1887

Abstract

The aim of the present study was to re-examine the taxonomic position and structure of taxon K (also known as group K) within the complex (Bcc). For this purpose, a representative set of strains was examined by a traditional polyphasic taxonomic approach, by multilocus sequence typing (MLST) analysis and by analysis of available whole-genome sequences. Analysis of the gene sequence revealed three different lineages, designated -I, -II and -III. DNA–DNA hybridization experiments demonstrated that -I and -II isolates each represented a single novel species. However, DNA–DNA hybridization values of -II strains towards -III strains and among -III strains were at the threshold level for species delineation. By MLST, -I isolates were clearly distinguished from the others and represented a distinct lineage referred to as MLST-I, whereas -II and -III isolates formed a second MLST lineage referred to as MLST-II. A divergence value of 3.5 % was obtained when MLST-I was compared with MLST-II. The internal level of concatenated sequence divergence within MLST-I and MLST-II was 1.4 and 2.7 %, respectively; by comparison with the level of concatenated sequence divergence in established Bcc species, these data demonstrate that the MLST-I and MLST-II lineages represent two distinct species within the Bcc. The latter conclusion was supported by comparison of the whole-genome average nucleotide identity (ANI) level of MLST-I and MLST-II strains with strains of established Bcc species and by a whole-genome-based phylogenetic analysis. We formally propose to classify taxon K bacteria from the MLST-I and MLST-II lineages as sp. nov. (with strain J2956 =LMG 23361 =CCUG 55526 as the type strain) and sp. nov. (with strain 383 =ATCC 17760 =LMG 22485 =CCUG 55525 as the type strain), respectively. The MLST approach was confirmed as a valuable instrument in polyphasic taxonomic studies; more importantly, the cumulative data for about 1000 Bcc isolates analysed demonstrate that the 3 % concatenated sequence divergence level correlates with the 70 % DNA–DNA hybridization or 95 % whole-genome ANI threshold levels for species delineation.

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2009-01-01
2019-08-21
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References

