Obstacles of multiplex real-time PCR for bacterial 16S rDNA: Primer specifity and DNA decontamination of Taq polymerase

Transfusion Medicine and Hemotherapy

Volumn 37, Issue 1, 2010, Pages 21-28

  Philipp, Sebastian ^a   Huemer, Hartwig P ^a   Irschick, Eveline U ^a   Gassner, Christoph ^b  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

^b UNIVERSITY HOSPITAL INNSBRUCK   (Austria)

Author keywords

DNA decontamination methods; Taq polymerase depleteted of bacterial DNA contamination

Indexed keywords

BACTERIAL DNA; DNA 16S; RESTRICTION ENDONUCLEASE; RESTRICTION ENDONUCLEASE SAU 3A1; TAQ POLYMERASE; UNCLASSIFIED DRUG;

ARTICLE; COLONY FORMING UNIT; CONTROLLED STUDY; ESCHERICHIA COLI; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; MICROFILTRATION; MYCOBACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; REAL TIME POLYMERASE CHAIN REACTION; STAPHYLOCOCCUS EPIDERMIDIS; UNINDEXED SEQUENCE;

EID: 77149141969     PISSN: 16603796     EISSN: None     Source Type: Journal    
DOI: 10.1159/000265571     Document Type: Article

References (23)

1. Mothershed EA, Whitney AM: Nucleic acid-based methods for the detection of bacterial pathogens: present and future considerations for the clinical laboratory. Clin Chim Acta 2006;363(1-2):206-20.
2. Barken KB, Haagensen JA, Tolker-Nielsen T: Advances in nucleic acid-based diagnostics of bacterial infections. Clin Chim Acta 2007;384(1-2):1-11.
3. Zhang T, Fang HH: Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl Microbiol Biotechnol 2006;70(3):281-9.
4. Corless CE, Guiver M, Borrow R, Edwards-Jones V, Kaczmarski EB, Fox AJ: Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J Clin Microbiol 2000;38(5):1747-52.
5. Rand KH, Houck H: Taq polymerase contains bacterial DNA of unknown origin. Mol Cell Probes 1990;4(6):445-50.
6. Corless CE, Guiver M, Borrow R, Edwards-Jones V, Fox AJ, Kaczmarski EB: Simultaneous detection of Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae in suspected cases of meningitis and septicemia using real-time PCR. J Clin Microbiol 2001;39(4):1553-8.
7. Carroll NM, Adamson P, Okhravi N: Elimination of bacterial DNA from Taq DNA polymerases by restriction endonuclease digestion. J Clin Microbiol 1999;37(10):3402-4.
8. Klaschik S, Lehmann LE, Raadts A, Hoeft A, Stuber F: Comparison of different decontamination methods for reagents to detect low concentrations of bacterial 16S DNA by real-time-PCR. Mol Biotechnol 2002;22(3):231-42.
9. Silkie SS, Tolcher MP, Nelson KL: Reagent decontamination to eliminate false-positives in Escherichia coli qPCR. J Microbiol Methods 2008; 72(3):275-82.
10. Yang S, Lin S, Kelen GD, Quinn TC, Dick JD, Gaydos CA, Rothman RE: Quantitative multiprobe PCR assay for simultaneous detection and identification to species level of bacterial pathogens. J Clin Microbiol 2002;40(9):3449-54.
11. Bremer H, Dennis PP: Escherichia coli and Salmonella typhimurium; in Neidhardt FC, Curtiss R III, Ingraham JL, Lin ECC, Low KB, et al. (eds): Cellular and Molecular Biology. Washington, DC, American Society for Microbiology, 1996, pp 1553-1569.
12. Klappenbach JA, Saxman PR, Cole JR, Schmidt TM: rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res 2001;29(1):181-4.
13. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, et al: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998;393(6685):537-44.
14. Mohammadi T, Pietersz RN, Vandenbroucke-Grauls CM, Savelkoul PH, Reesink HW: Detection of bacteria in platelet concentrates: comparison of broad-range real-time 16S rDNA polymerase chain reaction and automated culturing. Transfusion 2005;45(5):731-6.
15. Petershofen EK, Fislage R, Faber R, Schmidt H, Roth WK, Seifried E: Detection of nucleic acid sequences from bacterial species with molecular genetic methods. Transfus Sci 2000;23(1):21-7.
16. Rueckert A, Morgan HW: Removal of contaminating DNA from polymerase chain reaction using ethidium monoazide. J Microbiol Methods 2007; 68(3):596-600.
17. Tondeur S, Agbulut O, Menot ML, Larghero J, Paulin D, et al: Overcoming bacterial DNA contamination in real-time PCR and RT-PCR reactions for LacZ detection in cell therapy monitoring. Mol Cell Probes 2004;18(6):437-41.
18. Nadkarni MA, Martin FE, Jacques NA, Hunter N: Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology. 2002;148(Pt 1):257-66.
19. Mühl H, Kochem AJ, Disqué C, Sakka SG: Activity and DNA contamination of commercial polymerase chain reaction reagents for the universal 16S rDNA real-time polymerase chain reaction detection of bacterial pathogens in blood. Diagn Microbiol Infect Dis 2008; doi:10.1016/j.diagmicrobio. 2008.07.011.
20. Erlich HA, Gelfand D, Sninsky JJ: Recent advances in the polymerase chain reaction. Science 1991; 252(5013):1643-51.
21. Schmidt M, Hourfar MK, Heck J, Weis C, Montag T, Nicol SB, Seifried E: Scansystem™ enables rapid and sensitive bacterial detection in platelets stored in additive solution with implementation of standard positive control capsules. Transfus Med Hemother 2006;33(3):274-8.
22. Corash L: Inactivation of viruses, bacteria, protozoa and leukocytes in platelet and red cell concentrates. Dev Biol (Basel) 2000;102:115-23.
23. van Rhenen D, Gulliksson H, Cazenave JP, et al: Transfusion of pooled buffy coat platelet components prepared with photochemical pathogen inactivation treatment: the euroSPRITE trial. Blood 2003;101:2426-33.