1887

Abstract

The highly variable nature of the internal transcribed spacer region (ITS) has been claimed to represent an ideal target for designing species-specific probes/primers capable of differentiating between closely related species. However, several species contain multiple ITS copies of variable lengths, and these include , and . This study shows these length variations result from inter-genomic insertion/deletion events (indels) involving horizontal transfer of ITS fragments of other species and possibly unrelated bacteria, as shown previously by us. In some instances, indel incorporation results in the loss of probe target sites in the recipient cell ITS. In other cases, some indel sequences contain target sites for probes designed from a single ITS sequence to target other species. Hence, these can generate false positives. The largest of the indels that remove probe sites is 683 bp (labelled bay/i1-0), and it derives from the horizontal transfer of a complete ITS between BCRC15423 and strain ADP1. As a consequence, ITS sequencing or fingerprinting cannot be used to distinguish between the 683 bp ITS in these two strains.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.083600-0
2015-02-01
2019-10-19
Loading full text...

Full text loading...

/deliver/fulltext/micro/161/2/322.html?itemId=/content/journal/micro/10.1099/mic.0.083600-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Boguski M. S., Gish W., Wootton J. C.. ( 1994;). Issues in searching molecular sequence databases. . Nat Genet 6:, 119–129. [CrossRef][PubMed]
    [Google Scholar]
  2. Barbe V., Vallenet D., Fonknechten N., Kreimeyer A., Oztas S., Labarre L., Cruveiller S., Robert C., Duprat S.. & other authors ( 2004;). Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. . Nucleic Acids Res 32:, 5766–5779. [CrossRef][PubMed]
    [Google Scholar]
  3. Beacham A. M., Seviour R. J., Lindrea K. C., Livingston I.. ( 1990;). Genospecies diversity of Acinetobacter isolates obtained from a biological nutrient removal pilot plant of modified UCT configuration. . Water Res 24:, 23–29. [CrossRef]
    [Google Scholar]
  4. Bouvet P. J. M., Grimont P. A. D.. ( 1986;). Taxonomy of the genus Acinetobacter with the recognition Acinetobacter baumannii sp. nov., Acinetobacter haemolyticus sp. nov., Acinetobacter johnsonii sp. nov., Acinetobacter junii sp. nov. and emended descriptions of Acinetobacter calcoaceticus and Acinetobacter lwoffii. . Int J Syst Bacteriol 36:, 228–240. [CrossRef]
    [Google Scholar]
  5. Carr E. L., Gürtler V., Seviour R. J.. ( 2004;). Variation of 16S-23S rRNA intergenic spacer regions (ISRs) in Acinetobacter baylyi (strain B2) isolated from activated sludge. . Syst Appl Microbiol 27:, 478–491. [CrossRef][PubMed]
    [Google Scholar]
  6. Chang H. C., Wei Y. F., Dijkshoorn L., Vaneechoutte M., Tang C. T., Chang T. C.. ( 2005;). Species-level identification of isolates of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex by sequence analysis of the 16S-23S rRNA gene spacer region. . J Clin Microbiol 43:, 1632–1639. [CrossRef][PubMed]
    [Google Scholar]
  7. Chen T. L., Siu L. K., Wu R. C.-C., Shaio M. F., Huang L. Y., Fung C. P., Lee C. M., Cho W. L.. ( 2007;). Comparison of one-tube multiplex PCR, automated ribotyping and intergenic spacer (ITS) sequencing for rapid identification of Acinetobacter baumannii. . Clin Microbiol Infect 13:, 801–806. [CrossRef][PubMed]
    [Google Scholar]
  8. Chen T. L., Siu L. K., Lee Y. T., Chen C. P., Huang L. Y., Wu R. C.-C., Cho W.-L., Fung C.-P.. ( 2008;). Acinetobacter baylyi as a pathogen for opportunistic infection. . J Clin Microbiol 46:, 2938–2944. [CrossRef][PubMed]
    [Google Scholar]
  9. Dijkshoorn L., Nemec A.. ( 2008;). The diversity of the genus Acinetobacter. . In Acinetobacter Molecular Biology, pp. 1–34. Edited by Gerischer U... Norfolk:: Caister Academic Press;.
    [Google Scholar]
  10. Gürtler V.. ( 1999;). The role of recombination and mutation in 16S-23S rDNA spacer rearrangements. . Gene 238:, 241–252. [CrossRef][PubMed]
    [Google Scholar]
