spa Typing Method for Discriminating among Staphylococcus aureus Isolates: Implications for Use of A Single Marker to Detect Genetic Micro- and Macrovariation

Journal of Clinical Microbiology

Volumn 42, Issue 2, 2004, Pages 792-799

  Koreen, Larry ^a,b   Ramaswamy, Srinivas V ^c   Graviss, Edward A ^c   Naidich, Steven ^d   Musser, James M ^c,e   Kreiswirth, Barry N ^a  

^a PUBLIC HEALTH RESEARCH INSTITUTE   (United States)

^b RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

^d eGenomics   (United States)

^e NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN A;

ARTICLE; BACTERIAL GENE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; DNA MICROARRAY; DNA SEQUENCE; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC VARIABILITY; MULTILOCUS ENZYME ELECTROPHORESIS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; SEQUENCE ANALYSIS; SPA GENE; STAPHYLOCOCCUS AUREUS;

ANTIGENS, BACTERIAL; BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; DNA PRIMERS; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; GENETIC MARKERS; GENOTYPE; GEOGRAPHY; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; POLYMERASE CHAIN REACTION; STAPHYLOCOCCUS AUREUS; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); POSIBACTERIA; STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS;

EID: 1242336848     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.42.2.792-799.2004     Document Type: Article

References (38)

