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f Identification of species of the complex by sequence analysis of the gene

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Identification of species of the complex by sequence analysis of the gene, Page 1 of 1

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  • Bacteria of the complex (Bcc) are opportunistic human pathogens that can cause serious infections in the lungs of cystic fibrosis patients. The Bcc is a complex taxonomic group and comprises 17 closely related species of both biotechnological and clinical importance that have been discriminated by a polyphasic taxonomic approach. In this study we focused on the gene, which encodes a 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino] imidazole-4-carboxamide isomerase involved in histidine biosynthesis, as a new target gene to discriminate among the Bcc species. PCR primers were designed to amplify a DNA fragment of 442 bp from 78 strains representative of all the 17 Bcc species known at the time of writing. The nucleotide sequences of the amplicons were determined and aligned with the 54 Bcc sequences available in databases. Then a phylogenetic tree was constructed on the basis of this alignment and this revealed that this region allows discrimination of all Bcc species, suggesting that this gene fragment can be used for the identification of Bcc strains. In addition, an 11 nucleotide letter code for the rapid discrimination of Bcc species was identified.

  • The GenBank/EMBL/DDBJ accession numbers for the gene sequences of the 78 Bcc strains are given in Supplementary Table S1 available with the online journal.

  • A table of strain information and figures of sequence analyses are available as supplementary data with the online version of this paper.

