1887

Abstract

The genetic relationship and population structure of subspecies I strains were analysed using nucleotide sequences of four genes (, , and ). Fifteen strains from the reference collection B (SARB), belonging to 13 serovars, were analysed. Sequence data of two housekeeping genes, and , of the same 15 strains reported by Brown (2003) ( , 15676–15681) were also included in the analyses. Phylogenetic analysis revealed that there was a lack of congruence among the six gene trees. Split decomposition analysis resolved only five strains with a network structure, while others showed a star phylogeny. Compatibility values for the SARB strains were the lowest in comparison to those for strains representing different subspecies of . These results showed that the genes studied have undergone frequent recombination, suggesting a low level of clonality within subspecies I of .

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.28486-0
2006-04-01
2020-04-10
Loading full text...

Full text loading...

/deliver/fulltext/micro/152/4/1099.html?itemId=/content/journal/micro/10.1099/mic.0.28486-0&mimeType=html&fmt=ahah

References

  1. Bandelt H. J, Dress A. W. 1992; Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol1:242–252[CrossRef]
    [Google Scholar]
  2. Bastin D. A, Romana L. K, Reeves P. R. 1991; Molecular cloning and expression in Escherichia coli K-12 of the rfb gene cluster determining the O antigen of an E. coli O111 strain. Mol Microbiol5:2223–2231[CrossRef]
    [Google Scholar]
  3. Baumler A, Tsolis R, Ficht T, Adams L. 1998; Evolution of host adaptation in Salmonella enterica . Infect Immun66:4579–4587
    [Google Scholar]
  4. Beltran P, Musser J. M, Helmuth R.8 other authors 1988; Toward a population genetic analysis of Salmonella : genetic diversity and relationships among strains of serotypes S. choleraesuis , S. derby , S. dublin , S. enteritidis , S. heidelberg , S. infantis , S. newport ,and S. typhimurium . . Proc Natl Acad Sci U S A85:7753–7757[CrossRef]
    [Google Scholar]
  5. Beltran P, Plock S. A, Smith N. H, Whittam T. S, Old D. C, Selander R. K. 1991; Reference collection of strains of the Salmonella typhimurium complex from natural populations. J Gen Microbiol137:601–606[CrossRef]
    [Google Scholar]
  6. Boyd E. F, Wang F.-S, Beltran P, Plock S. A, Nelson K, Selander R. K. 1993; Salmonella reference collection B (SARB): strains of 37 serovars of subspecies 1. J Gen Microbiol139:1125–1132[CrossRef]
    [Google Scholar]
  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 U S A91:1280–1284[CrossRef]
    [Google Scholar]
  8. Boyd E. F, Wang F. S, Whittam T. S, Selander R. K. 1996; Molecular genetic relationships of the salmonellae. Appl Environ Microbiol62:804–808
    [Google Scholar]
  9. Brenner F. W, Villar R. G, Angulo F. J, Tauxe R, Swaminathan B. 2000; Salmonella nomenclature. J Clin Microbiol38:2465–2467
    [Google Scholar]
  10. Brown E. W, Kotewicz M. L, Cebula T. A. 2002; Detection of recombination among Salmonella enterica strains using the incongruence length difference test. Mol Phylogenet Evol24:102–120[CrossRef]
    [Google Scholar]
  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 U S A100:15676–15681[CrossRef]
    [Google Scholar]
  12. Crosa J. H, Brenner D. J, Ewing W. H, Falkow S. 1973; Molecular relationships among the Salmonellae . J Bacteriol115:307–315
    [Google Scholar]
  13. Deng W, Liou S. R, Plunkett G., 3rd, Mayhew G. F, Rose D. J, Burland V, Kodoyianni V, Schwartz D. C, Blattner F. R. 2003; Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol185:2330–2337[CrossRef]
    [Google Scholar]
  14. Dolz R. 1994; gcg: comparison of sequences. Methods Mol Biol24:64–82
    [Google Scholar]
  15. Feil E. J, Smith J. M, Enright M. C, Spratt B. G. 2000; Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics154:1439–1450
    [Google Scholar]
  16. Feil E. J, Holmes E. C, Bessen D. E.9 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 A98:182–187[CrossRef]
    [Google Scholar]
  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 Bacteriol186:1518–1530[CrossRef]
    [Google Scholar]
  18. Felsenstein J. 1989; phylip – phylogeny inference package. Cladistics5:164–166
    [Google Scholar]
  19. Gordon D, Abajian C, Green P. 1998; consed – a graphical tool for sequence finishing. Genome Res8:195–202[CrossRef]
    [Google Scholar]
  20. Hoorfar J, Baggesen D. L, Porting P. H. 1999; A PCR-based strategy for simple and rapid identification of rough presumptive Salmonella isolates. J Microbiol Methods35:77–84[CrossRef]
    [Google Scholar]
  21. Jakobsen I. B, Easteal S. 1996; A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. CABIOS12:291–295
    [Google Scholar]
  22. 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 Evol2:39–45[CrossRef]
    [Google Scholar]
