Chapter 5 : The Staphylococci: A Postgenomic View

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

The Staphylococci: A Postgenomic View, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815530/9781555814519_Chap05-1.gif /docserver/preview/fulltext/10.1128/9781555815530/9781555814519_Chap05-2.gif


Staphylococci that can cause disease in humans are ,, , , , , , subsp. , subsp. , and . This chapter briefly discusses the often complex biology of the organism before the genomic insights determined from the sequence. One of the most valuable tools that can arise from whole genome sequences are whole-genome microarrays. A study on core variable genes revealed new information about the genome and its evolution. are generally more resistant to antiobiotics than other staphylococci, and it could be that they accumulate more of these genes than other species. As the methods for classifying strains into dominant types become more widespread, further epidemiological patterns and associations between certain lineages, toxins, and the infections they cause are being considered. Unlike the genomic islands in other staphylococci that are often associated with virulence, the arginine catabolism mobile element (ACME) island is associated with drug resistance. Each of the sequenced staphylococcal genomes carries genes common to all other sequenced staphylococci, genes specific to particular species, genes specific to particular lineages, and mobile genetic elements (MGEs).

Citation: Lindsay J, Holden M. 2007. The Staphylococci: A Postgenomic View, p 120-140. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch5
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

Phylogenetic relationships of staphylococcal species based on 16S rRNA sequences. Symbols after the names of the species indicate the host association: *, human; +, animals and birds; no symbol, other. Maximum-likelihood tree built from 16S rRNA sequences downloaded from the Ribosomal Database Project-I (http://rdp.cme.msu.edu) ( ) by ClustalX ( ), Phylip (version 3.6) ( ) and NJplot ( ). The numbers at the tree branches are percentage bootstrap values indicating the confident levels at that node where congruent ( ). The bar indicates the genetic distance between species (1 nucleotide substitution per 100) as displayed in the branch lengths. Sequences used to construct the tree are (accession number X68417), (AJ421446), (Y15750), (AJ517414), (S83566), (AB009933), (AB009934), (AB009935), (AB009936), (AB009937), (AB009938), (AB009939), (AB009940), (AB009941), (AB009943), (AB009945), (AB009946), (AF004220), (D83358), (D83360), (D83363), (D83364), (D83366), (D83367), (D83368), (D83369), (D83370), (D83371), (D83373), (D83374), (L37601), (L37602), (L37603), (AF041361), (AY727530), and (AJ780976). Currently recognized species missing from the tree are ( ) and ( ); these species were not included in the tree because the 16S rRNA sequences available for these species are <600 bp.

Citation: Lindsay J, Holden M. 2007. The Staphylococci: A Postgenomic View, p 120-140. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

Pairwise comparisons of NCTC8325, USA300, COL, Mu50, N315, MW2, MSSA476, MRSA252, and RF122 chromosomes displayed using the Artemis Comparison Tool (ACT) ( ). The sequences have been aligned from the predicted replication origins (; right), with the terminus of replication in the center. The dark gray bars separating each genome represent orthologous matches identified by reciprocal FASTA analysis ( ), with an identity cutoff of 30% and a length-of-match cutoff of 80%. Variable regions of the chromosomes containing mobile genetic elements such as prophages, plasmids, transposons, SaPIs, and other genomic islands are marked as boxes within the genomes and vary significantly between each strain.

Citation: Lindsay J, Holden M. 2007. The Staphylococci: A Postgenomic View, p 120-140. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3

Distribution of orthologous CDSs in . Venn diagram showing the number of genes unique or shared between three strains (MRSA252, MSSA476, and N315). The associated pie charts show the breakdown of the functional groups assigned for CDSs in relevant sections of the Venn diagram. Orthologous matches were identified as previously described for Fig. 2 . Grayscale code for the functional groups in the pie charts is displayed.

Citation: Lindsay J, Holden M. 2007. The Staphylococci: A Postgenomic View, p 120-140. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4

Pairwise comparisons of the MRSA252, ATCC 12228, RP62A, , and chromosomes. The comparisons are displayed using the Artemis Comparison Tool (ACT) ( ). The sequences have been aligned from the predicted replication origins (; right). The gray bars separating each genome represent orthologous matches identified by reciprocal FASTA analysis as previously described for Fig. 2 . The intensity of the gray matches indicates the relative identity of the orthologous match; the darker the gray, the higher the identity.

