European Journal of Microbiology and Immunology
Volume/Issue:
Volume 5: Issue 1
Comparison of an automated nucleic acid extraction system with the column-based procedure
Authors:
Hagen Frickmann

Search for other papers by Hagen Frickmann in
Current site
Google Scholar
PubMed Close
,
Rebecca Hinz German Armed Forces Hospital of Hamburg Department of Tropical Medicine at the Bernhard Nocht Institute Bernhard Nocht street 74 D-20359 Hamburg Germany

Search for other papers by Rebecca Hinz in
Current site
Google Scholar
PubMed Close
, and
Ralf Hagen German Armed Forces Hospital of Hamburg Department of Tropical Medicine at the Bernhard Nocht Institute Bernhard Nocht street 74 D-20359 Hamburg Germany

Search for other papers by Ralf Hagen in
Current site
Google Scholar
PubMed Close
Pages:
94–102
Online Publication Date:
26 Mar 2015
Publication Date:
01 Mar 2015
Article Category:
Research Article
DOI:
https://doi.org/10.1556/eujmi-d-14-00040
Keywords:
nucleic acid extraction; DNA; RNA; column; EZ1; automate; inhibition
Open access

Here, we assessed the extraction efficiency of a deployable bench-top nucleic acid extractor EZ1 in comparison to the column-based approach with complex sample matrices.A total of 48 EDTA blood samples and 81 stool samples were extracted by EZ1 automated extraction and the column-based QIAamp DNA Mini Kit. Blood sample extractions were assessed by two real-time malaria PCRs, while stool samples were analyzed by six multiplex real-time PCR assays targeting bacterial, viral, and parasitic stool pathogens. Inhibition control PCR testing was performed as well.In total, 147 concordant and 13 discordant pathogen-specific PCR results were obtained. The latter comprised 11 positive results after column-based extraction only and two positive results after EZ1 extraction only. EZ1 extraction showed a higher frequency of inhibition. This phenomenon was, however, inconsistent for the different PCR schemes. In case of concordant PCR results, relevant differences of cycle threshold numbers for the compared extraction schemes were not observed.Switches from well-established column-based extraction to extraction with the automated EZ1 system do not lead to a relevantly reduced yield of target DNA when complex sample matrices are used. If sample inhibition is observed, column-based extraction from another sample aliquot may be considered.

  • Akutsu T, Kitayama T, Watanabe K, Sakurada K: Comparison of automated and manual purification of total RNA for mRNA-based identification of body fluids. Forensic Sci Int Genet 14, 11–17 (2015) [Epub Sep 17, 2014]

    Sakurada K , 'Comparison of automated and manual purification of total RNA for mRNA-based identification of body fluids ' (2015 ) 14 Forensic Sci Int Genet : 11 -17 .

    • Search Google Scholar

  • Aebischer A, Beer M, Hoffmann B: Development and validation of rapid magnetic particle based extraction protocols. Virol J 11, 137 (2014)

    Hoffmann B , 'Development and validation of rapid magnetic particle based extraction protocols ' (2014 ) 11 Virol J : 137 -.

    • Search Google Scholar

  • Perry MD, White PL, Barnes RA: Comparison of four automated nucleic acid extraction platforms for the recovery of DNA from Aspergillus fumigatus. J Med Microbiol 63(Pt 9), 1160–1166 (2014)

    Barnes RA , 'Comparison of four automated nucleic acid extraction platforms for the recovery of DNA from Aspergillus fumigatus ' (2014 ) 63 J Med Microbiol : 1160 -1166 .

    • Search Google Scholar

  • Kim Y, Han MS, Kim J, Kwon A, Lee KA: Evaluation of three automated nucleic acid extraction systems for identification of respiratory viruses in clinical specimens by multiplex real-time PCR. Biomed Res Int 2014, 430650 (2014)

    Lee KA , 'Evaluation of three automated nucleic acid extraction systems for identification of respiratory viruses in clinical specimens by multiplex real-time PCR ' (2014 ) 2014 Biomed Res Int : 430650 -.

    • Search Google Scholar

  • Kalina WV, Douglas CE, Coyne SR, Minogue TD: Comparative assessment of automated nucleic acid sample extraction equipment for biothreat agents. J Clin Microbiol 52, 1232–1234 (2014)

    Minogue TD , 'Comparative assessment of automated nucleic acid sample extraction equipment for biothreat agents ' (2014 ) 52 J Clin Microbiol : 1232 -1234 .

