Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: Insights into the pneumococcal supragenome

Journal of Bacteriology

Volumn 189, Issue 22, 2007, Pages 8186-8195

  Hiller, N Luisa ^a   Janto, Benjamin ^a   Hogg, Justin S ^a   Boissy, Robert ^a   Yu, Susan ^a   Powell, Evan ^a   Keefe, Randy ^a   Ehrlich, Nathan E ^a   Shen, Kai ^a   Hayes, Jay ^a   Barbadora, Karen ^b   Klimke, William ^c   Dernovoy, Dmitry ^c   Tatusova, Tatiana ^c   Parkhill, Julian ^d   Bentley, Stephen D ^d   Post, J Christopher ^a,e   Ehrlich, Garth D ^a,e   Hu, Fen Z ^a,e  

^a ALLEGHENY GENERAL HOSPITAL   (United States)

^b CHILDREN S HOSPITAL OF PITTSBURGH   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e DREXEL UNIVERSITY COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENETICS; BACTERIAL STRAIN; CONFERENCE PAPER; CONTROLLED STUDY; GENE CLUSTER; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; STREPTOCOCCUS PNEUMONIAE;

GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; GENOMICS; MULTIGENE FAMILY; PHYLOGENY; STREPTOCOCCUS PNEUMONIAE;

BACTERIA (MICROORGANISMS); HAEMOPHILUS INFLUENZAE; STREPTOCOCCUS AGALACTIAE; STREPTOCOCCUS PNEUMONIAE;

EID: 36549020646     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00690-07     Document Type: Conference Paper

References (44)

