The PCR amplification of non-tuberculous mycobacterial 16S rRNA sequences from soil

FEMS Microbiology Letters

Volumn 185, Issue 2, 2000, Pages 189-192

  Mendum, Tom A ^a   Chilima, Ben Z ^a,b   Hirsch, Penny R ^a  

^a ROTHAMSTED RESEARCH   (United Kingdom)

^b LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

Author keywords

16S rRNA; Non tuberculous mycobacterium; PCR; Soil

Indexed keywords

BCG VACCINE; RNA 16S;

ARTICLE; GENE AMPLIFICATION; GENE SEQUENCE; MYCOBACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA SEQUENCE; SOIL;

GENES, BACTERIAL; GENES, RRNA; MOLECULAR SEQUENCE DATA; MYCOBACTERIA, ATYPICAL; MYCOBACTERIUM; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

CORYNEBACTERINEAE; MYCOBACTERIUM; MYCOBACTERIUM LENTIFLAVUM;

EID: 0034655879     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(00)00101-4     Document Type: Article

References (25)

1. Yajko D.M., Chin D.P., Gonzalez P.C., Nassos P.S., Hopewell P.C., Reingold A.L., Horsburgh C.R., Yakrus M.A., Ostreoff S.M. Mycobacterium avium complex in water, food and soil samples collected from the environment of HIV-infected individuals. J. Acquired Immun. Defic. Synd. Hum. Retrovirol. 9:1995;176-182.
2. Brooks R.W., Parker B.C., Gruft H., Falkinham J.O. III. Epidemiology of infection by nontuberculous mycobacteria V. Numbers in Eastern United States soils and correlation with soil characteristics. Am. Rev. Respir. Dis. 130:1984;630-633.
3. Iivanainen E. Isolation of mycobacteria from acidic forest soil samples-comparison of culture methods. J. Appl. Bacteriol. 78:1995;663-668.
4. Covert T.C., Rodgers M.R., Reyes A.L., Stelma G.N. Occurrence of nontuberculous mycobacteria in environmental samples. Appl. Environ. Microbiol. 65:1999;2492-2496.
5. Peters M., Müller C., Rüsch-Gerdes S., Seidel C., Göbel U., Pohle H.D., Ruf B. Isolation of atypical mycobacteria from tap water in hospitals and homes, is this a possible source of disseminated MAC infection in AIDS patients? J. Infect. 31:1995;39-44.
6. Wolinsky E. Nontuberculous mycobacteria and associated diseases. Am. Rev. Respir. Dis. 119:1979;107-159.
7. O'Brien R.J. The epidemiology of nontuberculous mycobacterial disease. Clin. Chest Med. 10:1989;407-418.
8. Fine P.E.M. Variation in protection by BCG: Implications of and for heterologous immunity. Lancet. 346:1995;1339-1345.
9. Cooney R., Kazda J., Quinn J., Cook B., Müller K., Monaghan M. Environmental mycobacteria in Ireland as a source of non-specific sensitisation to tuburculins. Ir. Vet. J. 50:1997;370-373.
10. Palmer C.E., Long M.W. Effects of infection with atypical mycobacteria on BCG vaccination and tuberculosis. Am. Rev. Respir. Dis. 94:1966;553-568.
11. Smith D., Reeser P., Musa S. Does infection with environmental mycobacteria suppress the protective response to subsequent vaccination with BCG? Tubercle. 66:1985;17-23.
12. Kamala T., Paramasivan C.N., Herbert D., Venkatesan P., Prabhakar R. Isolation and identification of environmental mycobacteria in the Mycobacterium bovis BCG trial area of South-India. Appl. Environ. Microbiol. 60:1994;2180-2183.
13. Kamala T., Paramasivan C.N., Herbert D., Venkatesan P., Prabhakar R. Evaluation of procedures for isolation of nontuberculous mycobacteria from soil and water. Appl. Environ. Microbiol. 60:1994;1021-1024.
14. McVeigh H.P., Munro J., Embley T.M. Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil. J. Ind. Microbiol. 17:1996;197-204.
15. Kox L.F.F., van Leeuwen J., Knijper S., Jansen H.M., Kolk A.H.J. PCR assay based on DNA coding for 16S ribosomal-RNA for detection and identification of mycobacteria in clinical samples. J. Clin. Microbiol. 33:1995;3225-3233.
16. Schwartz T., Kalmbach S., Hoffmann S., Szewzyk U., Obst U. PCR-based detection of mycobacteria in biofilms from a drinking water distribution system. J. Microbiol. Methods. 34:1998;113-123.
17. Cullen D.W., Hirsch P.R. A simple and rapid method for the direct extraction of microbial DNA from soil for PCR. Soil Biol. Biochem. 30:1998;983-993.
18. van Soolingen D., Hermans P.W.M., De Haas P.E.W., Soll D.R., van Embden J.D.A. Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains-evaluation of an insertion sequence-dependant DNA polymorphism as a tool in the epidemiology of tuberculosis. J. Clin. Microbiol. 29:1991;2578-2586.
19. Maidak B.L., Cole J.R., Parker C.T. Jr., Garrity G.M., Larsen N., Li B., Lilburn T.G., McCaughey M.J., Olsen G.J., Overbeek R., Pramanik S., Schmidt T.M., Tiedje J.M., Woese C.R. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27:1999;171-173.
20. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:1997;4876-4882.
21. Strimmer K., von Haeseler A. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 1:1996;964-969.
22. Felstein, J. (1994) PHYLIP V3.57 (phylogeny inference package) Distributed by author. Department of Genetics, University of Washington, Seattle, WA.
23. Govindaswami M., Feldhake D.J., Kinkle B.K., Mindell D.P., Loper J.C. Phylogenetic comparison of two polycyclic aromatic hydrocarbon-degrading mycobacteria. Appl. Environ. Microbiol. 61:1995;3221-3226.
24. Kleespies M., Kroppenstedt R.M., Rainey F.A., Webb L.E., Stackebrandt E. Mycobacterium hodleri sp. nov., a new member of the fast-growing mycobacteria capable of degrading polycyclic aromatic hydrocarbons. Int. J. Syst. Bacteriol. 46:1996;683-687.
25. Springer B., Wu W.-K., Bodmer T., Haase G., Pfyffer G.E., Kroppenstedt R.M., Schroder K.-H., Emler S., Telenti A., Coyle M.B., Böttger E.C. Isolation and characterization of a unique group of slowly growing mycobacteria: description of Mycobacterium lentiflavum sp. nov. J. Clin. Microbiol. 34:1996;1100-1107.