Impact of recombination on genetic variability within Staphylococcus aureus clonal complexes

Infection, Genetics and Evolution

Volumn 10, Issue 7, 2010, Pages 1117-1123

  Basic Hammer, Nevena ^a   Vogel, Valérie ^a   Basset, Patrick ^a   Blanc, Dominique S ^a  

^a LAUSANNE UNIVERSITY HOSPITAL   (Switzerland)

Author keywords

Clonal complexes; Genetic diversity; Recombination; Selection; Staphylococcus aureus

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIUM ISOLATE; CLONAL VARIATION; CONTROLLED STUDY; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAPLOTYPE; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; STAPHYLOCOCCUS AUREUS;

BACTERIAL PROTEINS; BACTERIAL TYPING TECHNIQUES; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC VARIATION; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; RECOMBINATION, GENETIC; STAPHYLOCOCCUS AUREUS;

STAPHYLOCOCCUS AUREUS;

EID: 77956262774     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2010.07.013     Document Type: Article

References (43)

1. Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annual Review of Microbiology 2008, 62:53-70.
2. Brown C.J., Garner E.C., Dunker A.K., Joyce P. The power to detect recombination using the coalescent. Molecular Biology and Evolution 2001, 18:1421-1424.
3. Bruen T.C., Philippe H., Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics 2006, 172:2665-2681.
4. Clement M., Posada D., Crandall K.A. TCS: a computer program to estimate gene genealogies. Molecular Ecology 2000, 9:1657-1659.
5. Cooper J.E., Feil E.J. Multilocus sequence typing-what is resolved?. Trends in Microbiology 2004, 12:373-377.
6. Cooper J.E., Feil E.J. The phylogeny of Staphylococcus aureus-which genes make the best intra-species markers?. Microbiology-Sgm 2006, 152:1297-1305.
7. de Queiroz K. Different species problems and their resolution. Bioessays 2005, 27:1263-1269.
8. Didelot X., Falush D. Inference of bacterial microevolution using multilocus sequence data. Genetics 2007, 175:1251-1266.
9. Enright M.C., Day N.P., Davies C.E., Peacock S.J., Spratt B.G. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. Journal of Clinical Microbiology 2000, 38:1008-1015.
10. Feil E.J. Small change: keeping pace with microevolution. Nature Reviews Microbiology 2004, 2:483-495.
11. Feil E.J., Cooper J.E., Grundmann H., Robinson D.A., Enright M.C., Berendt T., Peacock S.J., Smith J.M., Murphy M., Spratt B.G., Moore C.E., Day N.P. How clonal is Staphylococcus aureus?. Journal of Bacteriology 2003, 185:3307-3316.
12. Fitzgerald J.R., Reid S.D., Ruotsalainen E., Tripp T.J., Liu M., Cole R., Kuusela P., Schlievert P.M., Jarvinen A., Musser J.M. Genome diversification in Staphylococcus aureus: molecular evolution of a highly variable chromosomal region encoding the Staphylococcal exotoxin-like family of proteins. Infection and Immunity 2003, 71:2827-2838.
13. Guttman D.S., Dykhuizen D.E. Clonal divergence in Escherichia-coli as a result of recombination. Not mutation. Science 1994, 266:1380-1383.
14. Halkett F., Simon J.C., Balloux F. Tackling the population genetics of clonal and partially clonal organisms. Trends in Ecology & Evolution 2005, 20:194-201.
15. Hall T.A. BioEdit: a user friendly biological sequence alignment editor and analyses program for Windows 95/98/NT. Nucleic Acids Symposium Series 1999, 41:95-98.
16. Hanage W.P., Fraser C., Spratt B.G. The impact of homologous recombination on the generation of diversity in bacteria. Journal of Theoretical Biology 2006, 239:210-219.
17. Harris S.R., Feil E.J., Holden M.T.G., Quail M.A., Nickerson E.K., Chantratita N., Gardete S., Tavares A., Day N., Lindsay J.A., Edgeworth J.D., de Lencastre H., Parkhill J., Peacock S.J., Bentley S.D. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327:469-474.