    • Search Google Scholar

  • Fujii K, Inokuchi S, Kitayama T, Nakahara H, Mizuno N, Sekiguchi K: A comparison of DNA extraction using AutoMate Express™ and EZ1 advanced XL from liquid blood, bloodstains, and semen stains. J Forensic Sci 58, 981–988 (2013)

    Sekiguchi K , 'A comparison of DNA extraction using AutoMate Express™ and EZ1 advanced XL from liquid blood, bloodstains, and semen stains ' (2013 ) 58 J Forensic Sci : 981 -988 .

    • Search Google Scholar

  • Khelaifia S, Ramonet PY, Bedotto Buffet M, Drancourt M: A semi-automated protocol for Archaea DNA extraction from stools. BMC Res Notes 6, 186 (2013)

    Drancourt M , 'A semi-automated protocol for Archaea DNA extraction from stools ' (2013 ) 6 BMC Res Notes : 186 -.

    • Search Google Scholar

  • Yama IN, Garba M, Britton-Davidian J, Thiberville SD, Dobigny G, Gould EA, de Lamballerie X, Charrel RN: Comparative analysis of rodent tissue preservation methods and nucleic acid extraction techniques for virus screening purposes. J Virol Methods 189, 311–316 (2013)

    Charrel RN , 'Comparative analysis of rodent tissue preservation methods and nucleic acid extraction techniques for virus screening purposes ' (2013 ) 189 J Virol Methods : 311 -316 .

    • Search Google Scholar

  • Sam SS, Lebel KA, Bissaillon CL, Tafe LJ, Tsongalis GJ, Lefferts JA: Automation of genomic DNA isolation from formalin-fixed, paraffin-embedded tissues. Pathol Res Pract 208, 705–707 (2012)

    Lefferts JA , 'Automation of genomic DNA isolation from formalin-fixed, paraffin-embedded tissues ' (2012 ) 208 Pathol Res Pract : 705 -707 .

    • Search Google Scholar

  • Brownlow RJ, Dagnall KE, Ames CE: A comparison of DNA collection and retrieval from two swab types (cotton and nylon flocked swab) when processed using three QIAGEN extraction methods. J Forensic Sci 57, 713–717 (2012)

    Ames CE , 'A comparison of DNA collection and retrieval from two swab types (cotton and nylon flocked swab) when processed using three QIAGEN extraction methods ' (2012 ) 57 J Forensic Sci : 713 -717 .

    • Search Google Scholar

  • Davis CP, King JL, Budowle B, Eisenberg AJ, Turnbough MA: Extraction platform evaluations: a comparison of AutoMate Express™, EZ1® Advanced XL, and Maxwell® 16 Bench-top DNA extraction systems. Leg Med (Tokyo) 14, 36–39 (2012)

    Turnbough MA , 'Extraction platform evaluations: a comparison of AutoMate Express™, EZ1® Advanced XL, and Maxwell® 16 Bench-top DNA extraction systems ' (2012 ) 14 Leg Med (Tokyo) : 36 -39 .

    • Search Google Scholar

  • Liégeois F, Boué V, Mouinga-Ondémé A, Lékané DK, Mongo D, Sica J, Rouet F: Suitability of an open automated nucleic acid extractor for high-throughput plasma HIV-1 RNA quantitation in Gabon (Central Africa). J Virol Methods 179, 269–271 (2012)

    Rouet F , 'Suitability of an open automated nucleic acid extractor for high-throughput plasma HIV-1 RNA quantitation in Gabon (Central Africa) ' (2012 ) 179 J Virol Methods : 269 -271 .

    • Search Google Scholar

  • Bravo D, Clari MÁ, Costa E, Muñoz-Cobo B, Solano C, José Remigia M, Navarro D: Comparative evaluation of three automated systems for DNA extraction in conjunction with three commercially available real-time PCR assays for quantitation of plasma Cytomegalovirus DNAemia in allogeneic stem cell transplant recipients. J Clin Microbiol 49, 2899–2904 (2011)

    Navarro D , 'Comparative evaluation of three automated systems for DNA extraction in conjunction with three commercially available real-time PCR assays for quantitation of plasma Cytomegalovirus DNAemia in allogeneic stem cell transplant recipients ' (2011 ) 49 J Clin Microbiol : 2899 -2904 .

