S., Blattner, F.R., Perry, R.D., 2002. Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184, 4601-4611.
15. Enright, M.C., Spratt, B.G., 1999. Multilocus sequence typing. Trends Microbiol. 7, 482-487.
16. Feil, E.J., Holmes, E.C., Bessen, D.E., Chan, M.-S., Day, N.P.J., Enright, M.C., Goldstein, R., Hood, D.W., Kalia, A., Moore, C.E., Zhou, J., Spratt, B.G., 2001. Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic comparisons. Proc. Natl. Acad. Sci. USA 98, 182-187.
17. 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.
18. Gagneux, S., Wirth, T., Hodgson, A., Ehrhard, I., Morelli, G., Kriz, P., Genton, B., Smith, T., Binka, F., Pluschke, G., Achtman, M., 2002a. Clonal groupings in serogroup X Neisseria meningitidis. Emerg. Infect. Dis. 8, 462-466.
19. Gagneux, S.P., Hodgson, A., Smith, T.A., Wirth, T., Erhard, I., Morelli, G., Genton, B., Binka, F.N., Achtman, M., Pluschke, G., 2002b. Prospective study of a serogroup X Neisseria meningitidis outbreak in northern Ghana. J. Infect. Dis. 185, 618-626.
20. Guiyoule, A., Grimont, F., Iteman, I., Grimont, P.A.D., Lefèvre, M., Carniel, E., 1994. Plague pandemics investigated by ribotyping of Yersinia pestis strains. J. Clin. Microbiol. 32, 634-641.
21. Gutacker, M.M., Smoot, J.C., Migliaccio, C.A., Ricklefs, S.M., Hua, S., Cousins, D.V., Graviss, E.A., Shashkina, E., Kreiswirth, B.N., Musser, J.M., 2002. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms. Resolution of genetic relationships among closely related microbial strains. Genetics 162, 1533-1543.
22. Hassan-King, M.K.A., Wall, R.A., Greenwood, B.M., 1988. Meningococcal carriage, meningococcal disease and vaccination. J. Infect. 16, 55-59.
23. Hill, K.K., Ticknor, L.O., Okinaka, R.T., Asay, M., Blair, H., Bliss, K.A., Laker, M., Pardington, P.E., Richardson, A.P., Tonks, M., Beecher, D.J., Kemp, J.D., Kolsto, A.B., Wong, A.C., Keim, P., Jackson, P.J., 2004. Fluorescent amplified fragment length polymorphism analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis isolates. Appl. Environ. Microbiol. 70, 1068-1080.
24. Joy, D.A., Feng, X., Mu, J., Furuya, T., Chotivanich, K., Krettli, A.U., Ho, M., Wang, A., White, N.J., Suh, E., Beerli, P., Su, X.Z., 2003. Early origin and recent expansion of Plasmodium falciparum. Science 300, 318-321.
25. Keim, P., Klevytska, A.M., Price, L.B., Schupp, J.M., Zinser, G., Smith, K.L., Hugh-Jones, M.E., Okinaka, R., Hill, K.K., Jackson, P.J., 1999. Molecular diversity in Bacillus anthracis. J. Appl. Microbiol. 87, 215-217.
26. Kidgell, C., Reichard, U., Wain, J., Linz, B., Torpdahl, M., Dougan, G., Achtman, M., 2002. Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old. Infect. Genet. Evol. 2, 39-45.
27. Lawrence, J.G., Ochman, H., 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44, 383-397.
28. Linz, B., Schenker, M., Zhu, P., Achtman, M., 2000. Frequent interspecific genetic exchange between commensal neisseriae and Neisseria meningitidis. Mol. Microbiol. 36, 1049-1058.
29. Maiden, M.C.J., Bygraves, J.A., Feil, E., Morelli, G., Russell, J.E., Urwin, R., Zhang, Q., Zhou, J., Zurth, K., Caugant, D.A., Feavers, I.M., Achtman, M., Spratt, B.G., 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.
30. 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.
31. Meyers, L.A., Levin, B.R., Richardson, A.R., Stojiljkovic, I., 2003. Epidemiology, hypermutation, within-host evolution and the virulence of Neisseria meningitidis. Proc. R. Soc. London B Biol. Sci. 270, 1667-1677.
32. Motin, V.L., Georgescu, A.M., Elliott, J.M., Hu, P., Worsham, P.L., Ott, L.L., Slezak, T.R., Sokhansanj, B.A., Regala, W.M., Brubaker, R.R., Garcia, E., 2002. Genetic variability of Yersinia pestis isolates as predicted by PCR-based IS100 genotyping and analysis of structural genes encoding glycerol-3-phosphate dehydrogenase (glpD). J. Bacteriol. 184, 1019-1027.