  1. Baldwin, A., Mahenthiralingam, E., Thickett, K. M., Honeybourne, D., Maiden, M. C., Govan, J. R., Speert, D. P., LiPuma, J. J., Vandamme, P. & Dowson, C. G. ( 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]
  2. Berriatua, E., Ziluaga, I., Miguel-Virto, C., Uribarren, P., Juste, R., Laevens, S., Vandamme, P. & Govan, J. R. ( 2001; ). Outbreak of subclinical mastitis in a flock of dairy sheep associated with Burkholderia cepacia complex infection. J Clin Microbiol 39, 990–994.[CrossRef]
    [Google Scholar]
  3. Campana, S., Taccetti, G., Ravenni, N., Favari, F., Cariani, L., Sciacca, A., Savoia, D., Collura, A., Fiscarelli, E. & other authors ( 2005; ). Transmission of Burkholderia cepacia complex: evidence for new epidemic clones infecting cystic fibrosis patients in Italy. J Clin Microbiol 43, 5136–5142.[CrossRef]
    [Google Scholar]
  4. Castresana, J. ( 2000; ). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17, 540–552.[CrossRef]
    [Google Scholar]
  5. Coenye, T. & Vandamme, P. ( 2003; ). Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ Microbiol 5, 719–729.[CrossRef]
    [Google Scholar]
  6. Coenye, T., Vandamme, P., Govan, J. R. & LiPuma, J. J. ( 2001; ). Taxonomy and identification of the Burkholderia cepacia complex. J Clin Microbiol 39, 3427–3436.[CrossRef]
    [Google Scholar]
  7. Cunha, M. V., Pinto-de-Oliveira, A., Meirinhos-Soares, L., Salgado, M. J., Melo-Cristino, J., Correia, S., Barreto, C. & Sá-Correia, I. ( 2007; ). Exceptionally high representation of Burkholderia cepacia among B. cepacia complex isolates recovered from the major Portuguese cystic fibrosis center. J Clin Microbiol 45, 1628–1633.[CrossRef]
    [Google Scholar]
  8. Dalmastri, C., Pirone, L., Tabacchioni, S., Bevivino, A. & Chiarini, L. ( 2005; ). Efficacy of species-specific recA PCR tests in the identification of Burkholderia cepacia complex environmental isolates. FEMS Microbiol Lett 246, 39–45.[CrossRef]
    [Google Scholar]
  9. Dalmastri, C., Baldwin, A., Tabacchioni, S., Bevivino, A., Mahenthiralingam, E., Chiarini, L. & Dowson, C. ( 2007; ). Investigating Burkholderia cepacia complex populations recovered from Italian maize rhizosphere by multilocus sequence typing. Environ Microbiol 9, 1632–1639.[CrossRef]
    [Google Scholar]
  10. Edgar, R. C. ( 2004; ). muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792–1797.[CrossRef]
    [Google Scholar]
  11. Ezaki, T., Hashimoto, Y. & Yabuuchi, E. ( 1989; ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.[CrossRef]
    [Google Scholar]
  12. Goris, J., Suzuki, K., De Vos, P., Nakase, T. & Kersters, K. ( 1998; ). Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. Can J Microbiol 44, 1148–1153.[CrossRef]
    [Google Scholar]
  13. Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P. & Tiedje, J. M. ( 2007; ). DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57, 81–91.[CrossRef]
    [Google Scholar]
  14. Guindon, S. & Gascuel, O. ( 2003; ). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696–704.[CrossRef]
    [Google Scholar]
  15. Haubold, B. & Hudson, R. R. ( 2000; ). lian 3.0: detecting linkage disequilibrium in multilocus data. Linkage analysis. Bioinformatics 16, 847–848.[CrossRef]
    [Google Scholar]
  16. Henry, D. A., Campbell, M. E., LiPuma, J. J. & Speert, D. P. ( 1997; ). Identification of Burkholderia cepacia isolates from patients with cystic fibrosis and use of a simple new selective medium. J Clin Microbiol 35, 614–619.
    [Google Scholar]
  17. Henry, D. A., Mahenthiralingam, E., Vandamme, P., Coenye, T. & Speert, D. P. ( 2001; ). Phenotypic methods for determining genomovar status of the Burkholderia cepacia complex. J Clin Microbiol 39, 1073–1078.[CrossRef]
    [Google Scholar]
  18. Jolley, K. A., Chan, M.-S. & Maiden, M. C. ( 2004; ). mlstdbNet – distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 5, 86 [CrossRef]
    [Google Scholar]
  19. Jones, D. T., Taylor, W. R. & Thornton, J. M. ( 1992; ). The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8, 275–282.
    [Google Scholar]
  20. Jukes, T. H. & Cantor, C. R. ( 1969; ). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  21. Kenna, D. T., Yesilkaya, H., Forbes, K. J., Barcus, V. A., Vandamme, P. & Govan, J. R. ( 2006; ). Distribution and genomic location of active insertion sequences in the Burkholderia cepacia complex. J Med Microbiol 55, 1–10.[CrossRef]
    [Google Scholar]
  22. Konstantinidis, K. T. & Tiedje, J. M. ( 2005a; ). Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102, 2567–2572.[CrossRef]
    [Google Scholar]
  23. Konstantinidis, K. T. & Tiedje, J. M. ( 2005b; ). Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187, 6258–6264.[CrossRef]
    [Google Scholar]
  24. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  25. Lessie, T. G., Hendrickson, W., Manning, B. D. & Devereux, R. ( 1996; ). Genomic complexity and plasticity of Burkholderia cepacia. FEMS Microbiol Lett 144, 117–128.[CrossRef]
    [Google Scholar]
  26. Li, L., Stoeckert, C. J., Jr & Roos, D. S. ( 2003; ). OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13, 2178–2189.[CrossRef]
    [Google Scholar]