Citation: Lindsay J, Holden M. 2007. The Staphylococci: A Postgenomic View, p 120-140. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5

Distribution of orthologous CDSs in staphylococci. (A) Circular diagrams show the number of genes unique or shared between MRSA252 and RP62A; MRSA252 and ; and MRSA252 and . (B) Functional distribution of orthologous CDSs. Orthologous matches were identified as previously described for Fig. 2 .

Citation: Lindsay J, Holden M. 2007. The Staphylococci: A Postgenomic View, p 120-140. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Anonymous. 1999. Four pediatric deaths from community-acquired methicillin-resistant Staphylococcus aureus: Minnesota and North Dakota, 1997.–1999. Morb. Mortal. Wkly. Rep. 48: 707710.
2. Anonymous. 2002. Staphylococcus aureus resistant to vancomycin—United States, 2002. Morb. Mortal. Wkly. Rep. 51: 565567.
3. Anonymous. 2004. Vancomycin resistant Staphylococcus aureus—New York, 2004. Morb. Mortal. Wkly. Rep. 53: 322323.
4. Anonymous. 2002. Vancomycin-resistant Staphylococcus aureus—Pennsylvania, 2002. Morb. Mortal. Wkly. Rep. 51: 902.
5. Baba, T.,, F. Takeuchi,, M. Kuroda,, H. Yuzawa,, K. Aoki,, A. Oguchi,, Y. Nagai,, N. Iwama,, K. Asano,, T. Naimi,, H. Kuroda,, L. Cui,, K. Yamamoto, and, K. Hiramatsu. 2002. Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 359: 18191827.
6. Bae, T.,, A. K. Banger,, A. Wallace,, E. M. Glass,, F. Aslund,, O. Schneewind, and, D. M. Missiakas. 2004. Staphylococcus aureus virulence genes identified by bursa aurealis mutagenesis and nematode killing. Proc. Natl. Acad. Sci. USA 101: 1231212317.
7. Bannerman, T. L.,, G. A. Hancock,, F. C. Ten-over, and, J. M. Miller. 1995. Pulsed-field gel electrophoresis as a replacement for bacteriophage typing of Staphylococcus aureus. J. Clin. Microbiol. 33: 551555.
8. Becker, S. A., and, B. O. Palsson. 2005. Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol. 5: 8.
9. Beenken, K. E.,, P. M. Dunman,, F. McAleese,, D. Macapagal,, E. Murphy,, S. J. Projan,, J. S. Blevins, and, M. S. Smeltzer. 2004. Global gene expression in Staphylococcus aureus biofilms. J. Bacteriol. 186: 46654684.
10. Begun, J.,, C. D. Sifri,, S. Goldman,, S. B. Calderwood, and, F. M. Ausubel. 2005. Staphylococcus aureus virulence factors identified by using a high-throughput Caenorhabditis elegans– killing model. Infect. Immun. 73: 872877.
11. Betley, M. J., and, J. J. Mekalanos. 1985. Staphylococcal enterotoxin A is encoded by phage. Science 229: 185187.
12. Bohach, G. A.,, D. J. Fast,, R. D. Nelson, and, P. M. Schlievert. 1990. Staphylococcal and streptococcal pyrogenic toxins involved in toxic shock syndrome and related illnesses. Crit. Rev. Microbiol. 17: 251272.
13. Buckling, A.,, J. Neilson,, J. Lindsay,, R. ffrench-Constant,, M. Enright,, N. Day, and, R. C. Massey. 2005. Clonal distribution and phase-variable expression of a major histocompatibility complex analogue protein in Staphylococcus aureus. J. Bacteriol. 187: 29172919.
14. Carver, T. J.,, K. Rutherford,, M. Berriman,, M. A. Rajandream,, B. Barrell, and, J. Parkhill. 2005. ACT: the Artemis comparison tool. Bioinformatics 21: 34223423.
15. Chambers, H. F. 2005. Community-associated MRSA—resistance and virulence converge. N. Engl. J. Med. 352: 14851487.
16. 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: 13421347.
