Evaluation of inhibition and cross-reaction effects on real-time PCR applied to the total DNA of wastewater samples for the quantification of bacterial antibiotic resistance genes and taxon-specific targets

Molecular and Cellular Probes

Volumn 21, Issue 2, 2007, Pages 125-133

  Volkmann, Holger ^a   Schwartz, Thomas ^a   Kirchen, Silke ^a   Stofer, Carmen ^a   Obst, Ursula ^a  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

Author keywords

Competition; Impurities; Inhibition; Real time PCR; Wastewater

Indexed keywords

DNA; RIBOSOME DNA;

ANTIBIOTIC RESISTANCE; ARTICLE; COMPARATIVE STUDY; CONCENTRATION (PARAMETERS); CROSS REACTION; DNA EXTRACTION; DNA PROBE; DNA SEQUENCE; ENTEROCOCCUS FAECALIS; ENTEROCOCCUS FAECIUM; GENE AMPLIFICATION; GENE FUNCTION; GENE TARGETING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; TAXON; TAXONOMY; WASTE WATER; WATER SAMPLING;

AMINO ACID SEQUENCE; BACTERIA; BASE SEQUENCE; DNA PRIMERS; DNA, BACTERIAL; DRUG RESISTANCE; ENTEROBACTER; ENVIRONMENT; METHICILLIN RESISTANCE; POLYMERASE CHAIN REACTION; STAPHYLOCOCCUS AUREUS; WASTE DISPOSAL, FLUID; WATER; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS); ENTEROCOCCUS; PSEUDOMONAS AERUGINOSA;

EID: 33846118670     PISSN: 08908508     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mcp.2006.08.009     Document Type: Article

References (30)