18. Hughes A.L., Friedman R. Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus. Journal of Bacteriology 2005, 187:2698-2704.
19. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 2006, 23:254-267.
20. Kuhn G., Francioli P., Blanc D.S. Evidence for clonal evolution among highly polymorphic genes in methicillin-resistant Staphylococcus aureus. Journal of Bacteriology 2006, 188:169-178.
21. Martin D.P., Williamson C., Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 2005, 21:260-262.
22. Maydt J., Lengauer T. Recco: recombination analysis using cost optimization. Bioinformatics 2006, 22:1064-1071.
23. Narra H.P., Ochman H. Of what use is sex to bacteria?. Current Biology 2006, 16:R705-R710.
24. Nei M. Molecular Evolutionary Genetics 1987, Columbia University Press, New York.
25. Nubel U., Dordel J., Kurt K., Strommenger B., Westh H., Shukla S.K., Zemlickova H., Leblois R., Wirth T., Jombart T., Balloux F., Witte W. A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus. PLoS Pathogens 2010, 6.
26. Nübel U., Roumagnac P., Feldkamp M., Song J.H., Ko K.S., Huang Y.C., Coombs G., Ip M., Westh H., Skov R., Struelens M.J., Goering R.V., Strommenger B., Weller A., Witte W., Achtman M. Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:14130-14135.
27. Padidam M., Sawyer S., Fauquet C.M. Possible emergence of new geminiviruses by frequent recombination. Virology 1999, 265:218-225.
28. Posada D. Evaluation of methods for detecting recombination from DNA sequences: empirical data. Molecular Biology and Evolution 2002, 19:708-717.
29. Posada D., Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proceedings of the National Academy of Sciences of the United States of America 2001, 98:13757-13762.
30. Robinson D.A., Enright M.C. Evolutionary models of the emergence of methicillin-resistant Staphylococcus aureus. Antimicrobial Agents and Chemotherapy 2003, 47:3926-3934.
31. Robinson D.A., Enright M.C. Evolution of Staphylococcus aureus by large chromosomal replacements. Journal of Bacteriology 2004, 186:1060-1064.
32. Rozas J., Sanchez-DelBarrio J.C., Messeguer X., Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003, 19:2496-2497.
33. Schneider S., Roessli D., Excoffier L. Arlequin Version 2.000: A Software for Population Genetics Data analysis 2000, Genetics and Biometry Laboratory,University of Geneva, Switzerland.
34. Smith J.M. Analyzing the mosaic structure of genes. Journal of Molecular Evolution 1992, 34:126-129.
35. Smith J.M., Smith N.H., O'Rourke M., Spratt B.G. How clonal are bacteria?. Proceedings of the National Academy of Sciences of the United States of America 1993, 90:4384-4388.
36. Stumpf M.P.H., McVean G.A.T. Estimating recombination rates from population-genetic data. Nature Reviews Genetics 2003, 4:959-968.
37. Tibayrenc M. Population genetics of parasitic protozoa and other microorganisms. Advances in Parasitology 1995, 36:48-115.
38. Turner K.M.E., Feil E.J. The secret life of the multilocus sequence type. International Journal of Antimicrobial Agents 2007, 29:129-135.
39. Vos M. Why do bacteria engage in homologous recombination?. Trends in Microbiology 2009, 17:226-232.
40. Waldron D.E., Lindsay J.A. Sau1: a novel lineage-specific type I restriction-modification system that blocks horizontal gene transfer into Staphylococcus aureus and between S. aureus isolates of different lineages. Journal of Bacteriology 2006, 188:5578-5585.
41. Yang Z.H. PAML: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences 1997, 13:555-556.
42. Yang Z.H., Nielsen R., Goldman N., Pedersen A.M.K. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 2000, 155:431-449.
43. Yang Z.H., Wong W.S.W., Nielsen R. Bayes empirical Bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution 2005, 22:1107-1118.