1. Avery, O. T., C. M. MacLeod, and M. McCarty. 1944. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Inductions of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J. Exp. Med. 79:137-158.
2. Brueggemann, A. B., D. T. Griffiths, E. Meats, T. Peto, D. W. Crook, and B. G. Spratt. 2003. Clonal relationships between invasive and carriage Streptococcus pneumoniae and serotype- and clone-specific differences in invasive disease potential. J. Infect. Dis. 187:1424-1432.
3. Claverys, J. P., and L. S. Havarstein. 2002. Extracellular-peptide control of competence for genetic transformation in Streptococcus pneumoniae. Front. Biosci. 7:d1798-d1814.
4. Daraselia, N., D. Dernovoy, Y. Tian, M. Borodovsky, R. Tatusov, and T. Tatusova. 2003. Reannotation of Shewanella oneidensis genome. OMICS 7:171-175.
5. Del Beccaro, M. A., P. M. Mendelman, A. F. Inglis, M. A. Richardson, N. O. Duncan, C. R. Clausen, and T. L. Stull. 1992. Bacteriology of acute otitis media: a new perspective. J. Pediatr. 120:81-84.
6. Delcher, A. L., S. Kasif, R. D. Fleischmann, J. Peterson, O. White, and S. L. Salzberg. 1999. Alignment of whole genomes. Nucleic Acids Res. 27:2369-2376.
7. Ehrlich, G. D., F. Z. Hu, K. Shen, P. Stoodley, and J. C. Post. 2005. Bacterial plurality as a general mechanism driving persistence in chronic infections. Clin. Orthop. Relat. Res. 2005:20-24.
8. Ehrlich, G. D., R. Veeh, X. Wang, J. W. Costerton, J. D. Hayes, F. Z. Hu, B. J. Daigle, M. D. Ehrlich, and J. C. Post. 2002. Mucosal biofilm formation on middle-ear mucosa in the chinchilla model of otitis media. JAMA 287:1710-1715.
9. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
10. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
11. Farjo, R. S., B. Foxman, M. J. Patel, L. Zhang, M. M. Pettigrew, S. I. McCoy, C. F. Marrs, and J. R. Gilsdorf. 2004. Diversity and sharing of Haemophilus influenzae strains colonizing healthy children attending day-care centers. Pediatr. Infect. Dis. J. 23:41-46.
12. Gates, G. A. 1996. Cost-effectiveness considerations in otitis media treatment. Otolaryngol. Head Neck Surg. 114:525-530.
13. Gordon, D. 2004. Viewing and editing assembled sequences using Consed. John Wiley & Co., New York, NY.
14. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
15. Hall-Stoodley, L., F. Z. Hu, A. Gieseke, L. Nistico, D. Nguyen, J. Hayes, M. Forbes, D. P. Greenberg, B. Dice, A. Burrows, P. A. Wackym, P. Stoodley, J. C. Post, G. D. Ehrlich, and J. E. Kerschner. 2006. Direct detection of bacterial biofilms on the middle-ear mucosa of children with chronic otitis media. JAMA 296:202-211.
16. Hiltke, T. J., A. T. Schiffmacher, A. J. Dagonese, S. Sethi, and T. F. Murphy. 2003. Horizontal transfer of the gene encoding outer membrane protein P2 of nontypeable Haemophilus influenzae, in a patient with chronic obstructive pulmonary disease. J. Infect. Dis. 188:114-117.
17. Hoberman, A., D. P. Greenberg, J. L. Paradise, H. E. Rockette, J. R. Lave, D. H. Kearney, D. K. Colborn, M. Kurs-Lasky, M. A. Haralam, C. J. Byers, L. M. Zoffel, I. A. Fabian, B. S. Bernard, and J. D. Kerr. 2003. Effectiveness of inactivated influenza vaccine in preventing acute otitis media in young children: a randomized controlled trial. JAMA 290:1608-1616.
18. Hogg, J. S., F. Z. Hu, B. Janto, R. Boissy, J. Hayes, R. Keefe, J. C. Post, and G. D. Ehrlich. 2007. Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol. 8:R103. [Epub ahead of print.]
19. Hoskins, J., W. E. Alborn, Jr., J. Arnold, L. C. Blaszczak, S. Burgett, B. S. DeHoff, S. T. Estrem, L. Fritz, D. J. Fu, W. Fuller, C. Geringer, R. Gilmour, J. S. Glass, H. Khoja, A. R. Kraft, R. E. Lagace, D. J. LeBlanc, L. N. Lee, E. J. Lefkowitz, J. Lu, P. Matsushima, S. M. McAhren, M. McHenney, K. McLeaster, C. W. Mundy, T. I. Nicas, F. H. Norris, M. O'Gara, R. B. Peery, G. T. Robertson, P. Rockey, P. M. Sun, M. E. Winkler, Y. Yang, M. Young-Bellido, G. Zhao, C. A. Zook, R. H. Baltz, S. R. Jaskunas, P. R. Rosteck, Jr., P. L. Skatrud, and J. I. Glass. 2001. Genome of the bacterium Streptococcus pneumoniae strain R6. J. Bacteriol. 183:5709-5717.
20. Kelly, T., J. P. Dillard, and J. Yother. 1994. Effect of genetic switching of capsular type on virulence of Streptococcus pneumoniae. Infect. Immun. 62:1813-1819.
21. Klein, J. O. 1999. Management of acute otitis media in an era of increasing antibiotic resistance. Int. J. Pediatr. Otorhinolaryngol. 49(Suppl. 1):S15-S17.
22. Kunsch, C. A., G. H. Choi, P. S. Dillon, C. A. Rosen, S. C. Barash, M. R. Fannon, and B. A. Dougherty. 16 July 2002. Streptococcus pneumoniae polynucleotides and sequences. U.S. patent 6,420,135.
23. Lanie, J. A., W. L. Ng, K. M. Kazmierczak, T. M. Andrzejewski, T. M. Davidsen, K. J. Wayne, H. Tettelin, J. I. Glass, and M. E. Winkler. 2007. Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6. J. Bacteriol. 189:38-51.
24. Lowe, T. M., and S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
25. Marchler-Bauer, A., J. B. Anderson, M. K. Derbyshire, C. DeWeese-Scott, N. R. Gonzales, M. Gwadz, L. Hao, S. He, D. I. Hurwitz, J. D. Jackson, Z. Ke, D. Krylov, C. J. Lanczycki, C. A. Liebert, C. Liu, F. Lu, S. Lu, G. H. Marchler, M. Mullokandov, J. S. Song, N. Thanki, R. A. Yamashita, J. J. Yin, D. Zhang, and S. H. Bryant. 2007. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 35:D237-D240.