    • Search Google Scholar

  • Persson S, de Boer RF, Kooistra-Smid AM, Olsen KE: Five commercial DNA extraction systems tested and compared on a stool sample collection. Diagn Microbiol Infect Dis 69, 240–244 (2011)

    Olsen KE , 'Five commercial DNA extraction systems tested and compared on a stool sample collection ' (2011 ) 69 Diagn Microbiol Infect Dis : 240 -244 .

    • Search Google Scholar

  • Yang G, Erdman DE, Kodani M, Kools J, Bowen MD, Fields BS: Comparison of commercial systems for extraction of nucleic acids from DNA/RNA respiratory pathogens. J Virol Methods 171, 195–199 (2011)

    Fields BS , 'Comparison of commercial systems for extraction of nucleic acids from DNA/RNA respiratory pathogens ' (2011 ) 171 J Virol Methods : 195 -199 .

    • Search Google Scholar

  • Miller S, Seet H, Khan Y, Wright C, Nadarajah R: Comparison of QIAGEN automated nucleic acid extraction methods for CMV quantitative PCR testing. Am J Clin Pathol 133, 558–563 (2010)

    Nadarajah R , 'Comparison of QIAGEN automated nucleic acid extraction methods for CMV quantitative PCR testing ' (2010 ) 133 Am J Clin Pathol : 558 -563 .

    • Search Google Scholar

  • Yera H, Filisetti D, Bastien P, Ancelle T, Thulliez P, Delhaes L: Multicenter comparative evaluation of five commercial methods for toxoplasma DNA extraction from amniotic fluid. J Clin Microbiol 47, 3881–3886 (2009)

    Delhaes L , 'Multicenter comparative evaluation of five commercial methods for toxoplasma DNA extraction from amniotic fluid ' (2009 ) 47 J Clin Microbiol : 3881 -3886 .

    • Search Google Scholar

  • Schneider GJ, Kuper KG, Abravaya K, Mullen CR, Schmidt M, Bunse-Grassmann A, Sprenger-Haussels M: Performance evaluation of the QIAGEN EZ1 DSP Virus Kit with Abbott RealTime HIV-1, HBV and HCV assays. J Clin Virol 44, 292–296 (2009)

    Sprenger-Haussels M , 'Performance evaluation of the QIAGEN EZ1 DSP Virus Kit with Abbott RealTime HIV-1, HBV and HCV assays ' (2009 ) 44 J Clin Virol : 292 -296 .

    • Search Google Scholar

  • Dundas N, Leos NK, Mitui M, Revell P, Rogers BB: Comparison of automated nucleic acid extraction methods with manual extraction. J Mol Diagn 10, 311–316 (2008)

    Rogers BB , 'Comparison of automated nucleic acid extraction methods with manual extraction ' (2008 ) 10 J Mol Diagn : 311 -316 .

    • Search Google Scholar

  • Michelin BD, Hadzisejdic I, Bozic M, Grahovac M, Hess M, Grahovac B, Marth E, Kessler HH: Detection of cytomegalovirus (CMV) DNA in EDTA whole-blood samples: evaluation of the quantitative artus CMV LightCycler PCR kit in conjunction with automated sample preparation. J Clin Microbiol 46, 1241–1245 (2008)

    Kessler HH , 'Detection of cytomegalovirus (CMV) DNA in EDTA whole-blood samples: evaluation of the quantitative artus CMV LightCycler PCR kit in conjunction with automated sample preparation ' (2008 ) 46 J Clin Microbiol : 1241 -1245 .

    • Search Google Scholar

  • Legler TJ, Liu Z, Mavrou A, Finning K, Hromadnikova I, Galbiati S, Meaney C, Hultén MA, Crea F, Olsson ML, Maddocks DG, Huang D, Fisher SA, Sprenger-Haussels M, Soussan AA, van der Schoot CE: Workshop report on the extraction of foetal DNA from maternal plasma. Prenat Diagn 27, 824–829 (2007)

    Schoot CE , 'Workshop report on the extraction of foetal DNA from maternal plasma ' (2007 ) 27 Prenat Diagn : 824 -829 .