33. Ochman, H., Selander, R.K., 1984. Standard reference strains of Escherichia coli from natural populations. J. Bacteriol. 157, 690-693.
34. Old, D.C., Duguid, J.P., 1979. Transduction of fimbriation demonstrating common ancestry in FIRN strains of Salmonella typhimurium. J. Gen. Microbiol. 112, 251-259.
35. Olyhoek, T., Crowe, B.A., Achtman, M., 1987. Clonal population structure of Neisseria meningitidis serogroup A isolated from epidemics and pandemics between 1915 and 1983. Rev. Infect. Dis. 9, 665-692.
36. Ørskov, F., Ørskov, I., 1983. Summary of a workshop on the clone concept in the epidemiology, taxonomy, and evolution of the Enterobacteriaceae and other bacteria. J. Infect. Dis. 148, 346-357.
37. Ørskov, F., Ørskov, I., Evans Jr., D.J., Sack, R.B., Sack, D.A., Wadström, T., 1976. Special Escherichia coli serotypes among enterotoxigenic strains from diarrhoea in adults and children. Med. Microbiol. Immunol. 162, 73-80.
38. Parkhill, J., Wren, B.W., Thomson, N.R., Titball, R.W., Holden, M.T., Prentice, M.B., Sebaihia, M., James, K.D., Churcher, C., Mungall, K.L., Baker, S., Basham, D., Bentley, S.D., Brooks, K., Cerdeno-Tarraga, A.M., Chillingworth, T., Cronin, A., Davies, R.M., Davis, P., Dougan, G., Feltwell, T., Hamlin, N., Holroyd, S., Jagels, K., Karlyshev, A.V., Leather, S., Moule, S., Oyston, P.C., Quail, M., Rutherford, K., Simmonds, M., Skelton, J., Stevens, K., Whitehead, S., Barrell, B.G., 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413, 523-527.
39. Radnedge, L., Agron, P.G., Worsham, P.L., Andersen, G.L., 2002. Genome plasticity in Yersinia pestis. Microbiology 148, 1687-1698.
40. Rich, S.M., Licht, M.C., Hudson, R.R., Ayala, F.J., 1998. Malaria's Eve: evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum. Proc. Natl. Acad. Sci. USA 95, 4425-4430.
41. Richardson, A.R., Yu, Z., Popovic, T., Stojiljkovic, I., 2002. Mutator clones of Neisseria meningitidis in epidemic serogroup A disease. Proc. Natl. Acad. Sci. USA 99, 6103-6107.
42. 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, 873-884.
43. Selander, R.K., Levin, B.R., 1980. Genetic diversity and structure in Escherichia coli populations. Science 210, 545-547.
44. Sreevatsan, S., Pan, X., Stockbauer, K., Connell, N.D., Kreiswirth, B.N., Whittam, T.S., Musser, J.M., 1997. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94, 9869-9874.
45. Trebesius, K., Harmsen, D., Rakin, A., Schmelz, J., Heesemann, J., 1998. Development of rRNA-targeted PCR and in situ hybridization with fluorescently labelled oligonucleotides for detection of Yersinia species. J. Clin. Microbiol. 36, 2557-2564.
46. Vieusseux, M., 1806. Mémoire sur le maladie qui a régné à Genève au printemps de 1805. J. Med. Chirurg. Pharm. 11, 163-182.
47. Volkman, S.K., Barry, A.E., Lyons, E.J., Nielsen, K.M., Thomas, S.M., Choi, M., Thakore, S.S., Day, K.P., Wirth, D.F., Hartl, D.L., 2001. Recent origin of Plasmodium falciparum from a single progenitor. Science 293, 482-484.
48. Wang, J.-F., Caugant, D.A., Li, X., Hu, X., Poolman, J.T., Crowe, B.A., Achtman, M., 1992. Clonal and antigenic analysis of serogroup A Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in China. Infect. Immun. 60, 5267-5282.
49. Zhu, P., van der Ende, A., Falush, D., Brieske, N., Morelli, G., Linz, B., Popovic, T., Schuurman, I.G.A., Adegbola, R.A., Zurth, K., Gagneux, S., Platonov, A.E., Riou, J.-Y., Caugant, D.A., Nicolas, P., Achtman, M., 2001. Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis. Proc. Natl. Acad. Sci. USA 98, 5234-5239.