1887

Abstract

In a previous study, a molecular capsular type (MCT) prediction system for 51 serotypes was developed based on a combination of partial sequencing and serotype(s)/group(s)-specific PCR. In this study, another 169 isolates were added to the existing database of 427 isolates, including representatives of all 39 serotypes not previously studied. In addition to the authors’ own limited sequence data for all 90 serotypes, sequence data published by the capsular loci-sequencing group (http://www.sanger.ac.uk/Projects/S_pneumoniae/CPS/) at the Sanger Institute or available from GenBank were incorporated into the database. All serotypes, except 25A, were represented by at least two isolates. The number of sequence types identified was 138, of which 110 corresponded to single conventional serotypes (CSs); of these, 57 were represented by two or more isolates. Twenty-six sequence types were shared by between two and four CSs. To resolve these shared sequence types and increase the discriminatory power of our system, the genes encoding the capsular polysaccharide flippase () and polymerase () were annotated and 24 new serotype(s)/group(s)-specific PCRs targeting and two targeting were designed. Using both sequencing and / PCR, MCT correctly predicted the CSs of 516 (73 %) and the serogroup of an additional 155 (22 %) of the 708 isolates evaluated. For 5 % of isolates, MCT could not distinguish between members of five serotype pairs (37 isolates) containing members of different serogroups. Although further study of the relationship between MCT and CS is needed, this system now allows serotype or serogroup identification of 95 % of isolates.

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2005-04-01
2019-09-18
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References