1. Appel, R. D., A. Bairoch, and D. F. Hochstrasser. 1994. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem. Sci. 19:258-260.
2. Behr, M. A., M. A. Wilson, W. P. Gill, H. Salamon, G. K. Schoolnik, S. Rane, and P. M. Small. 1999. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284:1520-1523.
3. Chang, S., D. M. Sievert, J. C. Hageman, M. L. Boulton, F. C. Tenover, F. P. Downes, S. Shah, J. T. Rudrik, G. R. Pupp, W. J. Brown, D. Cardo, and S. K. Fridkin. 2003. Infection with vancomycin-resistant Staphylococcus aureus containing the vanA resistance gene. N. Engl. J. Med. 348:1342-1347.
4. Crisostomo, M. I., H. Westh, A. Tomasz, M. Chung, D. C. Oliveira, and H. de Lencastre. 2001. The evolution of methicillin resistance in Staphylococcus aureus: similarity of genetic backgrounds in historically early methicillin-susceptible and -resistant isolates and contemporary epidemic clones. Proc. Natl. Acad. Sci. USA 98:9865-9870.
5. Day, N. P., C. E. Moore, M. C. Enright, A. P. Berendt, J. M. Smith, M. F. Murphy, S. J. Peacock, B. G. Spratt, and E. J. Feil. 2001. A link between virulence and ecological abundance in natural populations of Staphylococcus aureus. Science 191:114-116. (Retraction, 295:971, 2002.)
6. Day, N. P., C. E. Moore, M. C. Enright, A. P. Berendt, J. M. Smith, M. F. Murphy, S. J. Peacock, B. G. Spratt, and E. J. Feil. 2001. A link between virulence and ecological abundance in natural populations of Staphylococcus aureus. Science 191:114-116. (Retraction, 295:971, 2002.)
7. de Lencastre, H., M. Chung, and H. Westh. 2000. Archaic strains of methicillin-resistant Staphylococcus aureus: molecular and microbiological properties of isolates from the 1960s in Denmark. Microb. Drug Resist. 6:1-10.
8. Deajardins, P., B. Picard, B. Kaltenbock, J. Elion, and E. Denamur. 1995. Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism. J. Mol. Evol. 41:440-448.
9. de Sousa, M. A., M. I. Crisostomo, I. S. Sanches, J. S. Wu, J. Fuzhong, A. Tomasz, and H. de Lencastre. 2003. Frequent recovery of a single clonal type of multidrug-resistant Staphylococcus aureus from patients in two hospitals in Taiwan and China. J. Clin. Microbiol. 41:159-163.
10. Enright, M. C., D. A. Robinson, G. Randle, E. J. Feil, H. Grundmann, and B. G. Spratt. 2002. The evolutionary history of methicillin-resistant Staphyloccocus aureus (MRSA). Proc. Natl. Acad. Sci. USA 99:7687-7692.
11. Enright, M. C., and B. G. Spratt. 1999. Multilocus sequence typing. Trends Microbiol. 7:482-487.
12. Feil, E. J., J. E. Cooper, H. Grundmann, D. A. Robinson, M. C. Enright, T. Berendt, S. J. Peacock, J. M. Smith, M. Murphy, B. G. Spratt, C. E. Moore, and N. P. Day. 2003. How clonal is Staphylococcus aureus? J. Bacteriol. 185:3307-3316.
13. Feil, E. J., E. C. Holmes, D. E. Bessen, M. S. Chan, N. P. Day, M. C. Enright, R. Goldstein, D. W. Hood, A. Kalia, C. E. Moore, J. Zhou, and B. G. Spratt. 2001. Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc. Natl. Acad. Sci. USA 98:182-187.
14. Fitzgerald, J. R., D. E. Sturdevant, S. M. Mackie, S. R. Gill, and J. M. Musser. 2001. Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. USA 98:8821-8826.
15. Hunter, P. R., and M. A. Gaston. 1988. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J. Clin. Microbiol. 26:2465-2466.
16. Hurst, L. D. 2002. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18:486.
17. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
18. Maiden, M. C., J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell, R. Urwin, Q. Zhang, J. Zhou, K. Zurth, D. A. Caugant, I. M. Feavers, M. Achtman, and B. G. Spratt. 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.
19. Milkman, R., and M. M. Bridges. 1990. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics 126:505-517.
20. Mostowy, S., D. Cousins, J. Brinkman, A. Aranaz, and M. A. Behr. 2002. Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J. Infect. Dis. 186:74-80.
21. Musser, J. M., and V. Kapur. 1992. Clonal analysis of methicillin-resistant Staphylococcus aureus strains from intercontinental sources: association of the mec gene with divergent phylogenetic lineages implies dissemination by horizontal transfer and recombination. J. Clin. Microbiol. 30:2058-2063.
22. National Nosocomial Infections Surveillance System. 1999. National Nosocomial Infections Surveillance (NNIS) System report, data summary from January 1990-May 1999, issued June 1999. Am. J. Infect. Control 27:520-532.
23. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
24. Okuma, K., K. Iwakawa, J. D. Turnidge, W. B. Grubb, J. M. Bell, F. G. O'Brien, G. W. Coombs, J. W. Pearman, F. C. Tenover, M. Kapi, C. Tiensasitorn, T. Ito, and K. Hiramatsu. 2002. Dissemination of new methicillin-resistant Staphylococcus aureus clones in the community. J. Clin. Microbiol. 40:4289-4294.
25. Oliveira, D. C., A. Tomasz, and H. de Lencastre. 2001. The evolution of pandemic clones of methicillin-resistant Staphylococcus aureus: identification of two ancestral genetic backgrounds and the associated mec elements. Microb. Drug Resist. 7:349-361.
26. Peacock, S. J., G. D. de Silva, A. Justice, A. Cowland, C. E. Moore, C. G. Winearls, and N. P. Day. 2002. Comparison of multilocus sequence typing and pulsed-field gel electrophoresis as tools for typing Staphylococcus aureus isolates in a microepidemiological setting. J. Clin. Microbiol. 40:3764-3770.
27. Peacock, S. J., C. E. Moore, A. Justice, M. Kantzanou, L. Story, K. Mackie, G. O'Neill, and N. P. Day. 2002. Virulent combinations of adhesin and toxin genes in natural populations of Staphylococcus aureus. Infect. Immun. 70:4987-4996.
28. Reid, S. D., C. J. Herbelin, A. C. Bumbaugh, R. K. Selander, and T. S. Whittam. 2000. Parallel evolution of virulence in pathogenic Escherichia coli. Nature 406:64-67.
29. Robinson, D. A., S. K. Hollingshead, J. M. Musser, A. J. Parkinson, D. E. Briles, and M. J. Crain. 1998. The IS1167 insertion sequence is a phylogenetically informative marker among isolates of serotype 6B Streptococcus pneumoniae. J. Mol. Evol. 47:222-229.
30. Salama, N., K. Guillemin, T. K. McDaniel, G. Sherlock, L. Tompkins, and S. Falkow. 2000. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc. Natl. Acad. Sci. USA 97:14668-14673.
31. Shopsin, B., M. Gomez, S. O. Montgomery, D. H. Smith, M. Waddington, D. E. Dodge, D. A. Bost, M. Riehman, S. Naidich, and B. N. Kreiswirth. 1999. Evaluation of protein A gene polymorphic region DNA sequencing for typing of Staphylococcus aureus strains. J. Clin. Microbiol. 37:3556-3563.
32. Shopsin, B., M. Gomez, M. Waddington, M. Riehman, and B. N. Kreiswirth. 2000. Use of coagulase gene (coa) repeat region nucleotide sequences for typing of methicillin-resistant Staphylococcus aureus strains. J. Clin. Microbiol. 38:3453-3456.
33. Smith, J., N. Smith, M. O'Rourke, and B. Spratt. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:4384-4388.
34. Snel, B., P. Bork, and M. A. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108-110.
35. Spratt, B. G., W. P. Hanage, and E. J. Feil. 2001. The relative contributions of recombination and point mutation to the diversification of bacterial clones. Curr. Opin. Microbiol. 4:602-606.
36. Tenover, F. C., R. D. Arbeit, R. V. Goering, P. A. Mickelsen, B. E. Murray, D. H. Persing, and B. Swaminathan. 1995. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33:2233-2239.
37. van Belkum, A., S. Scherer, L. van Alphen, and H. Verbrugh. 1998. Short-sequence DNA repeats in prokaryotic genomes. Microbiol. Mol. Biol. Rev. 62:275-293.
38. Versalovic, J., V. Kupur, E. O. Mason, Jr., U. Shah, T. Koeuth, J. R. Lupski, and J. M. Musser. 1993. Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones. J. Infect. Dis. 167:850-856.