Polymerase chain reaction-restriction fragment length polymorphism of the rpoB gene for identification of Mycobacterium avium subsp. paratuberculosis and differentiation of Mycobacterium avium subspecies

Diagnostic Microbiology and Infectious Disease

Volumn 70, Issue 1, 2011, Pages 65-71

  Whang, Jake ^a   Lee, Byung Soo ^a   Choi, Go Eun ^b   Cho, Sang Nae ^c   Kil, Park Young ^d   Collins, Michael T ^e   Shin, Sung Jae ^a  

^a Chungnam National University   (South Korea)

^b Pusan National University School of Medicine   (South Korea)

^c Yonsei University College of Medicine   (South Korea)

^d Korean Institute of Tuberculosis   (South Korea)

^e UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Mycobacterium avium complex; Mycobacterium avium subsp. paratuberculosis; Polymerase chain reaction restriction fragment length polymorphism

Indexed keywords

HAEIII RESTRICTION ENZYME; MSPI RESTRICTION ENZYME; RESTRICTION ENDONUCLEASE; SMAI RESTRICTION ENZYME; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; GENE SEQUENCE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MYCOBACTERIUM AVIUM; MYCOBACTERIUM PARATUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RPOB GENE; SPECIES IDENTIFICATION;

ANIMALS; BACTERIOLOGICAL TECHNIQUES; DEOXYRIBONUCLEASE HPAII; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; ENVIRONMENTAL MICROBIOLOGY; HUMANS; MYCOBACTERIUM AVIUM COMPLEX; MYCOBACTERIUM AVIUM-INTRACELLULARE INFECTION; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH;

EID: 79954996138     PISSN: 07328893     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.diagmicrobio.2011.01.014     Document Type: Article

References (39)