26. Margulies, M., M. Egholm, W. E. Altman, S. Attiya, J. S. Bader, L. A. Bemben, J. Berka, M. S. Braverman, Y. J. Chen, Z. Chen, S. B. Dewell, L. Du, J. M. Fierro, X. V. Gomes, B. C. Godwin, W. He, S. Helgesen, C. H. Ho, G. P. Irzyk, S. C. Jando, M. L. Alenquer, T. P. Jarvie, K. B. Jirage, J. B. Kim, J. R. Knight, J. R. Lanza, J. H. Leamon, S. M. Lefkowitz, M. Lei, J. Li, K. L. Lohman, H. Lu, V. B. Makhijani, K. E. McDade, M. P. McKenna, E. W. Myers, E. Nickerson, J. R. Nobile, R. Plant, B. P. Puc, M. T. Ronan, G. T. Roth, G. J. Sarkis, J. F. Simons, J. W. Simpson, M. Srinivasan, K. R. Tartaro, A. Tomasz, K. A. Vogt, G. A. Volkmer, S. H. Wang, Y. Wang, M. P. Weiner, P. Yu, R. F. Begley, and J. M. Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
27. Mavroidi, A., D. Godoy, D. M. Aanensen, D. A. Robinson, S. K. Hollingshead, and B. G. Spratt. 2004. Evolutionary genetics of the capsular locus of serogroup 6 pneumococci. J. Bacteriol. 186:8181-8192.
28. Molin, S., and T. Tolker-Nielsen. 2003. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr. Opin. Biotechnol. 14:255-261.
29. Moscoso, M., and J. P. Claverys. 2004. Release of DNA into the medium by competent Streptococcus pneumoniae: kinetics, mechanism and stability of the liberated DNA. Mol. Microbiol. 54:783-794.
30. Müller-Graf, C. D., A. M. Whatmore, S. J. King, K. Trzcinski, A. P. Pickerill, N. Doherty, J. Paul, D. Griffiths, D. Crook, and C. G. Dowson. 1999. Population biology of Streptococcus pneumoniae isolated from oropharyngeal carriage and invasive disease. Microbiology 145:3283-3293.
31. Murphy, T. F., S. Sethi, K. L. Klingman, A. B. Brueggemann, and G. V. Doern. 1999. Simultaneous respiratory tract colonization by multiple strains of nontypeable Haemophilus influenzae in chronic obstructive pulmonary disease: implications for antibiotic therapy. J. Infect. Dis. 180:404-409.
32. Oggioni, M. R., C. Trappetti, A. Kadioglu, M. Cassone, F. Iannelli, S. Ricci, P. W. Andrew, and G. Pozzi. 2006. Switch from planktonic to sessile life: a major event in pneumococcal pathogenesis. Mol. Microbiol. 61:1196-1210.
33. Pearson, W. R., and D. J. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85:2444-2448.
34. Peterson, S. N., C. K. Sung, R. Cline, B. V. Desai, E. C. Snesrud, P. Luo, J. Walling, H. Li, M. Mintz, G. Tsegaye, P. C. Burr, Y. Do, S. Ahn, J. Gilbert, R. D. Fleischmann, and D. A. Morrison. 2004. Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays. Mol. Microbiol. 51:1051-1070.
35. Prudhomme, M., L. Attaiech, G. Sanchez, B. Martin, and J. P. Claverys. 2006. Antibiotic stress induces genetic transformability in the human pathogen Streptococcus pneumoniae. Science 313:89-92.
36. Rozen, S., and H. Skaletsky. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132:365-386.
37. Shen, K., J. Gladitz, P. Antalis, B. Dice, B. Janto, R. Keefe, J. Hayes, A. Ahmed, R. Dopico, N. Ehrlich, J. Jocz, L. Krapp, S. Yu, L. Nistico, D. P. Greenberg, K. Barbadora, R. A. Preston, J. C. Post, G. D. Ehrlich, and F. Z. Hu. 2006. Characterization, distribution, and expression of novel genes among eight clinical isolates of Streptococcus pneumoniae. Infect. Immun. 74:321-330.
38. Smith, T., D. Lehmann, J. Montgomery, M. Gratten, I. D. Riley, and M. P. Alpers. 1993. Acquisition and invasiveness of different serotypes of Streptococcus pneumoniae in young children. Epidemiol. Infect. 111:27-39.
39. Smith-Vaughan, H. C., A. J. Leach, T. M. Shelby-James, K. Kemp, D. J. Kemp, and J. D. Mathews. 1996. Carriage of multiple ribotypes of non-encapsulated Haemophilus influenzae in aboriginal infants with otitis media. Epidemiol. Infect. 116:177-183.
40. Smith-Vaughan, H. C., K. S. Sriprakash, J. D. Mathews, and D. J. Kemp. 1995. Long PCR-ribotyping of nontypeable Haemophilus influenzae. J. Clin. Microbiol. 33:1192-1195.
41. Smith-Vaughan, H. C., K. S. Sriprakash, J. D. Mathews, and D. J. Kemp. 1997. Nonencapsulated Haemophilus influenzae in Aboriginal infants with otitis media: prolonged carriage of P2 porin variants and evidence for horizontal P2 gene transfer. Infect. Immun. 65:1468-1474.
42. Tatusov, R. L., M. Y. Galperin, D. A. Natale, and E. V. Koonin. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33-36.
43. 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 "pan-genome." Proc. Natl. Acad. Sci. USA 102:13950-13955.
44. Tettelin, H., K. E. Nelson, I. T. Paulsen, J. A. Eisen, T. D. Read, S. Peterson, J. Heidelberg, R. T. DeBoy, D. H. Haft, R. J. Dodson, A. S. Durkin, M. Gwinn, J. F. Kolonay, W. C. Nelson, J. D. Peterson, L. A. Umayam, O. White, S. L. Salzberg, M. R. Lewis, D. Radune, E. Holtzapple, H. Khouri, A. M. Wolf, T. R. Utterback, C. L. Hansen, L. A. McDonald, T. V. Feldblyum, S. Angiuoli, T. Dickinson, E. K. Hickey, I. E. Holt, B. J. Loftus, F. Yang, H. O. Smith, J. C. Venter, B. A. Dougherty, D. A. Morrison, S. K. Hollingshead, and C. M. Fraser. 2001. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293:498-506.