  23. Le Minor L, Popoff M. Y. 1987; Designation of Salmonella enterica sp. nov., nom. rev., as the type and only species of the genus Salmonella . Int J Syst Bacteriol37:465–468[CrossRef]
    [Google Scholar]
  24. Le Minor L, Popoff M. Y, Laurent B, Hermant D. 1986; Individualisation D'une septieme sous-espece de Salmonella: S.choleraesuis subsp. indica subsp. nov. Ann Inst Pasteur Microbiol137B:211–217
    [Google Scholar]
  25. Luk J. M. C, Kongmuang U, Reeves P. R, Lindberg A. A. 1993; Selective amplification of abequose and paratose synthase genes (rfb) by polymerase chain reaction for identification of Salmonella major serogroups (A, B, C2, and D). J Clin Microbiol31:2118–2123
    [Google Scholar]
  26. Matic I, Taddei F, Radman M. 1996; Genetic barriers among bacteria. Trends Microbiol4:69–73[CrossRef]
    [Google Scholar]
  27. Maynard Smith J, Smith N. H, O'Rourke M, Spratt B. G. 1993; How clonal are bacteria?. Proc Natl Acad Sci U S A90:4384–4388[CrossRef]
    [Google Scholar]
  28. 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 Bacteriol174:6886–6895
    [Google Scholar]
  29. Nelson K, Selander R. K. 1994; Intergenic transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria. Proc Natl Acad Sci U S A91:10227–10231[CrossRef]
    [Google Scholar]
  30. 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 U S A88:6667–6671[CrossRef]
    [Google Scholar]
  31. Nelson K, Wang F. S, Boyd E. F, Selander R. K. 1997; Size and sequence polymorphism in the isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella enterica and Escherichia coli . Genetics147:1509–1520
    [Google Scholar]
  32. Pabbaraju K, Miller W, Sanderson K. 2000; Distribution of intervening sequences in the genes for 23S rRNA and rRNA fragmentation among strains of the Salmonella reference collection B (SARB) and SARC sets. J Bacteriol182:1923–1929[CrossRef]
    [Google Scholar]
  33. Parkhill J, Dougan G, James K. D.38 other authors 2001; Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature413:848–852[CrossRef]
    [Google Scholar]
  34. Popoff M. Y. 2001; Antigenic Formulas of the Salmonella Serovars, 8th edn.. Paris, France: WHO Collaborating Centre for Reference and Research on Salmonella, Institut Pasteur;
    [Google Scholar]
  35. Radman M, Matic I, Taddei F. 1999; Evolution of evolvability. Ann N Y Acad Sci870:146–155[CrossRef]
    [Google Scholar]
  36. Rayssiguier C, Thaler D. S, Radman M. 1989; The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature342:396–400[CrossRef]
    [Google Scholar]
  37. Reeves M. W, Evins G. M, Heiba A. A, Plikaytis B. D, Farmer J. J., III. 1989; Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori . J Clin Microbiol27:313–320
    [Google Scholar]
  38. Reeves P. R, Farnell L, Lan R. 1994; multicomp: a program for preparing sequence data for phylogenetic analysis. CABIOS10:281–284
    [Google Scholar]
  39. Reid S. D, Herbelin C. J, Bumnaugh A. C, Selander R. K, Whittam T. S. 2000; Parallel evolution of virulence in pathogenic Escherichia coli. Nature40664–67[CrossRef]
    [Google Scholar]
  40. 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 Immun58:1891–1901
    [Google Scholar]
  41. Selander R. K, Beltran P, Smith N. H. & 7 other authors (1990b). Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers. Infect Immun58:2262–2275
    [Google Scholar]
  42. Selander R. K, Beltran P, Smith N. H. 1991; Evolutionary genetics of Salmonella. In Evolution at the Molecular Level pp 25–27 Edited by Selander R. K., Clark A. G., Whittam T. S.. Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  43. Selander R. K, Li J, Nelson K. 1996; Evolutionary genetics of Salmonella enterica. In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn. pp 2691–2707 Edited by Neidhardt F. C., Curtiss III R., Ingraham J. L., Lin E. C. C., Low K. B., Magasanik B., Reznikoff W. S., Riley M., Schaechter M., Umbarger H. E.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  44. Swofford D. L. 1998; paup – phylogenetic analysis using parsimony Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  45. Torpdahl M, Ahrens P. 2004; Population structurke of Salmonella investigated by amplified fragment length polymorphism. J Appl Microbiol97:566–573[CrossRef]
    [Google Scholar]
  46. Vulic M, Dionisio F, Taddei F, Radman M. 1997; Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc Natl Acad Sci U S A94:9763–9767[CrossRef]
    [Google Scholar]
  47. Wang F, Whittam T, Selander R. 1997; Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica . J Bacteriol179:6551–6559
    [Google Scholar]
  48. Worth L., Jr, Clark S. E, Radman M, Modrich P. 1994; Mismatch repair proteins MutS and MutL inhibit RecA-catalyzed strand transfer between diverged DNAs. Proc Natl Acad Sci U S A91:3238–3241[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.28486-0
Loading
/content/journal/micro/10.1099/mic.0.28486-0
Loading

Data & Media loading...

Most cited this month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error