  1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997;). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  2. Bateman, A., Birney, E., Cerruti, L. & 7 other authors ( 2002;). The Pfam protein families database. Nucleic Acids Res 30, 276–280.[CrossRef]
    [Google Scholar]
  3. Chen, Y., Yu, P., Luo, J. & Jiang, Y. ( 2003;). Secreted protein prediction system combining cj-sphmm, tmhmm, and psort. Mamm Genome 14, 859–865.[CrossRef]
    [Google Scholar]
  4. Coffey, T. J., Enright, M. C., Daniels, M., Morona, J. K., Morona, R., Hryniewicz, W., Paton, J. C. & Spratt, B. G. ( 1998;). Recombinational exchanges at the capsular polysaccharide biosynthetic locus lead to frequent serotype changes among natural isolates of Streptococcus pneumoniae. Mol Microbiol 27, 73–83.[CrossRef]
    [Google Scholar]
  5. Coffey, T. J., Daniels, M., Enright, M. C. & Spratt, B. G. ( 1999;). Serotype 14 variants of the Spanish penicillin-resistant serotype 9V clone of Streptococcus pneumoniae arose by large recombinational replacements of the cpsA–pbp1a region. Microbiology 145, 2023–2031.[CrossRef]
    [Google Scholar]
  6. Enright, M. C. & Spratt, B. G. ( 1998;). A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144, 3049–3060.[CrossRef]
    [Google Scholar]
  7. Enright, M. C. & Spratt, B. G. ( 1999;). Multilocus sequence typing. Trends Microbiol 7, 482–487.[CrossRef]
    [Google Scholar]
  8. Garcia, E., Llull, D., Munoz, R., Mollerach, M. & Lopez, R. ( 2000;). Current trends in capsular polysaccharide biosynthesis of Streptococcus pneumoniae. Res Microbiol 151, 429–435.[CrossRef]
    [Google Scholar]
  9. Gillespie, S. H. ( 1999;). The role of the molecular laboratory in the investigation of Streptococcus pneumoniae infections. Semin Respir Infect 14, 269–275.
    [Google Scholar]
  10. Hall, L. M. ( 1998;). Application of molecular typing to the epidemiology of Streptococcus pneumoniae. J Clin Pathol 51, 270–274.[CrossRef]
    [Google Scholar]
  11. Henrichsen, J. ( 1995;). Six newly recognized types of Streptococcus pneumoniae. J Clin Microbiol 33, 2759–2762.
    [Google Scholar]
  12. Hoskins, J., Alborn, W. E., Jr, Arnold, J. & 39 other authors ( 2001;). Genome of the bacterium Streptococcus pneumoniae strain R6. J Bacteriol 183, 5709–5717.[CrossRef]
    [Google Scholar]
  13. Jiang, S. M., Wang, L. & Reeves, P. R. ( 2001;). Molecular characterization of Streptococcus pneumoniae type 4, 6B, 8, and 18C capsular polysaccharide gene clusters. Infect Immun 69, 1244–1255.[CrossRef]
    [Google Scholar]
  14. Kong, F. & Gilbert, G. L. ( 2003;). Using cpsA–cpsB sequence polymorphisms and serotype-/group-specific PCR to predict 51 Streptococcus pneumoniae capsular serotypes. J Med Microbiol 52, 1047–1058.[CrossRef]
    [Google Scholar]
  15. Kumar, S., Tamura, K. & Nei, M. ( 1994;). mega: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput Appl Biosci 10, 189–191.
    [Google Scholar]
  16. Lawrence, E. R., Arias, C. A., Duke, B., Beste, D., Broughton, K., Efstratiou, A., George, R. C. & Hall, L. M. ( 2000;). Evaluation of serotype prediction by cpsA–cpsB gene polymorphism in Streptococcus pneumoniae. J Clin Microbiol 38, 1319–1323.
    [Google Scholar]
  17. Lawrence, E. R., Griffiths, D. B., Martin, S. A., George, R. C. & Hall, L. M. ( 2003;). Evaluation of semiautomated multiplex PCR assay for determination of Streptococcus pneumoniae serotypes and serogroups. J Clin Microbiol 41, 601–607.[CrossRef]
    [Google Scholar]
  18. Llull, D., Garcia, E. & Lopez, R. ( 2001;). Tts, a processive beta-glucosyltransferase of Streptococcus pneumoniae, directs the synthesis of the branched type 37 capsular polysaccharide in pneumococcus and other Gram-positive species. J Biol Chem 276, 21053–21061.[CrossRef]
    [Google Scholar]
  19. Magee, J. T., Fox, J. D. & Stubbs, S. L. ( 2001;). Cashing in your chips: speculation on the future of diagnostic laboratories in the era of DNA chips. J Med Microbiol 50, 111–115.
    [Google Scholar]
  20. McEllistrem, M. C., Noller, A. C., Visweswaran, S., Adams, J. M. & Harrison, L. H. ( 2004;). Serotype 14 variants of the France 9V−3 clone from Baltimore, Maryland, can be differentiated by the cpsB gene. J Clin Microbiol 42, 250–256.[CrossRef]
    [Google Scholar]
  21. Morona, J. K., Miller, D. C., Morona, R. & Paton, J. C. ( 2004;). The effect that mutations in the conserved capsular polysaccharide biosynthesis genes cpsA, cpsB, and cpsD have on virulence of Streptococcus pneumoniae. J Infect Dis 189, 1905–1913.[CrossRef]
    [Google Scholar]
  22. Rubin, L. G. & Rizvi, A. ( 2004;). PCR-based assays for detection of Streptococcus pneumoniae serotypes 3, 14, 19F and 23F in respiratory specimens. J Med Microbiol 53, 595–602.[CrossRef]
    [Google Scholar]
  23. Samuel, G. & Reeves, P. ( 2003;). Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly. Carbohydr Res 338, 2503–2519.[CrossRef]
    [Google Scholar]
  24. Tettelin, H., Nelson, K. E., Paulsen, I. T. & 36 other authors ( 2001;). Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293, 498–506.[CrossRef]
    [Google Scholar]
  25. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994;). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef]
    [Google Scholar]
  26. Trzcinski, K., Thompson, C. M. & Lipsitch, M. ( 2003;). Construction of otherwise isogenic serotype 6B, 7F, 14, and 19F capsular variants of Streptococcus pneumoniae strain TIGR4. Appl Environ Microbiol 69, 7364–7370.[CrossRef]
    [Google Scholar]
  27. van den Brule, A. J., Pol, R., Fransen-Daalmeijer, N., Schouls, L. M., Meijer, C. J. & Snijders, P. J. ( 2002;). GP5+/6+ PCR followed by reverse line blot analysis enables rapid and high-throughput identification of human papillomavirus genotypes. J Clin Microbiol 40, 779–787.[CrossRef]
    [Google Scholar]
  28. van Selm, S., van Cann, L. M., Kolkman, M. A., van der Zeijst, B. A. & van Putten, J. P. ( 2003;). Genetic basis for the structural difference between Streptococcus pneumoniae serotype 15B and 15C capsular polysaccharides. Infect Immun 71, 6192–6198.[CrossRef]
    [Google Scholar]
  29. Waite, R. D., Struthers, J. K. & Dowson, C. G. ( 2001;). Spontaneous sequence duplication within an open reading frame of the pneumococcal type 3 capsule locus causes high-frequency phase variation. Mol Microbiol 42, 1223–1232.
    [Google Scholar]
  30. Waite, R. D., Penfold, D. W., Struthers, J. K. & Dowson, C. G. ( 2003;). Spontaneous sequence duplications within capsule genes cap8E and tts control phase variation in Streptococcus pneumoniae serotypes 8 and 37. Microbiology 149, 497–504.[CrossRef]
    [Google Scholar]
  31. Wang, H., Kong, F., Jelfs, P., James, G. & Gilbert, G. L. ( 2004;). Simultaneous detection and identification of common cell culture contaminant and pathogenic mollicutes strains by reverse line blot hybridization. Appl Environ Microbiol 70, 1483–1486.[CrossRef]
    [Google Scholar]
  32. Weiller, G. F. ( 1998;). Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol 15, 326–335.[CrossRef]
    [Google Scholar]
  33. Zhang, L., Yuan, Z., Du, Z., Xiao, Y. & Ding, S. ( 1990;). Establishment of standard strains of serotypes (groups) of Streptococcus pneumoniae in China. Wei Sheng Wu Xue Bao 30, 389–392 (in Chinese).
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.45924-0
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Three phylogenetic trees ( Fig. S1, 20KB PDF; Fig. S3, 17KB PDF; Fig. S4, 17KB PDF), a schematic representation of related wzx genes ( Fig. S2, 26KB PDF) and five tables of data ( Table S1, 21KB PDF; Table S2, 40KB PDF; Table S3, 29KB PDF; Table S4, 15KB PDF; Table S5, 31KB PDF) are available to download.

