16S rRNA targeted sandwich hybridization method for direct quantification of mycobacteria in soils

Journal of Microbiological Methods

Volumn 67, Issue 1, 2006, Pages 44-55

  Nieminen, Timo ^a   Pakarinen, Jaakko ^b   Tsitko, Irina ^b   Salkinoja Salonen, Mirja ^b   Breitenstein, Antje ^c   Ali Vehmas, Terhi ^b   Neubauer, Peter ^a  

^a UNIVERSITY OF OULU   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

^c Scanbec GmbH   (Germany)

Author keywords

16S rRNA; Atypical; Fluorescence assay; Mycobacteria; Mycobacterium; Oligonucleotide probe; Sandwich hybridization; Soil

Indexed keywords

RIBOSOME RNA;

ARTICLE; BACTERIAL CELL; BACTERIUM CULTURE; BACTERIUM DETECTION; CONTROLLED STUDY; MYCOBACTERIUM; MYCOBACTERIUM CHLOROPHENOLICUM; NONHUMAN; NUCLEIC ACID AMPLIFICATION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA HYBRIDIZATION; SANDWICH HYBRIDIZATION; SOIL ANALYSIS;

DNA, RIBOSOMAL; MYCOBACTERIUM; NUCLEIC ACID HYBRIDIZATION; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SOIL MICROBIOLOGY;

CORYNEBACTERINEAE;

EID: 33747787044     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2006.02.015     Document Type: Article

References (44)