17. Chesneau, O.,, A. Morvan,, F. Grimont,, H. Labischinski, and, N. el Solh. 1993. Staphylococcus pasteuri sp. nov., isolated from human, animal, and food specimens. Int. J. Syst. Bacteriol. 43: 237244.
18. Clarke, S. R.,, L. G. Harris,, R. G. Richards, and, S. J. Foster. 2002. Analysis of Ebh, a 1.1-megadalton cell wall–associated fibronectin-binding protein of Staphylococcus aureus. Infect. Immun. 70: 66806687.
19. Cole, J. R.,, B. Chai,, R. J. Farris,, Q. Wang,, S. A. Kulam,, D. M. McGarrell,, G. M. Garrity, and, J. M. Tiedje. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33: D294D296.
20. Coulter, S. N.,, W. R. Schwan,, E. Y. Ng,, M. H. Langhorne,, H. D. Ritchie,, S. Westbrock-Wadman,, W. O. Hufnagle,, K. R. Folger,, A. S. Bayer, and, C. K. Stover. 1998. Staphylococcus aureus genetic loci impacting growth and survival in multiple infection environments. Mol. Microbiol. 30: 393404.
21. Cui, L.,, A. Iwamoto,, J. Q. Lian,, H. M. Neoh,, T. Maruyama,, Y. Horikawa, and, K. Hiramatsu. 2006. Novel mechanism of antibiotic resistance originating in vancomycin-intermediate Staphylococcus aureus. Antimicrob. Agents Chemother. 50: 428438.
22. Cui, L.,, X. Ma,, K. Sato,, K. Okuma,, F. C. Ten-over,, E. M. Mamizuka,, C. G. Gemmell,, M. N. Kim,, M. C. Ploy,, N. El-Solh,, V. Ferraz, and, K. Hiramatsu. 2003. Cell wall thickening is a common feature of vancomycin resistance in Staphylococcus aureus. J. Clin. Microbiol. 41: 514.
23. Diep, B. A.,, S. R. Gill,, R. F. Chang,, T. H. Phan,, J. H. Chen,, M. G. Davidson,, F. Lin,, J. Lin,, H. A. Carleton,, E. F. Mongodin,, G. F. Sensabaugh, and, F. Perdreau-Remington. 2006. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet 367: 731739.
24. Enright, M. C.,, N. P. J. Day,, C. E. Davies,, S. J. Peacock, and, B. G. Spratt. 2000. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J. Clin. Microbiol. 38: 10081015.
25. Enright, M. C.,, D. A. Robinson,, G. Randle,, E. J. Feil,, H. Grundmann, and, B. G. Spratt. 2002. The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proc. Natl. Acad. Sci. USA 99: 76877692.
26. Euzeby, J. P. 1997 List of bacterial names with standing in nomenclature: a folder available on the Internet. Int. J. Syst. Bacteriol. 47: 590592.
27. 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. J. Day. 2003. How clonal is Staphylococcus aureus? J. Bacteriol. 185: 33073316.
28. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783791.
29. Felsenstein, J. 1989. PHYLIP—Phylogeny Inference Package (version 3.2). Cladistics 5.
30. Fitzgerald, J. R.,, S. R. Monday,, T. J. Foster,, G. A. Bohach,, P. J. Hartigan,, W. J. Meaney, and, C. J. Smyth. 2001. Characterization of a putative pathogenicity island from bovine Staphylococcus aureus encoding multiple superantigens. J. Bacteriol. 183: 6370.
31. 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: 88218826.
32. Forehand, J. R., and, R. B. Johnston, Jr. 1994. Chronic granulomatous disease: newly defined molecular abnormalities explain disease variability and normal phagocyte physiology. Curr. Opin. Pediatr. 6: 668675.
33. Foster, G.,, H. M. Ross,, R. A. Hutson, and, M. D. Collins. 1997. Staphylococcus lutrae sp. nov., a new coagulase–positive species isolated from otters. Int. J. Syst. Bacteriol. 47: 724726.
