Establishment of a semi-automated pathogen DNA isolation from whole blood and comparison with commercially available kits

Journal of Microbiological Methods

Volumn 85, Issue 3, 2011, Pages 206-213

  Wiesinger Mayr, Herbert ^a   Jordana Lluch, Elena ^b   Martró, Elisa ^b,c   Schoenthaler, Silvia ^a   Noehammer, Christa ^a  

^a AIT AUSTRIAN INSTITUTE OF TECHNOLOGY   (Austria)

^b HOSPITAL UNIVERSITARI GERMANS TRIAS I PUJOL   (Spain)

^c CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

Author keywords

Automation; Bloodstream infection; DNA isolation; Molecular diagnostics; Sepsis

Indexed keywords

BACTERIAL DNA; RNA 16S;

ARTICLE; BACTERIAL CELL; BACTERIAL COUNT; BACTERIUM IDENTIFICATION; BLOOD ANALYSIS; CELL SUSPENSION; CENTRIFUGATION; CONTROLLED STUDY; CYTOLYSIS; DNA ISOLATION; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; LABORATORY AUTOMATION; LIMIT OF DETECTION; MICROARRAY ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SENSITIVITY ANALYSIS;

AUTOMATION; BACTERIA; BACTERIOLOGICAL TECHNIQUES; BLOOD CHEMICAL ANALYSIS; BLOOD-BORNE PATHOGENS; DNA, BACTERIAL; DNA, RIBOSOMAL; HUMANS; MICROARRAY ANALYSIS; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S;

BACTERIA (MICROORGANISMS);

EID: 79955094979     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2011.03.003     Document Type: Article

References (28)