1. Abubakar I., Myhill D., Aliyu S.H., Hunter P.R. Detection of Mycobacterium avium subspecies paratuberculosis from patients with Crohn's disease using nucleic acid-based techniques: a systematic review and meta-analysis. Inflamm. Bowel Dis. 2008, 14:401-410.
2. Aduriz J.J., Juste R.A., Cortabarria N. Lack of mycobactin dependence of mycobacteria isolated on Middlebrook 7H11 from clinical cases of ovine paratuberculosis. Vet. Microbiol. 1995, 45:211-217.
3. Alonso-Hearn M., Molina E., Geijo M., Vazquez P., Sevilla I., Garrido J.M., Juste R.A. Isolation of Mycobacterium avium subsp. paratuberculosis from muscle tissue of naturally infected cattle. Foodborne Pathog. Dis. 2009, 6:513-518.
4. Bannantine J.P., Baechler E., Zhang Q., Li L., Kapur V. Genome scale comparison of Mycobacterium avium subsp. paratuberculosis with Mycobacterium avium subsp. avium reveals potential diagnostic sequences. J. Clin. Microbiol. 2002, 40:1303-1310.
5. Behr M.A., Kapur V. The evidence for Mycobacterium paratuberculosis in Crohn's disease. Curr. Opin. Gastroenterol. 2008, 24:17-21.
6. Ben Salah I., Cayrou C., Raoult D., Drancourt M. Mycobacterium marseillense sp. nov., Mycobacterium timonense sp. nov. and Mycobacterium bouchedurhonense sp. nov., members of the Mycobacterium avium complex. Int. J. Syst. Evol. Microbiol. 2009, 59:2803-2808.
7. Ben Salah I., Drancourt M. Surviving within the amoebal exocyst: the Mycobacterium avium complex paradigm. BMC Microbiol. 2010, 10:99.
8. Beumer A., King D., Donohue M., Mistry J., Covert T., Pfaller S. Detection of Mycobacterium avium subsp. paratuberculosis in drinking water and biofilms by quantitative PCR. Appl. Environ. Microbiol. 2010, 76:7367-7370.
9. Cayrou C., Turenne C., Behr M.A., Drancourt M. Genotyping of Mycobacterium avium complex organisms using multispacer sequence typing. Microbiology 2010, 156:687-694.
10. Collins D.M., Gabric D.M., De Lisle G.W. Identification of a repetitive DNA sequence specific to Mycobacterium paratuberculosis. FEMS Microbiol. Lett. 1989, 51:175-178.
11. Cousins D.V., Whittington R., Marsh I., Masters A., Evans R.J., Kluver P. Mycobacteria distinct from Mycobacterium avium subsp. paratuberculosis isolated from the faeces of ruminants possess IS900-like sequences detectable IS900 polymerase chain reaction: implications for diagnosis. Mol. Cell. Probes 1999, 13:431-442.
12. Devallois A., Picardeau M., Paramasivan C.N., Vincent V., Rastogi N. Molecular characterization of Mycobacterium avium complex isolates giving discordant results in AccuProbe tests by PCR-restriction enzyme analysis, 16S rRNA gene sequencing, and DT1-DT6 PCR. J. Clin. Microbiol. 1997, 35:2767-2772.
13. Ellingson J.L., Anderson J.L., Koziczkowski J.J., Radcliff R.P., Sloan S.J., Allen S.E., Sullivan N.M. Detection of viable Mycobacterium avium subsp. paratuberculosis in retail pasteurized whole milk by two culture methods and PCR. J. Food Prot. 2005, 68:966-972.
14. Eltholth M.M., Marsh V.R., Van Winden S., Guitian F.J. Contamination of food products with Mycobacterium avium paratuberculosis: a systematic review. J. Appl. Microbiol. 2009, 107:1061-1071.
15. Englund S., Bolske G., Johansson K.E. An IS900-like sequence found in a Mycobacterium sp. other than Mycobacterium avium subsp. paratuberculosis. FEMS Microbiol. Lett. 2002, 209:267-271.
16. Feller M., Huwiler K., Stephan R., Altpeter E., Shang A., Furrer H., Pfyffer G.E., Jemmi T., Baumgartner A., Egger M. Mycobacterium avium subspecies paratuberculosis and Crohn's disease: a systematic review and meta-analysis. Lancet Infect. Dis. 2007, 7:607-613.
17. Glickman S.E., Kilburn J.O., Butler W.R., Ramos L.S. Rapid identification of mycolic acid patterns of mycobacteria by high-performance liquid chromatography using pattern recognition software and a Mycobacterium library. J. Clin. Microbiol. 1994, 32:740-745.
18. Gumber S., Whittington R.J. Comparison of BACTEC 460 and MGIT 960 systems for the culture of Mycobacterium avium subsp. paratuberculosis S strain and observations on the effect of inclusion of ampicillin in culture media to reduce contamination. Vet. Microbiol. 2007, 119:42-52.
19. Juste R.A., Marco J.C., Saez de Ocariz C., Aduriz J.J. Comparison of different media for the isolation of small ruminant strains of Mycobacterium paratuberculosis. Vet. Microbiol. 1991, 28:385-390.
20. Kim B.J., Lee K.H., Park B.N., Kim S.J., Bai G.H., Kook Y.H. Differentiation of mycobacterial species by PCR-restriction analysis of DNA (342 base pairs) of the RNA polymerase gene (rpoB). J. Clin. Microbiol. 2001, 39:2102-2109.