34. Freney, J.,, W. E. Kloos,, V. Hajek,, J. A. Webster,, M. Bes,, Y. Brun, and, C. Vernozy-Rozand. 1999. Recommended minimal standards for description of new staphylococcal species. Subcommittee on the taxonomy of staphylococci and streptococci of the International Committee on Systematic Bacteriology. Int. J. Syst. Bacteriol. 49 (Pt. 2): 489502.
35. Gill, S. R.,, D. E. Fouts,, G. L. Archer,, E. F. Mongodin,, R. T. DeBoy,, J. Ravel,, I. T. Paulsen,, J. F. Kolonay,, L. Brinkac,, M. Beanan,, R. J. Dodson,, S. C. Daugherty,, R. Madupu,, S. V. Angiuoli,, A. S. Durkin,, D. H. Haft,, J. Vamathevan,, H. Khouri,, T. Utter-back,, C. Lee,, G. Dimitrov,, L. X. Jiang,, H. Y. Qin,, J. Weidman,, K. Tran,, K. Kang,, I. R. Hance,, K. E. Nelson, and, C. M. Fraser. 2005. Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J. Bacteriol. 187: 24262438.
36. Gillaspy, A. F.,, V. Worrell,, J. Orvis,, B. A. Roe,, D. W. Dyer, and, J. J. Iandolo. 2006. The Staphylococcus aureus NCTC8325 genome, p. 381–412. In V. Fischetti,, R. Novick,, J. Ferretti,, D. Portnoy, and, J. Rood (ed.), Gram-Positive Pathogens. ASM Press, Washington, D. C.
37. Goerke, C.,, S. M.Y. Papenberg,, S. Dasbach,, K. Dietz,, R. Ziebach,, B. C. Kahl, and, C. Wolz. 2004. Increased frequency of genomic alterations in Staphylococcus aureus during chronic infection is in part due to phage mobilization. J. Infect. Dis. 189: 724734.
38. Heinemann, M.,, A. Kummel,, R. Ruinatscha, and, S. Panke. 2005. In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol. Bioeng. 92: 850864.
39. Holden, M. T. G.,, E. J. Feil,, J. A. Lindsay,, S. J. Peacock,, N. P. J. Day,, M. C. Enright,, T. J. Foster,, C. E. Moore,, L. Hurst,, R. Atkin,, A. Barron,, N. Bason,, S. D. Bentley,, C. Chilling-worth,, T. Chillingworth,, C. Churcher,, L. Clark,, C. Corton,, A. Cronin,, J. Doggett,, L. Dowd,, T. Feltwell,, Z. Hance,, B. Harris,, H. Hauser,, S. Holroyd,, K. Jagels,, K. D. James,, N. Lennard,, A. Line,, R. Mayes,, S. Moule,, K. Mungall,, D. Ormond,, M.A. Quail,, E. Rabbi-nowitsch,, K. Rutherford,, M. Sanders,, S. Sharp,, M. Simmonds,, K. Stevens,, S. White-head,, B. G. Barrell,, B. G. Spratt, and, J. Parkhill. 2004. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc. Natl. Acad. Sci. USA 101: 97869791.
40. Jensen, M. A.,, J. A. Webster, and, N. Straus. 1993. Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl. Environ. Microbiol. 59: 945952.
41. Johnson, A. P.,, H. M. Aucken,, S. Cavendish,, M. Ganner,, M. C. J. Wale,, M. Warner,, D. M. Livermore, and, B. D. Cookson. 2001. Dominance of EMRSA-15 and -16 among MRSA causing nosocomial bacteraemia in the United Kingdom: analysis of isolates from the European Antimicrobial Resistance Surveillance System (EARSS). J. Antimicrob. Chemother. 48: 143144.
42. Jones, R. N. 2003. Global epidemiology of antimicrobial resistance among community-acquired and nosocomial pathogens: a five-year summary from the SENTRY Antimicrobial Surveillance Program (1997–2001). Semin. Respir. Crit. Care Med. 24: 121134.
43. Kazakova, S. V.,, J. C. Hageman,, M. Matava,, A. Srinivasan,, L. Phelan,, B. Garfinkel,, T. Boo,, S. McAllister,, J. Anderson,, B. Jensen,, D. Dodson,, D. Lonsway,, L. K. McDougal,, M. Arduino,, V. J. Fraser,, G. Killgore,, F. C. Ten-over,, S. Cody, and, D. B. Jernigan. 2005. A clone of methicillin-resistant Staphylococcus aureus among professional football players. N. Engl. J. Med. 352: 468475.