1. Al-Soud W., Radstrom P. Effects of amplification facilitators on diagnostic PCR in the presence of blood, feces, and meat. J. Clin. Microbiol. 2000, 38:4463-4470.
2. Al-Soud W.A., Radstrom P. Purification and characterization of PCR-inhibitory components in blood cells. J. Clin. Microbiol. 2001, 39:485-493.
3. Al-Soud W.A., Ouis I.S., Li D.Q., Ljungh S., Wadstrom T. Characterization of the PCR inhibitory effect of bile to optimize real-time PCR detection of Helicobacter species. FEMS Immunol. Med. Microbiol. 2005, 44:177-182.
4. de Boer R., Peters R., Gierveld S., Schuurman T., Kooistra-Smid M., Savelkoul P. Improved detection of microbial DNA after bead-beating before DNA isolation. J. Microbiol. Methods 2010, 80:209-211.
5. Disque C., Mühl H., Lorenz M. High performance DNA clean-up. Euro. Biotech. News 2004, 3:44-45.
6. Disque C., Kaling M., Wolkersdorfer U.M., Lorenz M. Automatisierte Probenaufbereitung für die PCR-Diagnostik von Sepsis. BIOspectrum 2006, 1.
7. Duarte G.R., Price C.W., Littlewood J.L., Haverstick D.M., Ferrance J.P., Carrilho E., et al. Characterization of dynamic solid phase DNA extraction from blood with magnetically controlled silica beads. Analyst 2010, 135:531-537.
8. Dzik S., Aubuchon J., Jeffries L., Kleinman S., Manno C., Murphy M.F., et al. Leukocyte reduction of blood components: public policy, new technology. Transfus. Med. Rev. 2000, 14:34-52.
9. Handschur M., Karlic H., Hertel C., Pfeilstocker M., Haslberger A.G. Preanalytic removal of human DNA eliminates false signals in general 16S rDNA PCR monitoring of bacterial pathogens in blood. Comp. Immunol. Microbiol. Infect. Dis. 2009, 32:207-219.
10. Hansen W.L., Bruggeman C.A., Wolffs P.F. Evaluation of new preanalysis sample treatment tools and DNA isolation protocols to improve bacterial pathogen detection in whole blood. J. Clin. Microbiol. 2009, 47:2629-2631.
11. Jordan J.A., Durso M.B. Comparison of 16S rRNA gene PCR and BACTEC 9240 for detection of neonatal bacteremia. J. Clin. Microbiol. 2000, 38:2574-2578.
12. Kang K., Choi J., Nam J.H., Lee S.C., Kim K.J., Lee S.W., et al. Preparation and characterization of chemically functionalized silica-coated magnetic nanoparticles as a DNA separator. J. Phys. Chem. B 2009, 113:536-543.
13. Lehner A., Loy A., Behr T., Gaenge H., Ludwig W., Wagner M., et al. Oligonucleotide microarray for identification of Enterococcus species. FEMS Microbiol. Lett. 2005, 246:133-142.
14. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, et al. ARB: a software environment for sequence data. Nucleic Acids Res. 2004, 32:1363-1371.
15. Mahalanabis M., Al-Muayad H., Kulinski M.D., Altman D., Klapperich C.M. Cell lysis and DNA extraction of gram-positive and gram-negative bacteria from whole blood in a disposable microfluidic chip. Lab Chip 2009, 9:2811-2817.
16. Morin N., Vallaeys T., Hendrickx L., Natalie L., Wilmotte A. An efficient DNA isolation protocol for filamentous cyanobacteria of the genus Arthrospira. J. Microbiol. Methods 2010, 80:148-154.
17. Mothershed E.A., Whitney A.M. Nucleic acid-based methods for the detection of bacterial pathogens: present and future considerations for the clinical laboratory. Clin. Chim. Acta 2006, 363:206-220.
18. Muhl H., Kochem A.J., Disque C., Sakka S.G. 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. 2010, 66:41-49.
19. Nylund L., Heilig H.G., Salminen S., de Vos W.M., Satokari R. Semi-automated extraction of microbial DNA from feces for qPCR and phylogenetic microarray analysis. J. Microbiol. Methods 2010, 83:231-235.
20. Radstrom P., Knutsson R., Wolffs P., Lovenklev M., Lofstrom C. Pre-PCR processing: strategies to generate PCR-compatible samples. Mol. Biotechnol. 2004, 26:133-146.
21. Rock G., Berger R., Romans R.A., Russell N.M., Owens W.A. An in vitro method for predicting the efficacy of WBC separation using different starch preparations and anticoagulant ratios. Transfusion 2000, 40:1442-1445.
22. Schulz B., Weber K., Radecke C., Scheer C., Ruhnke M. Effect of different sample volumes on the DNA extraction of Aspergillus fumigatus from whole blood. Clin. Microbiol. Infect. 2009, 15:686-688.
23. Shang S., Chen G., Wu Y., DU L., Zhao Z. Rapid diagnosis of bacterial sepsis with PCR amplification and microarray hybridization in 16S rRNA gene. Pediatr. Res. 2005, 58:143-148.
24. Wellinghausen N., Kochem A.J., Disque C., Muhl H., Gebert S., Winter J., et al. Diagnosis of bacteremia in whole-blood samples by use of a commercial universal 16S rRNA gene-based PCR and sequence analysis. J. Clin. Microbiol. 2009, 47:2759-2765.
25. Wiesinger-Mayr H., Vierlinger K., Pichler R., Kriegner A., Hirschl A.M., Presterl E., et al. Identification of human pathogens isolated from blood using microarray hybridisation and signal pattern recognition. BMC Microbiol. 2007, 7:78.
26. Wilson I.G. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 1997, 63:3741-3751.
27. Wolffs P., Grage H., Hagberg O., Radstrom P. Impact of DNA polymerases and their buffer systems on quantitative real-time PCR. J. Clin. Microbiol. 2004, 42:408-411.
28. Yadav A.K., Wilson C.G., Prasad P.L., Menon P.K. Polymerase chain reaction in rapid diagnosis of neonatal sepsis. Indian Pediatr. 2005, 42:681-685.