21. Kim B.J., Lee K.H., Yun Y.J., Park E.M., Park Y.G., Bai G.H., Cha C.Y., Kook Y.H. Simultaneous identification of rifampin-resistant Mycobacterium tuberculosis and nontuberculous mycobacteria by polymerase chain reaction-single strand conformation polymorphism and sequence analysis of the RNA polymerase gene (rpoB). J. Microbiol. Methods 2004, 58:111-118.
22. Lee H., Park H.J., Cho S.N., Bai G.H., Kim S.J. Species identification of mycobacteria by PCR-restriction fragment length polymorphism of the rpoB gene. J. Clin. Microbiol. 2000, 38:2966-2971.
23. Manning E.J., Collins M.T. Mycobacterium avium subsp. paratuberculosis: pathogen, pathogenesis and diagnosis. Rev. Sci. Tech. 2001, 20:133-150.
24. Motiwala A.S., Strother M., Amonsin A., Byrum B., Naser S.A., Stabel J.R., Shulaw W.P., Bannantine J.P., Kapur V., Sreevatsan S. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis: evidence for limited strain diversity, strain sharing, and identification of unique targets for diagnosis. J. Clin. Microbiol. 2003, 41:2015-2026.
25. Naser S.A., Ghobrial G., Romero C., Valentine J.F. Culture of Mycobacterium avium subspecies paratuberculosis from the blood of patients with Crohn's disease. Lancet 2004, 364:1039-1044.
26. Pithua P., Wells S.J., Godden S.M., Sreevatsan S., Stabel J.R. Experimental validation of a nested polymerase chain reaction targeting the genetic element ISMAP02 for detection of Mycobacterium avium subspecies paratuberculosis in bovine colostrum. J. Vet. Diagn. Invest. 2010, 22:253-256.
27. Poupart P., Coene M., Van Heuverswyn H., Cocito C. Preparation of a specific RNA probe for detection of Mycobacterium paratuberculosis and diagnosis of Johne's disease. J. Clin. Microbiol. 1993, 31:1601-1605.
28. Prince D.S., Peterson D.D., Steiner R.M., Gottlieb J.E., Scott R., Israel H.L., Figueroa W.G., Fish J.E. Infection with Mycobacterium avium complex in patients without predisposing conditions. N. Engl. J. Med. 1989, 321:863-868.
29. Semret M., Turenne C.Y., Behr M.A. Insertion sequence IS900 revisited. J. Clin. Microbiol. 2006, 44:1081-1083.
30. Shin S.J., Lee B.S., Koh W.J., Manning E.J., Anklam K., Sreevatsan S., Lambrecht R.S., Collins M.T. Efficient differentiation of Mycobacterium avium complex species and subspecies by use of five-target multiplex PCR. J. Clin. Microbiol. 2010, 48:4057-4062.
31. Strommenger B., Stevenson K., Gerlach G.F. Isolation and diagnostic potential of ISMav2, a novel insertion sequence-like element from Mycobacterium avium subspecies paratuberculosis. FEMS Microbiol. Lett. 2001, 196:31-37.
32. Swanson D.S., Kapur V., Stockbauer K., Pan X., Frothingham R., Musser J.M. Subspecific differentiation of Mycobacterium avium complex strains by automated sequencing of a region of the gene (hsp65) encoding a 65-kilodalton heat shock protein. Int. J. Syst. Bacteriol. 1997, 47:414-419.
33. Turenne C.Y., Semret M., Cousins D.V., Collins D.M., Behr M.A. Sequencing of hsp65 distinguishes among subsets of the Mycobacterium avium complex. J. Clin. Microbiol. 2006, 44:433-440.
34. van Soolingen D., Hermans P.W., de Haas P.E., Soll D.R., van Embden J.D. Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J. Clin. Microbiol. 1991, 29:2578-2586.
35. Vary P.H., Andersen P.R., Green E., Hermon-Taylor J., McFadden J.J. Use of highly specific DNA probes and the polymerase chain reaction to detect Mycobacterium paratuberculosis in Johne's disease. J. Clin. Microbiol. 1990, 28:933-937.
36. Whittington R., Marsh I., Choy E., Cousins D. Polymorphisms in IS1311, an insertion sequence common to Mycobacterium avium and M. avium subsp. paratuberculosis, can be used to distinguish between and within these species. Mol. Cell. Probes 1998, 12:349-358.
37. Whittington R.J. Factors affecting isolation and identification of Mycobacterium avium subsp. paratuberculosis from fecal and tissue samples in a liquid culture system. J. Clin. Microbiol. 2009, 47:614-622.
38. Whittington R.J., Marsh I., Turner M.J., McAllister S., Choy E., Eamens G.J., Marshall D.J., Ottaway S. Rapid detection of Mycobacterium paratuberculosis in clinical samples from ruminants and in spiked environmental samples by modified BACTEC 12B radiometric culture and direct confirmation by IS900 PCR. J. Clin. Microbiol. 1998, 36:701-707.
39. Williams-Bouyer N., Yorke R., Lee H.I., Woods G.L. Comparison of the BACTEC MGIT 960 and ESP culture system II for growth and detection of mycobacteria. J. Clin. Microbiol. 2000, 38:4167-4170.