44. Kloos, W. E., and, T. L. Bannerman. 1994. Update on clinical significance of coagulase-negative staphylococci. Clin. Microbiol. Rev. 7: 117140.
45. Kluytmans, J.,, A. vanBelkum, and, H. Verbrugh. 1997. Nasal carriage of Staphylococcus aureus: epidemiology, underlying mechanisms, and associated risks. Clin. Microbiol. Rev. 10: 505520.
46. Koessler, T.,, P. Francois,, Y. Charbonnier,, A. Huyghe,, M. Bento,, S. Dharan,, G. Renzi,, D. Lew,, S. Harbarth,, D. Pittet, and, J. Schrenzel. 2006. Use of oligoarrays for characterization of community-onset methicillin-resistant Staphylococcus aureus. J. Clin. Microbiol. 44: 10401048.
47. Kozitskaya, S.,, M. E. Olson,, P. D. Fey,, W. Witte,, K. Ohlsen, and, W. Ziebuhr. 2005. Clonal analysis of Staphylococcus epidermidis isolates carrying or lacking biofilm-mediating genes by multilocus sequence typing. J. Clin. Microbiol. 43: 47514757.
48. Kuroda, M.,, H. Kuroda,, T. Oshima,, F. Takeuchi,, H. Mori, and, K. Hiramatsu. 2003. Two-component system VraSR positively modulates the regulation of cell-wall biosynthesis pathway in Staphylococcus aureus. Mol. Microbiol. 49: 807821.
49. Kuroda, M.,, T. Ohta,, I. Uchiyama,, T. Baba,, H. Yuzawa,, I. Kobayashi,, L. Z. Cui,, A. Oguchi,, K. Aoki,, Y. Nagai,, J. Q. Lian,, T. Ito,, M. Kanamori,, H. Matsumaru,, A. Maruyama,, H. Murakami,, A. Hosoyama,, Y. Mizutani-Ui,, N. K. Takahashi,, T. Sawano,, R. Inoue,, C. Kaito,, K. Sekimizu,, H. Hirakawa,, S. Kuhara,, S. Goto,, J. Yabuzaki,, M. Kanehisa,, A. Yamashita,, K. Oshima,, K. Furuya,, C. Yoshino,, T. Shiba,, M. Hattori,, N. Ogasawara,, H. Hayashi, and, K. Hiramatsu. 2001. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357: 12251240.
50. Kuroda, M.,, A. Yamashita,, H. Hirakawa,, M. Kumano,, K. Morikawa,, M. Higashide,, A. Maruyama,, Y. Inose,, K. Matoba,, H. Toh,, S. Kuhara,, M. Hattori, and, T. Ohta. 2005. Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection. Proc. Natl. Acad. Sci. USA 102: 1327213277.
51. Lina, G.,, Y. Piemont,, F. Godail-Gamot,, M. Bes,, M. O. Peter,, V. Gauduchon,, F. Vandenesch, and, J. Etienne. 1999. Involvement of Panton-Valentine leukocidin-producing Staphylococcus aureus in primary skin infections and pneumonia. Clin. Infect. Dis. 29: 11281132.
52. Lindsay, J. A., and, M. T. G. Holden. 2004. Staphylococcus aureus: superbug, super genome? Trends Microbiol. 12: 378385.
53. Lindsay, J. A.,, C. E. Moore,, N. P. Day,, S. J. Peacock,, A. A. Witney,, R. A. Stabler,, S. E. Husain,, P. D. Butcher, and, J. Hinds. 2006. Microarrays reveal that each of the ten dominant lineages of Staphylococcus aureus has a unique combination of surface-associated and regulatory genes. J. Bacteriol. 188: 669676.
54. Lindsay, J. A.,, A. Ruzin,, H. F. Ross,, N. Kurepina, and, R. P. Novick. 1998. The gene for toxic shock toxin is carried by a family of mobile pathogenicity islands in Staphylococcus aureus. Mol. Microbiol. 29: 527543.
55. Liolios, K.,, N. Tavernarakis,, P. Hugenholtz, and, N. C. Kyrpides. 2006. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 34: D332D334.
56. Lowe, A. M.,, D. T. Beattie, and, R. L. Deresiewicz. 1998. Identification of novel staphylococcal virulence genes by in vivo expression technology. Mol. Microbiol. 27: 967976.
