Amplified ribosomal DNA restriction analysis in the differentiation of related species of mycobacteria

Journal of Microbiological Methods

Volumn 55, Issue 1, 2003, Pages 83-90

  Kurabachew, Mekonnen ^a,b   Enger, Øivind ^c   Sandaa, Ruth Anne ^a   Lemma, Eshetu ^d   Bjorvatn, Bjarne ^a  

^a UNIVERSITY OF BERGEN   (Norway)

^b ADDIS ABABA UNIVERSITY   (Ethiopia)

^c Forninova AS   (Norway)

^d ETHIOPIAN PUBLIC HEALTH INSTITUTE   (Ethiopia)

Author keywords

ARDRA; Mycobacteria; rDNA; Restriction enzymes

Indexed keywords

DNA 16S; DNA 23S; ETHAMBUTOL; ISONIAZID; RESTRICTION ENDONUCLEASE; RIBOSOME DNA; RIFAMPICIN; SPACER DNA; STREPTOMYCIN; THIOACETAZONE; UNCLASSIFIED DRUG;

ACCURACY; ANALYTIC METHOD; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATE; CONTROLLED STUDY; GENE AMPLIFICATION; GENUS; MYCOBACTERIUM AFRICANUM; MYCOBACTERIUM BOVIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; REPRODUCIBILITY; RESTRICTION MAPPING; SPECIES DIFFERENCE;

CORYNEBACTERINEAE; MYCOBACTERIUM; MYCOBACTERIUM AFRICANUM; MYCOBACTERIUM BOVIS; MYCOBACTERIUM BOVIS BCG; MYCOBACTERIUM TUBERCULOSIS;

EID: 0142028187     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7012(03)00119-2     Document Type: Article

References (36)