1. Oliver J.D. The viable but nonculturable state in bacteria. J Microbiol 43 (2005) 93-100
2. López-Gutiérrez J.C., Henry S., Hallet S., Martin-Laurent F., Catroux G., and Philippot L. Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR. J Microbiol Meth 57 (2004) 399-407
3. Khan I., and Yadav J. Real-time PCR assays for genus-specific detection and quantification of culturable and non-culturable mycobacteria and pseudomonads in metalworking fluids. Mol Cell Probes 18 (2004) 67-73
4. Ludwig W., and Schleifer K.H. How quantitative is quantitative PCR?. System Appl Microbiol 23 (2000) 556-562
5. Becker S., Böger P., Oehlmann R., and Ernst A. PCR bias in ecological analysis: Case study for a quantitative Taq nuclease assay of microbial communities. Appl Eviron Microbiol 66 (2000) 4945-4953
6. Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acid Res 29 (2001) 2002-2007
7. Weyant R.S., Edmonds P., and Swaminathan B. Effect of ionic and nonionic detergents on the Taq polymerase. BioTechniques 9 (1990) 308-309
8. Schwartz T., Kohnen W., Jansen B., and Obst U. Detection of antibiotic-resistant bacteria and their resistance genes in wastewater, surface water, and drinking water biofilms. FEMS Microbiol Ecol 43 (2003) 325-335
9. Volkmann H., Schwartz T., Bischoff P., Kirchen S., and Obst U. Detection of clinically relevant antibiotic-resistance genes in municipal wastewater using real-time PCR (TaqMan). J Microbiol. Methods 56 (2004) 277-286
10. Schwartz T., Volkmann H., Kirchen S., Kohnen K., Schön-Hölz K., Jansen B., et al. Real-time PCR detection of Pseudomonas aeruginosa in clinical and municipal wastewater and genotyping of ciprofloxacin-resistant isolates. FEMS Microbiol Ecol 57 (2006) 158-167
11. Patel R., Uhl J., Kohner P., Hopkins M., and Cockerill F. Multiplex PCR detection of vanA, vanB, vanC-1, and vanC-2/3 genes in enterococci. J Clin Microbiol 35 (1997) 703-707
12. Singer V.L., Jones L.J., Yue S.T., and Haugland R.P. Characterization of PicoGreen reagent and development of a fluorescence-based solution assay for double-stranded DNA quantitation. Anal Biochem 249 (1997) 228-238
13. Vitzthum F., Geiger G., Bisswange H.S., Brunner H., and Bernhagen J. A quantitative fluorescence-based microplate assay for the determination of double-stranded DNA using SYBR Green I and a standard ultraviolet transilluminator gel imaging system. Anal Biochem 276 (1999) 59-64
14. Zipper H., Buta C., Lämmle K., Brunner H., Bernhagen J., and Vitzthum F. Mechanisms underlying the impact of humid acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments. Nucleic Acid Res 31 (2003) e39
15. Frahm E., and Obst U. Application of the fluorogenic probe technique (TaqMan PCR) to the detection of Enterococcus spp and Escherichia coli in water samples. J Microbiol Methods 52 (2003) 123-131
16. Pirnay J.P., DeVos D., Duinslaeger L., Reper P., Valdenvelde C., Cornelis P., et al. Quantitation of Pseudomonas aeruginosa in wound biopsy samples: from bacterial culture to rapid 'real-time' polymerase chain reaction. Crit Care 4 (2000) 255-261
17. Wellinghausen N., Frost C., and Marre R. Detection of Legionellae in hospital water samples by quantitative real-time LightCycler PCR. Appl Environ Microbiol 67 (2001) 3985-3993
18. Schabereiter-Gurtner C., Hirschl A.M., Dragosics B., Hufnagi P., Puz S., Kovách Z., et al. Novel real-time PCR assay for detection of Helicobacter pylori infection and simultaneous clarithromycin susceptibility testing of stool and biopsy specimens. J Clin Microbiol 42 (2004) 4512-4518
19. Hanna S.E., Connor C.J., and Wang H.H. Real-time polymerase chain reaction for food microbiologists: Technologies, applications, and limitations. J Food Sci 70 (2005) 49-53
20. Saleh-Lakha S., Miller M., Campbell R.G., Schneider K., Elahimanesh P., Hart M.M., et al. Microbial gene expression in soil: Methods, applications, and challenges. J Microbiol Meth 63 (2005) 1-19
21. Becker S., Fahrbach M., Böger P., and Ernst A. Quantitative tracing, by Taq nuclease assay, of Synechococcus ecotype in a highly diversified natural population. Appl and Environ Microbiol 68 (2002) 4486-4494
22. Kreader C.A. Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62 (1996) 1102-1106
23. Hartmann L.J., Coyne S.R., and Norwood D.A. Development of a novel internal positive control for Taqman based assays. Mol Cell Probes 19 (2005) 51-59
24. Wilson I. Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63 (1997) 3741-3751
25. Klocke M., Mundt K., Idler C., McEniry J., O'Kiely P., and Barth S. Monitoring Lactobacillus plantarum in grass silages with the aid of16S rDNA-based quantitative real-time PCR assays. Syst Appl Microbiol 29 (2006) 49-58
26. Rinttilä T., Kassinen A., Malinen E., Krogius L., and Palva A. Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in fecal samples by real-time PCR. J Appl Microbiol 97 (2004) 1166-1177
27. Rodrigues J., Aiello M., Urbance J., Tsoi T., and Tedje J. Use of both 16S rRNA and engeneered functional genes with real-time PCR to quantify an engeneered, PCB-degrading Rhodococcus in soil. J Microbiol Methods 51 (2002) 181-189
28. Stubner S. Quantification of Gram-negative sulphate reducing bacteria in rice field soil by 16s rRNA gene-targeted real-time PCR. J Microbiol Methods 57 (2004) 219-230
29. Smits T.H.M., Devenoges C., Szynalski K., Maillard J., and Holliger C. Development of a real-time PCR method for quantification of the three genera Dehalobacter, Dehalococcoides, and Desulfitobacterium in microbial communities. J Microbiol Methods 57 (2004) 369-378
30. Nogva H.K., and Rudi K. Potential influence of the first PCR cycles in real-time comparative gene quantifications. BioTechniques 37 (2004) 246-253