1. Andersson M.A., Nikulin M., Koljalg U., Andersson M.C., Rainey F., Reijula K., Hintikka E.L., and Salkinoja-Salonen M. Bacteria, molds, and toxins in water-damaged building materials. Appl. Environ. Microbiol. 63 (1997) 387-393
2. Bleve G., Rizzotti L., Dellaglio F., and Torriani S. Development of reverse transcription (RT)-PCR and real-time RT-PCR assays for rapid detection and quantification of viable yeasts and molds contaminating yogurts and pasteurized food products. Appl. Environ. Microbiol. 69 (2003) 4116-4122
3. Bremer H., and Dennis P.P. Modulation of chemical composition and other parameters of the cell by growth. In: Neidhardt F.C., Curtiss III R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Riley M., Schaechter M., and Umbarger H.E. (Eds). Escherichia and Salmonella. Cellular and Molecular Biology vol. 2 (1996), ASM Press, Washington 1553-1566
4. Briglia M., Eggen R.I.L., Vos W.d., and Elsas J.v. Rapid and sensitive method for the detection of Mycobacterium chlorophenolicum PCP-1 in soil based on 16S rRNA gene-targeted PCR. Appl. Environ. Microbiol. 62 (1996) 1478-1480
5. Brosius J., Palmer M.L., Kennedy P.J., and Noller H.F. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 75 (1978) 4801-4805
6. Duarte G.F., Rosado A.S., Seldin L., Keijzer-Wolters A.C., and van Elsas J.D. Extraction of ribosomal RNA and genomic DNA from soil for studying the diversity of the indigenous bacterial community. J. Microbiol. Methods 32 (1998) 21-29
7. Eilers H., Pernthaler J., Glockner F.O., and Amann R. Culturability and In situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66 (2000) 3044-3051
8. Falkinham III J.O. Epidemiology of infection by nontuberculous mycobacteria. Clin. Microbiol. Rev. 9 (1996) 177-215
9. Falkinham III J.O. Environmental sources of Mycobacterium avium linked to routes of exposure. In: Pedley S., Bartram J., Rees G., Dufour A., and Cotruvo J.A. (Eds). Pathogenic Mycobacteria in Water: a Guide to Public Health Consequences, Monitoring and Managment. WHO Emerging Issues in Water and Infectious Disease Series (2004), IWA Publishing, London 26-37
10. Fey A., Eichler S., Flavier S., Christen R., Hofle M.G., and Guzman C.A. Establishment of a real-time PCR-based approach for accurate quantification of bacterial RNA targets in water, using Salmonella as a model organism. Appl. Environ. Microbiol. 70 (2004) 3618-3623
11. Gabig-Ciminska M., Los M., Holmgren A., Albers J., Czyz A., Hintsche R., Wegrzyn G., and Enfors S.O. Detection of bacteriophage infection and prophage induction in bacterial cultures by means of electric DNA chips. Anal. Biochem. 324 (2004) 84-91
12. Griffiths R.I., Whiteley A.S., O'Donnel A.G., and Bailey M.J. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66 (2000) 5488-5491
13. Hurt R.A., Qiu X., Wu L., Roh Y., Palumbo A.V., Tiedje J.M., and Zhou J. Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67 (2001) 4495-4503
14. Iivanainen E., Martikainen P.J., Räisänen M.L., and Katila M.L. Mycobacteria in boreal coniferous forest soils. FEMS Microbiol. Ecol. 23 (1997) 325-332
15. Iivanainen E., Martikainen P.J., Vaananen P., and Katila M.L. Environmental factors affecting the occurrence of mycobacteria in brook sediments. J. Appl. Microbiol. 86 (1999) 673-681
16. Jussila J., Komulainen H., Huttunen K., Roponen M., Iivanainen E., Torkko P., Kosma V.M., Pelkonen J., and Hirvonen M.R. Mycobacterium terrae isolated from indoor air of a moisture-damaged building induces sustained biphasic inflammatory response in mouse lungs. Environ. Health Perspect. 110 (2002) 1119-1125
17. Keer J.T., and Birch L. Molecular methods for the assessment of bacterial viability. J. Microbiol. Methods 53 (2003) 175-183
18. Kemp P.F., Lee S., and LaRoche J. Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl. Environ. Microbiol. 59 (1993) 2594-2601
19. Kirschner P., Springer B., Vogel U., Meier A., Wrede A., Kiekenbeck M., Bange F.C., and 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
20. Komijn R.E., de Haas P.E., Schneider M.M., Eger T., Nieuwenhuijs J.H., van den Hoek R.J., Bakker D., Zijd Erveld F.G., and van Soolingen D. Prevalence of Mycobacterium avium in slaughter pigs in The Netherlands and comparison of IS1245 restriction fragment length polymorphism patterns of porcine and human isolates. J. Clin. Microbiol. 37 (1999) 1254-1259
21. Kramer J.G., and Singleton F.L. Variations in rRNA content of marine Vibrio spp. during starvation-survival and recovery. Appl. Environ. Microbiol. 58 (1992) 201-207
22. Lebuhn M., Effenberger M., Garces G., Gronauer A., and Wilderer P.A. Evaluating real-time PCR for the quantification of distinct pathogens and indicator organisms in environmental samples. Water Sci. Technol. 50 (2004) 263-270
23. Leskelä T., Tilsala-Timisjärvi A., Kusnetsov J., Neubauer P., and Breitenstein A. Sensitive and genus-specific detection of Legionella by a 16S rRNA based sandwich hybridization assay. J. Microbiol. Methods 62 (2005) 167-179
24. Los M., Los J.M., Blohm L., Spillner E., Grunwald T., Albers J., Hintsche R., and Wegrzyn G. Rapid detection of viruses using electrical biochips and anti-virion sera. Lett. Appl. Microbiol. 40 (2005) 479-485