57. Malachowa, N.,, A. Sabat,, M. Gniadkowski,, J. Krzyszton-Russjan,, J. Empel,, J. Miedzobrodzki,, K. Kosowska-Shick,, P. C. Appelbaum, and, W. Hryniewicz. 2005. Comparison of multiple-locus variable-number tandem-repeat analysis with pulsed-field gel electrophoresis, spa typing, and multilocus sequence typing for clonal characterization of Staphylococcus aureus isolates. J. Clin. Microbiol. 43: 30953100.
58. McDougal, L. K.,, C. D. Steward,, G. E. Kill-gore,, J. M. Chaitram,, S. K. McAllister, and, F. C. Tenover. 2003. Pulsed-field gel electrophoresis typing of oxacillin-resistant Staphylococcus aureus isolates from the United States: establishing a national database. J. Clin. Microbiol. 41: 51135120.
59. Mei, J. M.,, F. Nourbakhsh,, C. W. Ford, and, D. W. Holden. 1997. Identification of Staphylococcus aureus virulence genes in a murine model of bacteraemia using signature-tagged mutagenesis. Mol. Microbiol. 26: 399407.
60. Melish, M. E., and, L. A. Glasgow. 1970. The staphylococcal scalded-skin syndrome. N. Engl. J. Med. 282: 11141119.
61. Mongkolrattanothai, K.,, S. Boyle,, T. V. Murphy, and, R. S. Daum. 2004. Novel non- mecA-containing staphylococcal chromosomal cassette composite island containing pbp4 and tagF genes in a commensal staphylococcal species: a possible reservoir for antibiotic resistance islands in Staphylococcus aureus. Antimicrob. Agents Chemother. 48: 18231836.
62. Moore, P. C. L., and, J. A. Lindsay. 2001. Genetic variation among hospital isolates of methicillin-sensitive Staphylococcus aureus: evidence for horizontal transfer of virulence genes. J. Clin. Microbiol. 39: 27602767.
63. Nouwen, J.,, H. Boelens,, A. van Belkum, and, H. Verbrugh. 2004. Human factor in Staphylococcus aureus nasal carriage. Infect. Immun. 72: 66856688.
64. Ogston, A. 1881. Report upon micro-organisms in surgical diseases. Br. Med. J. 1: 369375.
65. Pan, E. S.,, B. A. Diep,, H. A. Carleton,, E. D. Charlebois,, G. F. Sensabaugh,, B. L. Haller, and, F. Perdreau-Remington. 2003. Increasing prevalence of methicillin-resistant Staphylococcus aureus infection in California jails. Clin. Infect. Dis. 37: 13841388.
66. Parkhill, J.,, M. Sebaihia,, A. Preston,, L. D. Murphy,, N. Thomson,, D. E. Harris,, M. T. G. Holden,, C. M. Churcher,, S. D. Bentley,, K. L. Mungall,, A. M. Cerdeno-Tarraga,, L. Temple,, K. James,, B. Harris,, M. A. Quail,, M. Achtman,, R. Atkin,, S. Baker,, D. Basham,, N. Bason,, I. Cherevach,, T. Chillingworth,, M. Collins,, A. Cronin,, P. Davis,, J. Doggett,, T. Feltwell,, A. Goble,, N. Hamlin,, H. Hauser,, S. Holroyd,, K. Jagels,, S. Leather,, S. Moule,, H. Norberczak,, S. O’Neil,, D. Ormond,, C. Price,, E. Rabbinowitsch,, S. Rutter,, M. Sanders,, D. Saunders,, K. Seeger,, S. Sharp,, M. Simmonds,, J. Skelton,, R. Squares,, S. Squares,, K. Stevens,, L. Unwin,, S. Whitehead,, B. G. Barrell, and, D. J. Maskell. 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35: 3240.
67. Parkhill, J.,, B. W. Wren,, N. R. Thomson,, R. W. Titball,, M. T. G. Holden,, M. B. Prentice,, M. Sebaihia,, K. D. James,, C. Churcher,, K. L. Mungall,, S. Baker,, D. Basham,, S. D. Bentley,, K. Brooks,, A. M. Cerdeno-Tarraga,, T. Chillingworth,, A. Cronin,, R. M. Davies,, P. Davis,, G. Dougan,, T. Feltwell,, N. Hamlin,, S. Holroyd,, K. Jagels,, A. V. Karlyshev,, S. Leather,, S. Moule,, P. C. F. Oyston,, M. Quail,, K. Rutherford,, M. Simmonds,, J. Skelton,, K. Stevens,, S. Whitehead, and, B. G. Barrell. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413: 523527.