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  • 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]
  • Baldwin, A., Mahenthiralingam, E., Thickett, K. M., Honeybourne, D., Maiden, M. C., Govan, J. R., Speert, D. P., Lipuma, J. J., Vandamme, P. & other authors ( 2005; ). Multilocus sequence typing scheme that provides both species and strain differentiation for the Burkholderia cepacia complex. J Clin Microbiol 43, 4665–4673.[CrossRef]
    [Google Scholar]
  • Berg, G., Eberl, L. & Hartmann, A. ( 2005; ). The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ Microbiol 7, 1673–1685.[CrossRef]
    [Google Scholar]
  • Bevivino, A., Dalmastri, C., Tabacchioni, S. & Chiarini, L. ( 2000; ). Efficacy of Burkholderia cepacia MCI 7 in disease suppression and growth promotion of maize. Biol Fertil Soils 31, 225–231.[CrossRef]
    [Google Scholar]
  • Dakin, C. J., Numa, A. H., Wang, H., Morton, J. R., Vertzyas, C. C. & Henry, R. L. ( 2002; ). Inflammation, infection, and pulmonary function in infants and young children with cystic fibrosis. Am J Respir Crit Care Med 165, 904–910.[CrossRef]
    [Google Scholar]
  • Fani, R., Brilli, M., Fondi, M. & Lio, P. ( 2007; ). The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case. BMC Evol Biol 7, S4.
     [Google Scholar]
  • Fries, M. R., Forney, L. J. & Tiedje, J. M. ( 1997; ). Phenol- and toluene-degrading microbial populations from an aquifer in which successful trichloroethene cometabolism occurred. Appl Environ Microbiol 63, 1523–1530.
     [Google Scholar]
  • Govan, J. R., Brown, P. H., Maddison, J., Doherty, C. J., Nelson, J. W., Dodd, M., Greening, A. P. & Webb, A. K. ( 1993; ). Evidence for transmission of Pseudomonas cepacia by social contact in cystic fibrosis. Lancet 342, 15–19.[CrossRef]
    [Google Scholar]
  • Hall, T. A. ( 1999; ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98.
     [Google Scholar]
  • Heungens, K. & Parke, J. L. ( 2000; ). Zoospore homing and infection events: effects of the biocontrol bacterium Burkholderia cepacia AMMDR1 on two oomycete pathogens of pea (Pisum sativum L.). Appl Environ Microbiol 66, 5192–5200.[CrossRef]
    [Google Scholar]
  • Holden, M. T. G., Drevinek, P., Seth-Smith, H., Bentley, S. D., Cerdeño-Tárraga, A. M., Crossman, L. C., Sebaihia, M., Thomson, N. R., Bason, N. & other authors ( 2009; ). The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol 191, 261–277.[CrossRef]
    [Google Scholar]
  • Holmes, A., Nolan, R., Taylor, R., Finley, R., Riley, M., Jiang, R. Z., Steinbach, S. & Goldstein, R. ( 1999; ). An epidemic of Burkholderia cepacia transmitted between patients with and without cystic fibrosis. J Infect Dis 179, 1197–1205.[CrossRef]
    [Google Scholar]
  • Mahenthiralingam, E., Bischof, J., Byrne, S. K., Radomski, C., Davies, J. E., Av-Gay, Y. & Vandamme, P. ( 2000; ). DNA-based diagnostic approaches for identification of Burkholderia cepacia complex, Burkholderia vietnamiensis, Burkholderia multivorans, Burkholderia stabilis, and Burkholderia cepacia genomovars I and III. J Clin Microbiol 38, 3165–3173.
     [Google Scholar]
  • Mahenthiralingam, E., Urban, T. A. & Goldberg, J. B. ( 2005; ). The multifarious, multireplicon Burkholderia cepacia complex. Nat Rev Microbiol 3, 144–156.[CrossRef]
    [Google Scholar]
  • Papaleo, M. C., Russo, E., Fondi, M., Emiliani, G., Frandi, A., Brilli, M., Pastorelli, R. & Fani, R. ( 2009; ). Structural, evolutionary and genetic analysis of the histidine biosynthetic “core” in the genus Burkholderia. Gene 448, 16–28.[CrossRef]
    [Google Scholar]
  • Saiman, L. & Siegel, J. ( 2004; ). Infection control in cystic fibrosis. Clin Microbiol Rev 17, 57–71.[CrossRef]
    [Google Scholar]
  • Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
     [Google Scholar]
  • Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 1989; ). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY. : Cold Spring Harbor Laboratory.
     [Google Scholar]
  • Sanger, F., Nicklen, S. & Coulson, A. R. ( 1977; ). DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74, 5463–5467.[CrossRef]
    [Google Scholar]
  • Smith, D. L., Gumery, L. B., Smith, E. G., Stableforth, D. E., Kaufmann, M. E. & Pitt, T. L. ( 1993; ). Epidemic of Pseudomonas cepacia in an adult cystic fibrosis unit: evidence of person-to-person transmission. J Clin Microbiol 31, 3017–3022.
     [Google Scholar]
  • Tamura, K., Dudley, J., Nei, M. & Kumar, S. ( 2007; ). mega4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0. Mol Biol Evol 24, 1596–1599.[CrossRef]
    [Google Scholar]
  • 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]
  • Tsui, L. C., Buchwald, M., Barker, D., Braman, J. C., Knowlton, R., Schumm, J. W., Eiberg, H., Mohr, J., Kennedy, D. & other authors ( 1985; ). Cystic fibrosis locus defined by a genetically linked polymorphic DNA marker. Science 230, 1054–1057.[CrossRef]
    [Google Scholar]
  • Vandamme, P., Holmes, B., Vancanneyt, M., Coenye, T., Hoste, B., Coopman, R., Revets, H., Lauwers, S., Gillis, M. & other authors ( 1997; ). Occurrence of multiple genomovars of Burkholderia cepacia in cystic fibrosis patients and proposal of Burkholderia multivorans sp. nov. Int J Syst Bacteriol 47, 1188–1200.[CrossRef]
    [Google Scholar]
  • Vandamme, P., Henry, D., Coenye, T., Nzula, S., Vancanneyt, M., LiPuma, J. J., Speert, D. P., Govan, J. R. W. & Mahenthiralingam, E. ( 2002; ). Burkholderia anthina sp. nov. and Burkholderia pyrrocinia, two additional Burkholderia cepacia complex bacteria, may confound results of new molecular diagnostic tools. FEMS Immunol Med Microbiol 33, 143–149.[CrossRef]
    [Google Scholar]
  • Vandamme, P., Holmes, B., Coenye, T., Goris, J., Mahenthiralingam, E., LiPuma, J. J. & Govan, J. R. W. ( 2003; ). Burkholderia cenocepacia sp. nov. – a new twist to an old story. Res Microbiol 154, 91–96.[CrossRef]
    [Google Scholar]
  • Vanlaere, E., Lipuma, J. J., Baldwin, A., Henry, D., De Brandt, E., Mahenthiralingam, E., Speert, D., Dowson, C. & Vandamme, P. ( 2008; ). Burkholderia latens sp. nov., Burkholderia diffusa sp. nov., Burkholderia arboris sp. nov., Burkholderia seminalis sp. nov. and Burkholderia metallica sp. nov., novel species within the Burkholderia cepacia complex. Int J Syst Evol Microbiol 58, 1580–1590.[CrossRef]
    [Google Scholar]
  • Vanlaere, E., Baldwin, A., Gevers, D., Henry, D., De Brandt, E., LiPuma, J. J., Mahenthiralingam, E., Speert, D. P., Dowson, C. & Vandamme, P. ( 2009; ). Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. Int J Syst Evol Microbiol 59, 102–111.[CrossRef]
    [Google Scholar]
  • Vermis, K., Coenye, T., Mahenthiralingam, E., Nelis, H. J. & Vandamme, P. ( 2002; ). Evaluation of species-specific recA-based PCR tests for genomovar level identification within the Burkholderia cepacia complex. J Med Microbiol 51, 937–940.
     [Google Scholar]
  • Whiteford, M. L., Wilkinson, J. D., McColl, J. H., Conlon, F. M., Michie, J. R., Evans, T. J. & Paton, J. Y. ( 1995; ). Outcome of Burkholderia (Pseudomonas) cepacia colonisation in children with cystic fibrosis following a hospital outbreak. Thorax 50, 1194–1198.[CrossRef]
    [Google Scholar]
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2010-10-01
2019-05-25
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