25. Martin-Casabona N., Bahrmand A.R., Bennedsen J., Thomsen V.O., Curcio M., Fauville-Dufaux M., Feldman K., Havelkova M., Katila M.L., Koksalan K., Pereira M.F., Rodrigues F., Pfyffer G.E., Portaels F., Urgell J.R., Rusch-Gerdes S., Tortoli E., Vincent V., and Watt B. Non-tuberculous mycobacteria: patterns of isolation. A multi-country retrospective survey. Int. J. Tuberc. Lung Dis. 8 (2004) 1186-1193
26. Matlova L., Dvorska L., Ayele W.Y., Bartos M., Amemori T., and Pavlik I. Distribution of Mycobacterium avium complex isolates in tissue samples of pigs fed peat naturally contaminated with mycobacteria as a supplement. J. Clin. Microbiol. 43 (2005) 1261-1268
27. Mendum T.A., Chilima B.Z., and Hirsch P.R. The PCR amplification of non-tuberculous mycobacterial 16S rRNA sequences from soil. FEMS Microbiol. Lett. 185 (2000) 189-192
28. Mijs W., De Vreese K., Devos A., Pottel H., Valgaeren A., Evans C., Norton J., Parker D., Rigouts L., Portaels F., Reischl U., Watterson S., Pfyffer G., and Rossau R. Evaluation of a commercial line probe assay for identification of mycobacterium species from liquid and solid culture. Eur. J. Clin. Microbiol. Infect. Dis. 21 (2002) 794-802
29. Niva M., Hernesmaa A., Haahtela K., Salkinoja-Salonen M., Sivonen K., and Haukka K. Actinobacterial communities of boreal forest soil and lake water are rich in mycobacteria. Boreal Env. Res. 11 (2006) 45-53
30. Parish T., and Stoker N.G. Mycobacteria: bugs and bugbears. In: Parish T., and Stoker N.G. (Eds). Mycobacteria Protocols. Methods in Molecular Biology (1998), Humana Press Inc., Totowa, New Jersey 1-15
31. Pavlik I., Matlova L., Dvorska L., Bartl J., Oktabcova L., Docekal J., and Parmova I. Tuberculous lesions in pigs in the Czech Republic during 1990-1999: occurrence, causal factors and economic losses. Vet. Med. - Czech. 48 (2003) 113-125
32. Primm T.P., Lucero C.A., and Falkinham III J.O. Health impacts of environmental mycobacteria. Clin. Microbiol. Rev. 17 (2004) 98-106
33. Rautio J., Barken K.B., Lahdenpera J., Breitenstein A., Molin S., and Neubauer P. Sandwich hybridisation assay for quantitative detection of yeast RNAs in crude cell lysates. Microb. Cell Fact. 2 (2003) 4
34. Schafer M.P., Martinez K.F., and Mathews E.S. Rapid detection and determination of the aerodynamic size range of airborne mycobacteria associated with whirlpools. Appl. Occup. Environ. Hyg. 18 (2003) 41-50
35. Sievert S.M., Ziebis W., Kuever J., and Sahm K. Relative abundance of archaea and bacteria along a thermal gradient of a shallow-water hydrothermal vent quantified by rRNA slot-blot hybridization. Microbiology 146 (2000) 1287-1293
36. Small J., Call D.R., Brockman F.J., Straub T.M., and Chandler D.P. Direct Detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl. Environ. Microbiol. 67 (2001) 4708-4716
37. Soini J., Falschlehner C., Mayer C., Bohm D., Weinel S., Panula J., Vasala A., and Neubauer P. Transient increase of ATP as a response to temperature up-shift in Escherichia coli. Microb. Cell Fact. 4 (2005) 9
38. Stinear T., Ford T., and Vincent V. Analytical methods for the detection of waterborne and environmental pathogenic mycobacteria. In: Pedley S., Bartram J., Rees G., Dufour A., and Cotruvo J.A. (Eds). Pathogenic Mycobacteria in Water: a Guide to Public Health Consequences, Monitoring and Managment. WHO Emerging Issues in Water & Infectious Disease Series (2004), IWA Publishing, London 55-73
39. Thomas J.C., Desrosiers M., St Pierre Y., Lirette P., Bisaillon J.G., Beaudet R., and Villemur R. Quantitative flow cytometric detection of specific microorganisms in soil samples using rRNA targeted fluorescent probes and ethidium bromide. Cytometry 27 (1997) 224-232
40. Torkko P., Suomalainen S., Iivanainen E., Suutari M., Tortoli E., Paulin L., and Katila M.L. Mycobacterium xenopi and related organisms isolated from stream waters in Finland and description of Mycobacterium botniense sp. nov. Int. J. Syst. Evol. Microbiol. 50 (2000) 283-289
41. van Elsas J.D., Mantynen V., and Wolters A.C. Soil DNA extraction and assessment of the fate of Mycobacterium chlorophenolicum strain PCP 1 in different soils by 16S ribosomal RNA gene sequence based most probable number PCR and immunofluorescence. Biol. Fertil. Soils 24 (1997) 188-195
42. von Dürrling H., Ludewig H., Uhlemann J., and Gericke R. Torf als Quelle einer Infektion mit aviären Mykobakterien bei Schweinen. Tierärztl. Umsch. 53 (1998) 259-261
43. von Reyn C.F., Waddell R.D., Eaton T., Arbeit R.D., Maslow J.N., Barber T.W., Brindle R.J., Gilks C.F., Lumio J., and Lahdevirta J. Isolation of Mycobacterium avium complex from water in the United States, Finland, Zaire, and Kenya. J. Clin. Microbiol. 31 (1993) 3227-3230
44. Vuorio R., Andersson M.A., Rainey F.A., Kroppenstedt R.M., Kampfer P., Busse H.J., Viljanen M., and Salkinoja-Salonen M. A new rapidly growing mycobacterial species, Mycobacterium murale sp. nov., isolated from the indoor walls of a children's day care centre. Int. J. Syst. Bacteriol. 49 (1999) 25-35