Evaluation of Inhibitor-Resistant Real-Time PCR Methods for Diagnostics in Clinical and Environmental Samples

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Trombley Hall, Adrienne ^a   McKay Zovanyi, Ashley ^a   Christensen, Deanna Rose ^a   Koehler, Jeffrey William ^a   Devins Minogue, Timothy ^a  

^a UNITED STATES ARMY MEDICAL RESEARCH INSTITUTE OF INFECTIOUS DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; GENOMIC DNA;

ARTICLE; BACTERIUM IDENTIFICATION; BLOOD SAMPLING; CONTROLLED STUDY; DIAGNOSTIC KIT; FECES ANALYSIS; FRANCISELLA TULARENSIS; GENE IDENTIFICATION; LIMIT OF DETECTION; NONHUMAN; PHIRE HOT START DNA POLYMERASE; PHUSION BLOOD DIRECT POLYMERASE CHAIN REACTION KIT; POLYMERASE CHAIN REACTION BOOST; PROCESS OPTIMIZATION; REAL TIME POLYMERASE CHAIN REACTION; SOIL ANALYSIS; SPUTUM ANALYSIS; STR BOOST; TERRA POLYMERASE CBAIN REACTION DIRECT POLYMERASE MIX;

DNA, BACTERIAL; ENVIRONMENTAL MICROBIOLOGY; FRANCISELLA TULARENSIS; HUMANS; REAGENT KITS, DIAGNOSTIC; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 84883625478     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0073845     Document Type: Article

References (24)

1. Shchelkunov SN, Shcherbakov DN, Maksyutov RA, Gavrilova EV, (2011) Species-specific identification of variola, monkeypox, cowpox, and vaccinia viruses by multiplex real-time PCR assay. J Virol Methods 175: 163-169. doi:10.1016/j.jviromet.2011.05.002. PubMed: 21635922.
2. Tomaso H, Jacob D, Eickhoff M, Scholz HC, Al Dahouk S, et al. (2008) Preliminary validation of real-time PCR assays for the identification of Yersinia pestis. Clin Chem Lab Med 46: 1239-1244. PubMed: 18783342.
3. Skottman T, Piiparinen H, Hyytiäinen H, Myllys V, Skurnik M, et al. (2007) Simultaneous real-time PCR detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis. Eur J Clin Microbiol Infect Dis 26: 207-211. doi:10.1007/s10096-007-0262-z. PubMed: 17294160.
4. Christensen DR, Hartman LJ, Loveless BM, Frye MS, Shipley MA, et al. (2006) Detection of biological threat agents by real-time PCR: comparison of assay performance on the R.A.P.I.D., the LightCycler, and the Smart Cycler platforms. Clin Chem 52: 141-145. doi:10.1373/clinchem.2005.052522. PubMed: 16391330.
5. Ryu C, Lee K, Yoo C, Seong WK, Oh HB, (2003) Sensitive and rapid quantitative detection of anthrax spores isolated from soil samples by real-time PCR. Microbiol Immunol 47: 693-699. PubMed: 14605435.
6. Makino SI, Cheun HI, Watarai M, Uchida I, Takeshi K, (2001) Detection of anthrax spores from the air by real-time PCR. Lett Appl Microbiol 33: 237-240. doi:10.1046/j.1472-765x.2001.00989.x. PubMed: 11555211.
7. Higgins JA, Ezzell J, Hinnebusch BJ, Shipley M, Henchal EA, et al. (1998) 5' nuclease PCR assay to detect Yersinia pestis. J Clin Microbiol 36: 2284-2288. PubMed: 9666006.
8. Belgrader P, Benett W, Hadley D, Long G, Mariella R Jr., et al. (1998) Rapid pathogen detection using a microchip PCR array instrument. Clin Chem 44: 2191-2194. PubMed: 9761255.
9. Wong ML, Medrano JF, (2005) Real-time PCR for mRNA quantitation. BioTechniques 39: 75-85. doi:10.2144/05391RV01. PubMed: 16060372.
10. Wilson IG, (1997) Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63: 3741-3751. PubMed: 9327537.
11. Akane A, Matsubara K, Nakamura H, Takahashi S, Kimura K, (1994) Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification. J Forensic Sci 39: 362-372. PubMed: 8195750.
12. Monteiro L, Bonnemaison D, Vekris A, Petry KG, Bonnet J, et al. (1997) Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. J Clin Microbiol 35: 995-998. PubMed: 9157172.
13. Widjojoatmodjo MN, Fluit AC, Torensma R, Verdonk GP, Verhoef J, (1992) The magnetic immuno polymerase chain reaction assay for direct detection of salmonellae in fecal samples. J Clin Microbiol 30: 3195-3199. PubMed: 1452702.
14. Tsai YL, Olson BH, (1992) Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl Environ Microbiol 58: 754-757. PubMed: 1610201.
15. Shipley MA, Koehler JW, Kulesh DA, Minogue TD, (2012) Comparison of nucleic acid extraction platforms for detection of select biothreat agents for use in clinical resource limited settings. J Microbiol Methods 91: 179-183. doi:10.1016/j.mimet.2012.06.008. PubMed: 22750394.
16. Rådström P, Knutsson R, Wolffs P, Lövenklev M, Löfström C, (2004) Pre-PCR processing: strategies to generate PCR-compatible samples. Mol Biotechnol 26: 133-146. doi:10.1385/MB:26:2:133. PubMed: 14764939.
17. Klein A, Barsuk R, Dagan S, Nusbaum O, Shouval D, et al. (1997) Comparison of methods for extraction of nucleic acid from hemolytic serum for PCR amplification of hepatitis B virus DNA sequences. J Clin Microbiol 35: 1897-1899. PubMed: 9196220.
18. Abu Al-Soud W, Rådström P, (2000) Effects of amplification facilitators on diagnostic PCR in the presence of blood, feces, and meat. J Clin Microbiol 38: 4463-4470. PubMed: 11101581.
19. Kreader CA, (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62: 1102-1106. PubMed: 8975603.
20. Kermekchiev MB, Kirilova LI, Vail EE, Barnes WM, (2009) Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples. Nucleic Acids Res 37: e40. doi:10.1093/nar/gkp361. PubMed: 19208643.
21. Kramvis A, Bukofzer S, Kew MC, (1996) Comparison of hepatitis B virus DNA extractions from serum by the QIAamp blood kit, GeneReleaser, and the phenol-chloroform method. J Clin Microbiol 34: 2731-2733. PubMed: 8897174.
22. Zhang Z, Kermekchiev MB, Barnes WM, (2010) Direct DNA amplification from crude clinical samples using a PCR enhancer cocktail and novel mutants of Taq. J Mol Diagn 12: 152-161. doi:10.2353/jmoldx.2010.090070. PubMed: 20075207.
23. Holland PM, Abramson RD, Watson R, Gelfand DH, (1991) Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci U S A 88: 7276-7280. doi:10.1073/pnas.88.16.7276. PubMed: 1871133.
24. Abu Al-Soud W, Râdström P, (1998) Capacity of nine thermostable DNA polymerases To mediate DNA amplification in the presence of PCR-inhibiting samples. Appl Environ Microbiol 64: 3748-3753. PubMed: 9758794.