PDF

Three phylogenetic trees ( Fig. S1, 20KB PDF; Fig. S3, 17KB PDF; Fig. S4, 17KB PDF), a schematic representation of related wzx genes ( Fig. S2, 26KB PDF) and five tables of data ( Table S1, 21KB PDF; Table S2, 40KB PDF; Table S3, 29KB PDF; Table S4, 15KB PDF; Table S5, 31KB PDF) are available to download.

PDF

Three phylogenetic trees ( Fig. S1, 20KB PDF; Fig. S3, 17KB PDF; Fig. S4, 17KB PDF), a schematic representation of related wzx genes ( Fig. S2, 26KB PDF) and five tables of data ( Table S1, 21KB PDF; Table S2, 40KB PDF; Table S3, 29KB PDF; Table S4, 15KB PDF; Table S5, 31KB PDF) are available to download.

PDF

Three phylogenetic trees ( Fig. S1, 20KB PDF; Fig. S3, 17KB PDF; Fig. S4, 17KB PDF), a schematic representation of related wzx genes ( Fig. S2, 26KB PDF) and five tables of data ( Table S1, 21KB PDF; Table S2, 40KB PDF; Table S3, 29KB PDF; Table S4, 15KB PDF; Table S5, 31KB PDF) are available to download.

PDF

Three phylogenetic trees ( Fig. S1, 20KB PDF; Fig. S3, 17KB PDF; Fig. S4, 17KB PDF), a schematic representation of related wzx genes ( Fig. S2, 26KB PDF) and five tables of data ( Table S1, 21KB PDF; Table S2, 40KB PDF; Table S3, 29KB PDF; Table S4, 15KB PDF; Table S5, 31KB PDF) are available to download.

PDF

Three phylogenetic trees ( Fig. S1, 20KB PDF; Fig. S3, 17KB PDF; Fig. S4, 17KB PDF), a schematic representation of related wzx genes ( Fig. S2, 26KB PDF) and five tables of data ( Table S1, 21KB PDF; Table S2, 40KB PDF; Table S3, 29KB PDF; Table S4, 15KB PDF; Table S5, 31KB PDF) are available to download.

PDF

Three phylogenetic trees ( Fig. S1, 20KB PDF; Fig. S3, 17KB PDF; Fig. S4, 17KB PDF), a schematic representation of related wzx genes ( Fig. S2, 26KB PDF) and five tables of data ( Table S1, 21KB PDF; Table S2, 40KB PDF; Table S3, 29KB PDF; Table S4, 15KB PDF; Table S5, 31KB PDF) are available to download.

PDF

Three phylogenetic trees ( Fig. S1, 20KB PDF; Fig. S3, 17KB PDF; Fig. S4, 17KB PDF), a schematic representation of related wzx genes ( Fig. S2, 26KB PDF) and five tables of data ( Table S1, 21KB PDF; Table S2, 40KB PDF; Table S3, 29KB PDF; Table S4, 15KB PDF; Table S5, 31KB PDF) are available to download.

PDF

Three phylogenetic trees ( Fig. S1, 20KB PDF; Fig. S3, 17KB PDF; Fig. S4, 17KB PDF), a schematic representation of related wzx genes ( Fig. S2, 26KB PDF) and five tables of data ( Table S1, 21KB PDF; Table S2, 40KB PDF; Table S3, 29KB PDF; Table S4, 15KB PDF; Table S5, 31KB PDF) are available to download.

PDF
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