1. Abed Y., Davin-Regli A., Bollet C., De Micco P. Efficient discrimination of Mycobacterium tuberculosis strains by 16S-23S spacer region-based random amplified polymorphic DNA analysis. J. Clin. Microbiol. 33:1995;1418-1420.
2. Avaniss-Aghajani E., Jones K., Holtzman A., Aronson T., Glover N., Boian M., Froman S., Brunk C.F. Molecular technique for rapid identification of mycobacteria. J. Clin. Microbiol. 34:1996;98-102.
3. Boddinghaus B., Rogall T., Flohr T., Blocker H., Bottger E.C. Detection and identification of mycobacteria by amplification of rRNA. J. Clin. Microbiol. 28:1990;1751-1759.
4. De Baere T., de Mendonca R., Claeys G., Verschraegen G., Mijs W., Verhelst R., Rottiers S., Van Simaey L., De Ganck C., Vaneechoutte M. Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of cultured mycobacteria in a diagnostic laboratory. BMC Microbiol. 2:2002;4.
5. Devallois A., Goh K.S., Rastogi N. Rapid identification of mycobacteria to species level by PCR-restriction fragment length polymorphism analysis of the hsp65 gene and proposition of an algorithm to differentiate 34 mycobacterial species. J. Clin. Microbiol. 35:1997;2969-2973.
6. Dobner P., Feldmann K., Rifai M., Loscher T., Rinder H. Rapid identification of mycobacterial species by PCR amplification of hypervariable 16S rRNA gene promoter region. J. Clin. Microbiol. 34:1996;866-869.
7. Finken M., Kirschner P., Meier A., Wrede A., Bottger E.C. Molecular basis of streptomycin resistance in Mycobacterium tuberculosis: alterations of the ribosomal protein S12 gene and point mutations within a functional 16S ribosomal RNA pseudoknot. Mol. Microbiol. 9:1993;1239-1246.
8. Frothingham R., Hills H.G., Wilson K.H. Extensive DNA sequence conservation throughout the Mycobacterium tuberculosis complex. J. Clin. Microbiol. 32:1994;1639-1643.
9. Frothingham R., Strickland P.L., Bretzel G., Ramaswamy S., Musser J.M., Williams D.L. Phenotypic and genotypic characterization of Mycobacterium africanum isolates from West Africa. J. Clin. Microbiol. 37:1999;1921-1926.
10. Glennon M., Smith T., Cormican M., Noone D., Barry T., Maher M., Dawson M., Gilmartin J.J., Gannon F. The ribosomal intergenic spacer region: a target for the PCR based diagnosis of tuberculosis. Tuber. Lung Dis. 75:1994;353-360.
11. Hernandez S.M., Morlock G.P., Butler W.R., Crawford J.T., Cooksey R.C. Identification of Mycobacterium species by PCR-restriction fragment length polymorphism analyses using fluorescence capillary electrophoresis. J. Clin. Microbiol. 37:1999;3688-3692.
12. Honore N., Cole S.T. Streptomycin resistance in mycobacteria. Antimicrob. Agents Chemother. 38:1994;238-242.
13. Hughes M.S., Skuce R.A., Beck L.A., Neill S.D. Identification of mycobacteria from animals by restriction enzyme analysis and direct DNA cycle sequencing of polymerase chain reaction-amplified 16S rRNA gene sequences. J. Clin. Microbiol. 31:1993;3216-3222.
14. Imaeda T. Deoxyribonucleic acid relatedness among selected strains of Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium bovis BCG, Mycobacterium microti and Mycobacterium africanum. Int. J. Syst. Bacteriol. 35:1985;147-150.
15. Ingianni A., Petruzzelli S., Madeddu M.A., Pompei R. Studies on the distribution of high-level gentamicin-resistant Enterococcus faecalis using ribotyping and restriction analysis of the 16S-23S rRNA intergenic spacer sequences. Microb. Drug Resist. 3:1997;271-275.
16. Jeng R.S., Svircev A.M., Myers A.L., Beliaeva L., Hunter D.M., Hubbes M. The use of 16S and 16S-23S rDNA to easily detect and differentiate common Gram-negative orchard epiphytes. J. Microbiol. Methods. 44:2001;69-77.
17. Kirschner P., Springer B., Vogel U., Meier A., Wrede A., Kiekenbeck M., Bange F.C., Bottger E.C. Genotypic identification of mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory. J. Clin. Microbiol. 31:1993;2882-2889.
18. Koeleman J.G., Stoof J., Biesmans D.J., Savelkoul P.H., Vandenbroucke-Grauls C.M. Comparison of amplified ribosomal DNA restriction analysis, random amplified polymorphic DNA analysis, and amplified fragment length polymorphism fingerprinting for identification of Acinetobacter genomic species and typing of Acinetobacter baumannii. J. Clin. Microbiol. 36:1998;2522-2529.
19. Kox L.F., van Leeuwen J., Knijper S., Jansen H.M., Kolk A.H. PCR assay based on DNA coding for 16S rRNA for detection and identification of mycobacteria in clinical samples. J. Clin. Microbiol. 33:1995;3225-3233.
20. Kubica G.P. Clinical microbiology. Kubica G.P., Wayne L.G. The Mycobacteria: A Source Book. 1984;133-175 Marcel Dekker, New York.
21. Kurabachew M., Wondimu A., Ryon J.J. Reverse transcription-PCR detection of Mycobacterium leprae in clinical specimens. J. Clin. Microbiol. 36:1998;1352-1356.
22. Lappayawichit P., Rienthong S., Rienthong D., Chuchottaworn C., Chaiprasert A., Panbangred W., Saringcarinkul H., Palittapongarnpim P. Differentiation of Mycobacterium species by restriction enzyme analysis of amplified 16S-23S ribosomal DNA spacer sequences. Tuber. Lung Dis. 77:1996;257-263.
23. Liebana E., Aranaz A., Francis B., Cousins D. Assessment of genetic markers for species differentiation within the Mycobacterium tuberculosis complex. J. Clin. Microbiol. 34:1996;933-938.
24. Meier A., Kirschner P., Bange F.C., Vogel U., Bottger E.C. Genetic alterations in streptomycin-resistant Mycobacterium tuberculosis: mapping of mutations conferring resistance. Antimicrob. Agents. Chemother. 38:1994;228-233.
25. Miller N., Infante S., Cleary T. Evaluation of the LiPA mycobacteria assay for identification of mycobacterial species from BACTEC 12B bottles. J. Clin. Microbiol. 38:2000;1915-1919.
26. Nair J., Rouse D.A., Bai G.H., Morris S.L. The rpsL gene and streptomycin resistance in single and multiple drug-resistant strains of Mycobacterium tuberculosis. Mol. Microbiol. 10:1993;521-527.
27. Niemann S., Harmsen D., Rusch-Gerdes S., Richter E. Differentiation of clinical Mycobacterium tuberculosis complex isolates by gyrB DNA sequence polymorphism analysis. J. Clin. Microbiol. 38:2000;3231-3234.
28. Plikaytis B.B., Plikaytis B.D., Yakrus M.A., Butler W.R., Woodley C.L., Silcox V.A., Shinnick T.M. Differentiation of slowly growing Mycobacterium species, including Mycobacterium tuberculosis, by gene amplification and restriction fragment length polymorphism analysis. J. Clin. Microbiol. 30:1992;1815-1822.
29. Ramaswamy S., Musser J.M. Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update. Tuber. Lung Dis. 79:1998;3-29.
30. Rogall T., Wolters J., Flohr T., Bottger E.C. Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium. Int. J. Syst. Bacteriol. 40:1990;323-330.
31. Roth A., Reischl U., Streubel A., Naumann L., Kroppenstedt R.M., Habicht M., Fischer M., Mauch H. Novel diagnostic algorithm for identification of mycobacteria using genus-specific amplification of the 16S-23S rRNA gene spacer and restriction endonucleases. J. Clin. Microbiol. 38:2000;1094-1104.
32. Sansila A., Hongmanee P., Chuchottaworn C., Rienthong S., Rienthong D., Palittapongarnpim P. Differentiation between Mycobacterium tuberculosis and Mycobacterium avium by amplification of the 16S-23S ribosomal DNA spacer. J. Clin. Microbiol. 36:1998;2399-2403.
33. Steingrube V.A., Gibson J.L., Brown B.A., Zhang Y., Wilson R.W., Rajagopalan M., Wallace R.J. Jr. PCR amplification and restriction endonuclease analysis of a 65-kilodalton heat shock protein gene sequence for taxonomic separation of rapidly growing mycobacteria. J. Clin. Microbiol. 33:1995;149-153.
34. Telenti A., Marchesi F., Balz M., Bally F., Bottger E.C., Bodmer T. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J. Clin. Microbiol. 31:1993;175-178.
35. Vaneechoutte M., De Beenhouwer H., Claeys G., Verschraegen G., De Rouck A., Paepe N., Elaichouni A., Portaels F. Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis. J. Clin. Microbiol. 31:1993;2061-2065.
36. Vaneechoutte M., Dijkshoorn L., Tjernberg I., Elaichouni A., de Vos P., Claeys G., Verschraegen G. Identification of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis. J. Clin. Microbiol. 33:1995;11-15.