68. Paulsen, I. T.,, N. Firth, and, R. A. Skurray. 1997. Resistance to antimicrobial agents other than b-lactams, p. 175–212. In K. B. Crossley and, G. L. Archer (ed.), The Staphylococci in Human Disease. Churchill Livingstone, New York, N. Y.
69. Pearson, W. R., and, D. J. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85: 24442448.
70. Perriere, G., and, M. Gouy. 1996. WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78: 364369.
71. Peters, G.,, R. Locci, and, G. Pulverer. 1982. Adherence and growth of coagulase-negative staphylococci on surfaces of intravenous catheters. J. Infect. Dis. 146: 479482.
72. Phillips, S., and, R. P. Novick. 1979. Tn 554— site-specific repressor-controlled transposon in Staphylococcus aureus. Nature 278: 476478.
73. Rosenbach, F. J. 1884. Mikroorganismen bei Wundinfektionskrankheiten des Menschen. Wies-baden, Germany.
74. Schlievert, P. M.,, K. N. Shands,, B. B. Dan,, G. P. Schmid, and, R. D. Nishimura. 1981. Identification and characterization of an exotoxin from Staphylococcus aureus associated with toxic-shock syndrome. J. Infect. Dis. 143: 509516.
75. Seybold, U.,, E. V. Kourbatova,, J. G. Johnson,, S. J. Halvosa,, Y. F. Wang,, M. D. King,, S. M. Ray, and, H. M. Blumberg. 2006. Emergence of community-associated methicillin-resistant Staphylococcus aureus USA300 genotype as a major cause of health care-associated blood stream infections. Clin. Infect. Dis. 42: 647656.
76. Sousa, C.,, V. de Lorenzo, and, A. Cebolla. 1997. Modulation of gene expression through chromosomal positioning in Escherichia coli. Micro-biology 143(Pt. 6): 20712078.
77. Stemper, M. E.,, S. K. Shukla, and, K. D. Reed. 2004. Emergence and spread of community-associated methicillin-resistant Staphylococcus aureus in rural Wisconsin, 1989 to 1999. J. Clin. Microbiol. 42: 56735680.
78. Takeuchi, F.,, S. Watanabe,, T. Baba,, H. Yuzawa,, T. Ito,, Y. Morimoto,, M. Kuroda,, L. Cui,, M. Takahashi,, A. Ankai,, S. Baba,, S. Fukui,, J. C. Lee, and, K. Hiramatsu. 2005. Whole-genome sequencing of Staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of human-colonizing staphylococcal species. J. Bacteriol. 187: 72927308.
79. Tenover, F. C.,, L. K. McDougal,, R. V. Goering,, G. Killgore,, S. J. Projan,, J. B. Patel, and, P. M. Dunman. 2006. Characterization of a strain of community-associated methicillin-resistant Staphylococcus aureus widely disseminated in the United States. J. Clin. Microbiol. 44: 108118.
80. Tettelin, H.,, V. Masignani,, M. J. Cieslewicz,, C. Donati,, D. Medini,, N. L. Ward,, S. V. Angiuoli,, J. Crabtree,, A. L. Jones,, A. S. Durkin,, R. T. Deboy,, T. M. Davidsen,, M. Mora,, M. Scarselli,, I. Margarit y Ros,, J. D. Peterson,, C. R. Hauser,, J. P. Sundaram,, W. C. Nelson,, R. Madupu,, L. M. Brinkac,, R. J. Dodson,, M. J. Rosovitz,, S. A. Sullivan,, S. C. Daugherty,, D. H. Haft,, J. Selengut,, M. L. Gwinn,, L. Zhou,, N. Zafar,, H. Khouri,, D. Radune,, G. Dimitrov,, K. Watkins,, K. J. O’-Connor,, S. Smith,, T. R. Utterback,, O. White,, C. E. Rubens,, G. Grandi,, L. C. Madoff,, D. L. Kasper,, J. L. Telford,, M. R. Wessels,, R. Rappuoli, and, C. M. Fraser. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pangenome.” Proc. Natl. Acad. Sci. USA 102: 1395013955.
