• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of transbhomepageaboutsubmitalertseditorial board
Philos Trans R Soc Lond B Biol Sci. Apr 29, 1999; 354(1384): 701–710.
PMCID: PMC1692550

Bacterial population genetics, evolution and epidemiology.

Abstract

Asexual bacterial populations inevitably consist of an assemblage of distinct clonal lineages. However, bacterial populations are not entirely asexual since recombinational exchanges occur, mobilizing small genome segments among lineages and species. The relative contribution of recombination, as opposed to de novo mutation, in the generation of new bacterial genotypes varies among bacterial populations and, as this contribution increases, the clonality of a given population decreases. In consequence, a spectrum of possible population structures exists, with few bacterial species occupying the extremes of highly clonal and completely non-clonal, most containing both clonal and non-clonal elements. The analysis of collections of bacterial isolates, which accurately represent the natural population, by nucleotide sequence determination of multiple housekeeping loci provides data that can be used both to investigate the population structure of bacterial pathogens and for the molecular characterization of bacterial isolates. Understanding the population structure of a given pathogen is important since it impacts on the questions that can be addressed by, and the methods and samples required for, effective molecular epidemiological studies.

Full Text

The Full Text of this article is available as a PDF (217K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Achtman M. Microevolution and epidemic spread of serogroup A Neisseria meningitidis--a review. Gene. 1997 Jun 11;192(1):135–140. [PubMed]
  • Altwegg M, Hickman-Brenner FW, Farmer JJ., 3rd Ribosomal RNA gene restriction patterns provide increased sensitivity for typing Salmonella typhi strains. J Infect Dis. 1989 Jul;160(1):145–149. [PubMed]
  • ATWOOD KC, SCHNEIDER LK, RYAN FJ. Periodic selection in Escherichia coli. Proc Natl Acad Sci U S A. 1951 Mar;37(3):146–155. [PMC free article] [PubMed]
  • Bandelt HJ, Dress AW. Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol. 1992 Sep;1(3):242–252. [PubMed]
  • Bowler LD, Zhang QY, Riou JY, Spratt BG. 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. 1994 Jan;176(2):333–337. [PMC free article] [PubMed]
  • Boyd EF, Nelson K, Wang FS, Whittam TS, Selander RK. Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica. Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1280–1284. [PMC free article] [PubMed]
  • Boyd EF, Wang FS, Whittam TS, Selander RK. Molecular genetic relationships of the salmonellae. Appl Environ Microbiol. 1996 Mar;62(3):804–808. [PMC free article] [PubMed]
  • Brown AH, Feldman MW, Nevo E. Multilocus Structure of Natural Populations of HORDEUM SPONTANEUM. Genetics. 1980 Oct;96(2):523–536. [PMC free article] [PubMed]
  • Caugant DA, Frøholm LO, Bøvre K, Holten E, Frasch CE, Mocca LF, Zollinger WD, Selander RK. Intercontinental spread of a genetically distinctive complex of clones of Neisseria meningitidis causing epidemic disease. Proc Natl Acad Sci U S A. 1986 Jul;83(13):4927–4931. [PMC free article] [PubMed]
  • Caugant DA, Frøholm LO, Bøvre K, Holten E, Frasch CE, Mocca LF, Zollinger WD, Selander RK. Intercontinental spread of Neisseria meningitidis clones of the ET-5 complex. Antonie Van Leeuwenhoek. 1987;53(6):389–394. [PubMed]
  • Caugant DA, Mocca LF, Frasch CE, Frøholm LO, Zollinger WD, Selander RK. Genetic structure of Neisseria meningitidis populations in relation to serogroup, serotype, and outer membrane protein pattern. J Bacteriol. 1987 Jun;169(6):2781–2792. [PMC free article] [PubMed]
  • Enright MC, Spratt BG. A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology. 1998 Nov;144(Pt 11):3049–3060. [PubMed]
  • Feil E, Zhou J, Maynard Smith J, Spratt BG. 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. 1996 Dec;43(6):631–640. [PubMed]
  • Go MF, Kapur V, Graham DY, Musser JM. Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure. J Bacteriol. 1996 Jul;178(13):3934–3938. [PMC free article] [PubMed]
  • Gutjahr TS, O'Rourke M, Ison CA, Spratt BG. Arginine-, hypoxanthine-, uracil-requiring isolates of Neisseria gonorrhoeae are a clonal lineage with a non-clonal population. Microbiology. 1997 Feb;143(Pt 2):633–640. [PubMed]
  • Guttman DS, Dykhuizen DE. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science. 1994 Nov 25;266(5189):1380–1383. [PubMed]