  27. Mahenthiralingam, E. & Drevinek, P. ( 2007; ). Comparative genomics of Burkholderia species. In Burkholderia: Molecular Microbiology and Genomics, pp. 53–79. Edited by T. Coenye & P. Vandamme. Wymondham, UK: Horizon Bioscience.
  28. Mahenthiralingam, E., Coenye, T., Chung, J. W., Speert, D. P., Govan, J. R., Taylor, P. & Vandamme, P. ( 2000a; ). Diagnostically and experimentally useful panel of strains from the Burkholderia cepacia complex. J Clin Microbiol 38, 910–913.
    [Google Scholar]
  29. Mahenthiralingam, E., Bischof, J., Byrne, S. K., Radomski, C., Davies, J. E., Av-Gay, Y. & Vandamme, P. ( 2000b; ). 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]
  30. Mahenthiralingam, E., Baldwin, A., Drevinek, P., Vanlaere, E., Vandamme, P., LiPuma, J. J. & Dowson, C. G. ( 2006; ). Multilocus sequence typing breathes life into a microbial metagenome. PLoS One 1, e17 [CrossRef]
    [Google Scholar]
  31. Mahenthiralingam, E., Baldwin, A. & Dowson, C. G. ( 2008; ). Burkholderia cepacia complex bacteria: opportunistic pathogens with important natural biology. J Appl Microbiol 104, 1539–1551.[CrossRef]
    [Google Scholar]
  32. Maynard Smith, J., Smith, N. H., O'Rourke, M. & Spratt, B. G. ( 1993; ). How clonal are bacteria? Proc Natl Acad Sci U S A 90, 4384–4388.[CrossRef]
    [Google Scholar]
  33. Mesbah, M. & Whitman, W. B. ( 1989; ). Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J Chromatogr 479, 297–306.[CrossRef]
    [Google Scholar]
  34. Naser, S. M., Dawyndt, P., Hoste, B., Gevers, D., Vandemeulebroecke, K., Cleenwerck, I., Vancanneyt, M. & Swings, J. ( 2007; ). Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 57, 2777–2789.[CrossRef]
    [Google Scholar]
  35. Parke, J. L. & Gurian-Sherman, D. ( 2001; ). Diversity of the Burkholderia cepacia complex and implications for risk assessment of biological control strains. Annu Rev Phytopathol 39, 225–258.[CrossRef]
    [Google Scholar]
  36. Payne, G. W., Vandamme, P., Morgan, S. H., LiPuma, J. J., Coenye, T., Weightman, A. J., Jones, T. H. & Mahenthiralingam, E. ( 2005; ). Development of a recA gene-based identification approach for the entire Burkholderia genus. Appl Environ Microbiol 71, 3917–3927.[CrossRef]
    [Google Scholar]
  37. Pitcher, D. G., Saunders, N. A. & Owen, R. J. ( 1989; ). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8, 151–156.[CrossRef]
    [Google Scholar]
  38. Rozas, J., Sanchez-Delbarrio, J. C., Messeguer, X. & Rozas, R. ( 2003; ). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496–2497.[CrossRef]
    [Google Scholar]
  39. Souza, A. V., Moreira, C. R., Pasternak, J., Hirata, M. L., Saltini, D. A., Caetano, V. C., Ciosak, S., Azevedo, F. M., Severino, P. & other authors ( 2004; ). Characterizing uncommon Burkholderia cepacia complex isolates from an outbreak in a haemodialysis unit. J Med Microbiol 53, 999–1005.[CrossRef]
    [Google Scholar]
  40. Stanier, R. Y., Palleroni, N. J. & Doudoroff, M. ( 1966; ). The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43, 159–271.[CrossRef]
    [Google Scholar]
  41. Storms, V., Van Den Vreken, N., Coenye, T., Mahenthiralingam, E., LiPuma, J. J., Gillis, M. & Vandamme, P. ( 2004; ). Polyphasic characterisation of Burkholderia cepacia-like isolates leading to the emended description of Burkholderia pyrrocinia. Syst Appl Microbiol 27, 517–526.[CrossRef]
    [Google Scholar]
  42. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  43. Vandamme, P., Holmes, B., Coenye, T., Goris, J., Mahenthiralingam, E., LiPuma, J. J. & Govan, J. R. ( 2003; ). Burkholderia cenocepacia sp. nov. – a new twist to an old story. Res Microbiol 154, 91–96.[CrossRef]
    [Google Scholar]
  44. Vanlaere, E., Coenye, T., Samyn, E., Van Den Plas, C., Govan, J., De Baets, F., De Boeck, K., Knoop, C. & Vandamme, P. ( 2005; ). A novel strategy for the isolation and identification of environmental Burkholderia cepacia complex bacteria. FEMS Microbiol Lett 249, 303–307.[CrossRef]
    [Google Scholar]
  45. 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]
  46. Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. & other authors ( 2004; ). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74.[CrossRef]
    [Google Scholar]
  47. 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]
  48. Waine, D. J., Henry, D. A., Baldwin, A., Speert, D. P., Honeybourne, D., Mahenthiralingam, E. & Dowson, C. G. ( 2007; ). Reliability of multilocus sequence typing of the Burkholderia cepacia complex in cystic fibrosis. J Cyst Fibros 6, 215–219.[CrossRef]
    [Google Scholar]
  49. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors ( 1987; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef]
    [Google Scholar]
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vol. , part 1, pp. 102 - 111

Average nucleotide identity (ANI) among the strains studied

DNA base ratios and DNA–DNA binding values (%) of all strains examined

Isolates examined by MLST, showing their source, ST and allelic profile

Single-copy core genes that were concatenated and used to construct a robust maximum-likelihood species tree

Biochemical characteristics useful for the differentiation of established Bcc species and novel taxon K clusters

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