Use of PCR-restriction Enzyme Pattern Analysis and Sequencing Database for Hsp65 Gene-based Identification of Nocardia Species

Overview

Journal J Clin Microbiol

Specialty Microbiology

Date 2006 Feb 4

PMID 16455910

Citations 53

Authors

Veronica Rodriguez-Nava

Andree Couble

Gregory Devulder

Jean-Pierre Flandrois

Patrick Boiron

Frederic Laurent

Affiliations

Soon will be listed here.

Abstract

Nocardia identification required laborious and time-consuming phenotypic and chemotaxonomic methods until molecular methods were developed in the mid-1990s. Here we reassessed the capacity of PCR-restriction enzyme pattern analysis (PRA) of the hsp65 gene to differentiate Nocardia species, including 36 new species. Our results confirm that hsp65 PRA must no longer be used for Nocardia species identification, as many species have the same restriction pattern. We then compared sequencing-based strategies using an hsp65 database and a 16S rRNA database and found that the hsp65 region contained sufficient polymorphisms for comprehensive Nocardia species identification.

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References

Conville P, Fischer S, Cartwright C, Witebsky F . Identification of nocardia species by restriction endonuclease analysis of an amplified portion of the 16S rRNA gene. J Clin Microbiol. 2000; 38(1):158-64. PMC: 86045. DOI: 10.1128/JCM.38.1.158-164.2000. View

Saitou N, Nei M . The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987; 4(4):406-25. DOI: 10.1093/oxfordjournals.molbev.a040454. View

Kim B, Lee K, Park B, Bai G, Kim S, Kook Y . Differentiation of mycobacterial species by PCR-restriction analysis of DNA (342 base pairs) of the RNA polymerase gene (rpoB). J Clin Microbiol. 2001; 39(6):2102-9. PMC: 88096. DOI: 10.1128/JCM.39.6.2102-2109.2001. View

Maldonado L, Hookey J, Ward A, Goodfellow M . The Nocardia salmonicida clade, including descriptions of Nocardia cummidelens sp. nov., Nocardia fluminea sp. nov. and Nocardia soli sp. nov. Antonie Van Leeuwenhoek. 2001; 78(3-4):367-77. DOI: 10.1023/a:1010230632040. View

Brunello F, Ligozzi M, Cristelli E, Bonora S, Tortoli E, Fontana R . Identification of 54 mycobacterial species by PCR-restriction fragment length polymorphism analysis of the hsp65 gene. J Clin Microbiol. 2001; 39(8):2799-806. PMC: 88242. DOI: 10.1128/JCM.39.8.2799-2806.2001. View

Turenne C, Tschetter L, Wolfe J, Kabani A . Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species. J Clin Microbiol. 2001; 39(10):3637-48. PMC: 88401. DOI: 10.1128/JCM.39.10.3638-3648.2001. View

Cloud J, Neal H, Rosenberry R, Turenne C, JAMA M, Hillyard D . Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries. J Clin Microbiol. 2002; 40(2):400-6. PMC: 153382. DOI: 10.1128/JCM.40.2.400-406.2002. View

Wallace Jr R, Steele L, Sumter G, Smith J . Antimicrobial susceptibility patterns of Nocardia asteroides. Antimicrob Agents Chemother. 1988; 32(12):1776-9. PMC: 176016. DOI: 10.1128/AAC.32.12.1776. View

Telenti A, Marchesi F, Balz M, Bally F, Bottger E, Bodmer T . Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol. 1993; 31(2):175-8. PMC: 262730. DOI: 10.1128/jcm.31.2.175-178.1993. View

10.

Goebel B, Stackebrandt E . Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl Environ Microbiol. 1994; 60(5):1614-21. PMC: 201525. DOI: 10.1128/aem.60.5.1614-1621.1994. View

11.

McNeil M, Brown J . The medically important aerobic actinomycetes: epidemiology and microbiology. Clin Microbiol Rev. 1994; 7(3):357-417. PMC: 358331. DOI: 10.1128/CMR.7.3.357. View

12.

Thompson J, Higgins D, Gibson T . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

13.

Zolg J . The superoxide dismutase gene, a target for detection and identification of mycobacteria by PCR. J Clin Microbiol. 1994; 32(11):2801-12. PMC: 264162. DOI: 10.1128/jcm.32.11.2801-2812.1994. View

14.

Wallace Jr R, Brown B, Blacklock Z, Ulrich R, Jost K, Brown J . New Nocardia taxon among isolates of Nocardia brasiliensis associated with invasive disease. J Clin Microbiol. 1995; 33(6):1528-33. PMC: 228209. DOI: 10.1128/jcm.33.6.1528-1533.1995. View

15.

Steingrube V, Brown B, Gibson J, Wilson R, Brown J, Blacklock Z . DNA amplification and restriction endonuclease analysis for differentiation of 12 species and taxa of Nocardia, including recognition of four new taxa within the Nocardia asteroides complex. J Clin Microbiol. 1995; 33(12):3096-101. PMC: 228651. DOI: 10.1128/jcm.33.12.3096-3101.1995. View

16.

Galtier N, Gouy M, Gautier C . SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci. 1996; 12(6):543-8. DOI: 10.1093/bioinformatics/12.6.543. View

17.

Steingrube V, Wilson R, Brown B, Jost Jr K, Blacklock Z, Gibson J . Rapid identification of clinically significant species and taxa of aerobic actinomycetes, including Actinomadura, Gordona, Nocardia, Rhodococcus, Streptomyces, and Tsukamurella isolates, by DNA amplification and restriction endonuclease analysis. J Clin Microbiol. 1997; 35(4):817-22. PMC: 229682. DOI: 10.1128/jcm.35.4.817-822.1997. View

18.

McNabb A, Shuttleworth R, Behme R, Colby W . Fatty acid characterization of rapidly growing pathogenic aerobic actinomycetes as a means of identification. J Clin Microbiol. 1997; 35(6):1361-8. PMC: 229749. DOI: 10.1128/jcm.35.6.1361-1368.1997. View

19.

Roth A, Fischer M, Hamid M, Michalke S, Ludwig W, Mauch H . Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J Clin Microbiol. 1998; 36(1):139-47. PMC: 124824. DOI: 10.1128/JCM.36.1.139-147.1998. View

20.

Laurent F, Provost F, Boiron P . Rapid identification of clinically relevant Nocardia species to genus level by 16S rRNA gene PCR. J Clin Microbiol. 1998; 37(1):99-102. PMC: 84177. DOI: 10.1128/JCM.37.1.99-102.1999. View