81. Thompson, J. D.,, T. J. Gibson,, F. Plewniak,, F. Jeanmougin, and, D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 48764882.
82. Tiemersma, E. W.,, S. Bronzwaer,, O. Lyytikainen,, J. E. Degener,, P. Schrijnemakers,, N. Bruinsma,, J. Monen,, W. Witte, and, H. Grundmann. 2004. Methicillin-resistant Staphylococcus aureus in Europe, 1999–2002. Emerg. Infect. Dis. 10: 16271634.
83. Varaldo, P. E.,, R. Kilpper-Bälz,, F. Biavasco,, G. Satta, and, K. H. Schleifer. 1988. Staphylococcus delphini sp. nov., a coagulase-positive species isolated from dolphins. Int. J. Syst. Bacteriol. 38: 436439.
84. Vernozy-Rozand, C.,, C. Mazuy,, H. Meugnier,, M. Bes,, Y. Lasne,, F. Fiedler,, J. Etienne, and, J. Freney. 2000. Staphylococcus fleurettii sp. nov., isolated from goat’s milk cheeses. Int. J. Syst. Evol. Microbiol. 50(Pt 4): 15211527.
85. Wang, X. M.,, L. Noble,, B. N. Kreiswirth,, W. Eisner,, W. McClements,, K. U. Jansen, and, A. S. Anderson. 2003. Evaluation of a multilocus sequence typing system for Staphylococcus epidermidis. J. Med. Microbiol. 52: 989998.
86. Webster, J. A.,, T. L. Bannerman,, R. J. Hubner,, D. N. Ballard,, E. M. Cole,, J. L. Bruce,, F. Fiedler,, K. Schubert, and, W. E. Kloos. 1994. Identification of the Staphylococcus sciuri species group with EcoRI fragments containing rRNA sequences and description of Staphylococcus vitulus sp. nov. Int. J. Syst. Bacteriol. 44: 454460.
87. Weigel, L. M.,, D. B. Clewell,, S. R. Gill,, N. C. Clark,, L. K. McDougal,, S. E. Flannagan,, J. F. Kolonay,, J. Shetty,, G. E. Killgore, and, F. C. Tenover. 2003. Genetic analysis of a high-level vancomycin-resistant isolate of Staphylococcus aureus. Science 302: 15691571.
88. Wisplinghoff, H.,, A. E. Rosato,, M. C. En-right,, M. Noto,, W. Craig, and, G. L. Archer. 2003. Related clones containing SCC mec type IV predominate among clinically significant Staphylococcus epidermidis isolates. Antimicrob. Agents Chemother. 47: 35743579.
89. Witney, A. A.,, M. Marsden,, T. G. Holden,, R. A. Stabler,, S. E. Husain,, J. K. Vass,, P. D. Butcher,, J. Hinds, and, J. A. Lindsay. 2005. Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics. Appl. Environ. Microbiol. 71: 75047514.
90. Yao, Y.,, D. E. Sturdevant, and, M. Otto. 2005. Genomewide analysis of gene expression in Staphylococcus epidermidis biofilms: insights into the pathophysiology of S. epidermidis biofilms and the role of phenol-soluble modulins in formation of biofilms. J. Infect. Dis. 191: 289298.
91. Yao, Y. F.,, D. E. Sturdevant,, A. Villaruz,, L. Xu,, Q. Gao, and, M. Otto. 2005. Factors characterizing Staphylococcus epidermidis invasiveness determined by comparative genomics. Infect. Immun. 73: 18561860.
92. Zhang, Y. Q.,, S. X. Ren,, H. L. Li,, Y. X. Wang,, G. Fu,, J. Yang,, Z. Q. Qin,, Y. G. Miao,, W. Y. Wang,, R. S. Chen,, Y. Shen,, Z. Chen,, Z. H. Yuan,, G. P. Zhao,, D. Qu,, A. Danchin, and, Y. M. Wen. 2003. Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228). Mol. Microbiol. 49: 15771593.


Generic image for table

Clonal complex (CC) and sequence type (ST) of the sequenced isolates

Citation: Lindsay J, Holden M. 2007. The Staphylococci: A Postgenomic View, p 120-140. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch5

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error