  11. Gürtler V., Subrahmanyam G., Shaka M., Maiti B., Karunasagar J.. ( 2014;). Bacterial typing and identification by genomic analysis of 16S–23S rRNA intergenic spacer (ITS) sequences. . In Methods in Microbiology, vol. 41, pp. 253–274. Edited by Goodfellow M., Sutcliffe I... London:: Elsevier;.
    [Google Scholar]
  12. Ko W.-C., Lee N.-Y., Su S. C., Dijkshoorn L., Vaneechoutte M., Wang L.-R., Yan J.-J., Chang T. C.. ( 2008;). Oligonucleotide array-based identification of species in the Acinetobacter calcoaceticus-A. baumannii complex in isolates from blood cultures and antimicrobial susceptibility testing of the isolates. . J Clin Microbiol 46:, 2052–2059. [CrossRef][PubMed]
    [Google Scholar]
  13. Kuo S.-C., Fung C.-P., Lee Y.-T., Chen C.-P., Chen T.-L.. ( 2010;). Bacteremia due to Acinetobacter genomic species 10. . J Clin Microbiol 48:, 586–590. [CrossRef][PubMed]
    [Google Scholar]
  14. Liao D.. ( 2000;). Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea. . J Mol Evol 51:, 305–317.[PubMed]
    [Google Scholar]
  15. Lin Y. C., Sheng W. H., Chang S. C., Wang J. T., Chen Y. C., Wu R. J., Hsia K. C., Li S. Y.. ( 2008;). Application of a microsphere-based array for rapid identification of Acinetobacter spp. with distinct antimicrobial susceptibilities. . J Clin Microbiol 46:, 612–617. [CrossRef][PubMed]
    [Google Scholar]
  16. Maslunka C., Carr E., Gürtler V., Kämpfer P., Seviour R.. ( 2006;). Estimation of ribosomal RNA operon (rrn) copy number in Acinetobacter isolates and potential of patterns of rrn operon-containing fragments for typing strains of members of this genus. . Syst Appl Microbiol 29:, 216–228. [CrossRef][PubMed]
    [Google Scholar]
  17. Maslunka C., Gürtler V., Carr E. L., Seviour R. J.. ( 2008;). Unique organization of the 16S-23S intergenic spacer regions of strains of Acinetobacter baylyi provides a means for its identification from other Acinetobacter species. . J Microbiol Methods 73:, 227–236. [CrossRef][PubMed]
    [Google Scholar]
  18. Maslunka C., Gifford B., Tucci J., Gürtler V., Seviour R. J.. ( 2014;). Insertions or deletions (indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members. . PLoS ONE 9:, e105390. [CrossRef][PubMed]
    [Google Scholar]
  19. McConnell M. J., Actis L., Pachón J.. ( 2013;). Acinetobacter baumannii: human infections, factors contributing to pathogenesis and animal models. . FEMS Microbiol Rev 37:, 130–155.[PubMed]
    [Google Scholar]
  20. Nemec A., Krizova L., Maixnerova M., van der Reijden T. J. K., Deschaght P., Passet V., Vaneechoutte M., Brisse S., Dijkshoorn L.. ( 2011;). Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp. nov. (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp. nov. (formerly Acinetobacter genomic species 13TU). . Res Microbiol 162:, 393–404. [CrossRef][PubMed]
    [Google Scholar]
  21. Pérez Luz S., Rodríguez-Valera F., Lan R., Reeves P. R.. ( 1998;). Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies. . J Bacteriol 180:, 2144–2151.[PubMed]
    [Google Scholar]
  22. Stewart F. J., Cavanaugh C. M.. ( 2007;). Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in bacteria. . J Mol Evol 65:, 44–67. [CrossRef][PubMed]
    [Google Scholar]
  23. Su S. C., Vaneechoutte M., Dijkshoorn L., Wei Y. F., Chen Y. L., Chang T. C.. ( 2009;). Identification of non-fermenting Gram-negative bacteria of clinical importance by an oligonucleotide array. . J Med Microbiol 58:, 596–605. [CrossRef][PubMed]
    [Google Scholar]
  24. Vaneechoutte M., Young D. M., Ornston L. N., De Baare T., Nemec A., van der Reijden T., Carr E., Tjernberg I., Dijkshoorn L.. ( 2006;). Naturally transformable Acinetobacter sp. strain ADP1 belongs to the newly described species Acinetobacter baylyi. . Appl Environ Microbiol 72:, 932–936. [CrossRef][PubMed]
    [Google Scholar]
  25. Zarrilli R., Giannouli M., Di Popolo A., Tomasone F., Chu Y.-W.. ( 2009;). Identification of Acinetobacter genomic species 13TU by sequence analysis of the 16S-23S rRNA gene spacer region. . J Clin Microbiol 47:, 1281. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.083600-0
Loading
/content/journal/micro/10.1099/mic.0.083600-0
Loading

Data & Media loading...

Supplements

Supplementary Data



PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error