  • Kohl PK, Knapp JS, Hofmann H, Gruender K, Petzoldt D, Tams MR, Holmes KK. Epidemiological analysis of Neisseria gonorrhoeae in the Federal Republic of Germany by auxotyping and serological classification using monoclonal antibodies. Genitourin Med. 1986 Jun;62(3):145–150. [PMC free article] [PubMed]
  • Lorenz MG, Wackernagel W. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev. 1994 Sep;58(3):563–602. [PMC free article] [PubMed]
  • Maiden MC. Horizontal genetic exchange, evolution, and spread of antibiotic resistance in bacteria. Clin Infect Dis. 1998 Aug;27 (Suppl 1):S12–S20. [PubMed]
  • Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):3140–3145. [PMC free article] [PubMed]
  • Maynard Smith J, Smith NH. Detecting recombination from gene trees. Mol Biol Evol. 1998 May;15(5):590–599. [PubMed]
  • Smith JM, Dowson CG, Spratt BG. Localized sex in bacteria. Nature. 1991 Jan 3;349(6304):29–31. [PubMed]
  • Smith JM, Smith NH, O'Rourke M, Spratt BG. How clonal are bacteria? Proc Natl Acad Sci U S A. 1993 May 15;90(10):4384–4388. [PMC free article] [PubMed]
  • Morelli G, Malorny B, Müller K, Seiler A, Wang JF, del Valle J, Achtman M. Clonal descent and microevolution of Neisseria meningitidis during 30 years of epidemic spread. Mol Microbiol. 1997 Sep;25(6):1047–1064. [PubMed]
  • Musser JM. Molecular population genetic analysis of emerged bacterial pathogens: selected insights. Emerg Infect Dis. 1996 Jan-Mar;2(1):1–17. [PMC free article] [PubMed]
  • Navarro F, Llovet T, Echeita MA, Coll P, Aladueña A, Usera MA, Prats G. Molecular typing of Salmonella enterica serovar typhi. J Clin Microbiol. 1996 Nov;34(11):2831–2834. [PMC free article] [PubMed]
  • Nelson K, Selander RK. 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. 1992 Nov;174(21):6886–6895. [PMC free article] [PubMed]
  • Nelson K, Whittam TS, Selander RK. Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. Proc Natl Acad Sci U S A. 1991 Aug 1;88(15):6667–6671. [PMC free article] [PubMed]
  • O'Rourke M, Ison CA, Renton AM, Spratt BG. Opa-typing: a high-resolution tool for studying the epidemiology of gonorrhoea. Mol Microbiol. 1995 Sep;17(5):865–875. [PubMed]
  • Reeves PR. Variation in O-antigens, niche-specific selection and bacterial populations. FEMS Microbiol Lett. 1992 Dec 15;100(1-3):509–516. [PubMed]
  • Salaün L, Audibert C, Le Lay G, Burucoa C, Fauchère JL, Picard B. Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. FEMS Microbiol Lett. 1998 Apr 15;161(2):231–239. [PubMed]
  • Sawyer S. Statistical tests for detecting gene conversion. Mol Biol Evol. 1989 Sep;6(5):526–538. [PubMed]
  • Selander RK, Caugant DA, Ochman H, Musser JM, Gilmour MN, Whittam TS. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl Environ Microbiol. 1986 May;51(5):873–884. [PMC free article] [PubMed]
  • Selander RK, Beltran P, Smith NH, Barker RM, Crichton PB, Old DC, Musser JM, Whittam TS. Genetic population structure, clonal phylogeny, and pathogenicity of Salmonella paratyphi B. Infect Immun. 1990 Jun;58(6):1891–1901. [PMC free article] [PubMed]
  • Selander RK, Beltran P, Smith NH, Helmuth R, Rubin FA, Kopecko DJ, Ferris K, Tall BD, Cravioto A, Musser JM. Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers. Infect Immun. 1990 Jul;58(7):2262–2275. [PMC free article] [PubMed]
  • Shortridge VD, Stone GG, Flamm RK, Beyer J, Versalovic J, Graham DW, Tanaka SK. Molecular typing of Helicobacter pylori isolates from a multicenter U.S. clinical trial by ureC restriction fragment length polymorphism. J Clin Microbiol. 1997 Feb;35(2):471–473. [PMC free article] [PubMed]
  • Sved JA. The stability of linked systems of loci with a small population size. Genetics. 1968 Aug;59(4):543–563. [PMC free article] [PubMed]
  • Vázquez JA, Berrón S, O'Rourke M, Carpenter G, Feil E, Smith NH, Spratt BG. Interspecies recombination in nature: a meningococcus that has acquired a gonococcal PIB porin. Mol Microbiol. 1995 Mar;15(6):1001–1007. [PubMed]
  • Whittam TS, Ochman H, Selander RK. Multilocus genetic structure in natural populations of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1751–1755. [PMC free article] [PubMed]
  • Zhou J, Bowler LD, Spratt BG. Interspecies recombination, and phylogenetic distortions, within the glutamine synthetase and shikimate dehydrogenase genes of Neisseria meningitidis and commensal Neisseria species. Mol Microbiol. 1997 Feb;23(4):799–812. [PubMed]

Articles from Philosophical Transactions of the Royal Society B: Biological Sciences are provided here courtesy of The Royal Society

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Cited in Books
    Cited in Books
    PubMed Central articles cited in books
  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...