    • Search Google Scholar

  • Kishore R, Reef Hardy W, Anderson VJ, Sanchez NA, Buoncristiani MR: Optimization of DNA extraction from low-yield and degraded samples using the BioRobot EZ1 and BioRobot MJ Forensic Sci 51, 1055–1061 (2006)

    Buoncristiani MR , 'Optimization of DNA extraction from low-yield and degraded samples using the BioRobot EZ1 and BioRobot MJ ' (2006 ) 51 Forensic Sci : 1055 -1061 .

    • Search Google Scholar

  • Barkham T: BioRobot EZ1 workstation compares well with manual spin kits for extraction of viral RNA from sera and saves substantial staff time. J Clin Microbiol 44, 1598 (2006)

    Barkham T , 'BioRobot EZ1 workstation compares well with manual spin kits for extraction of viral RNA from sera and saves substantial staff time ' (2006 ) 44 J Clin Microbiol : 1598 -.

    • Search Google Scholar

  • Tang YW, Sefers SE, Li H, Kohn DJ, Procop GW: Comparative evaluation of three commercial systems for nucleic acid extraction from urine specimens. J Clin Microbiol 43, 4830–4833 (2005)

    Procop GW , 'Comparative evaluation of three commercial systems for nucleic acid extraction from urine specimens ' (2005 ) 43 J Clin Microbiol : 4830 -4833 .

    • Search Google Scholar

  • Montpetit SA, Fitch IT, O’Donnell PT: A simple automated instrument for DNA extraction in forensic casework. J Forensic Sci 50, 555–563 (2005)

    O’Donnell PT , 'A simple automated instrument for DNA extraction in forensic casework ' (2005 ) 50 J Forensic Sci : 555 -563 .

    • Search Google Scholar

  • Anslinger K, Bayer B, Rolf B, Keil W, Eisenmenger W: Application of the BioRobot EZ1 in a forensic laboratory. Leg Med (Tokyo) 7, 164–168 (2005)

    Eisenmenger W , 'Application of the BioRobot EZ1 in a forensic laboratory ' (2005 ) 7 Leg Med (Tokyo) : 164 -168 .

    • Search Google Scholar

  • Scholl PF, Kongkasuriyachai D, Demirev PA, Feldman AB, Lin JS, Sullivan DJ Jr, Kumar N: Rapid detection of malaria infection in vivo by laser desorption mass spectrometry. Am J Trop Med Hyg 71, 546–551 (2004)

    Kumar N , 'Rapid detection of malaria infection in vivo by laser desorption mass spectrometry ' (2004 ) 71 Am J Trop Med Hyg : 546 -551 .

    • Search Google Scholar

  • Nyunt M, Pisciotta J, Feldman AB, Thuma P, Scholl PF, Demirev PA, Lin JS, Shi L, Kumar N, Sullivan DJ Jr: Detection of Plasmodium falciparum in pregnancy by laser desorption mass spectrometry. Am J Trop Med Hyg 73, 485–490 (2005)

    Sullivan DJ , 'Detection of Plasmodium falciparum in pregnancy by laser desorption mass spectrometry ' (2005 ) 73 Am J Trop Med Hyg : 485 -490 .

    • Search Google Scholar

  • Mangold KA, Manson RU, Koay ES, Stephens L, Regner M, Thomson RB Jr, Peterson LR, Kaul KL: Real-time PCR for detection and identification of Plasmodium spp. J Clin Microbiol 43, 2435–2440 (2005)

    Kaul KL , 'Real-time PCR for detection and identification of Plasmodium spp ' (2005 ) 43 J Clin Microbiol : 2435 -2440 .

    • Search Google Scholar

  • Wiemer D, Loderstaedt U, von Wulffen H, Priesnitz S, Fischer M, Tannich E, Hagen RM: Real-time multiplex PCR for simultaneous detection of Campylobacter jejuni, Salmonella, Shigella, and Yersinia species in fecal samples. Int J Med Microbiol 311, 577–584 (2011)

    Hagen RM , 'Real-time multiplex PCR for simultaneous detection of Campylobacter jejuni, Salmonella, Shigella, and Yersinia species in fecal samples ' (2011 ) 311 Int J Med Microbiol : 577 -584 .

    • Search Google Scholar

  • Frickmann H, Dekker D, Boahen K, Acquah S, Sarpong N, Adu-Sarkodie Y, Schwarz NG, May J, Marks F, Poppert S, Wiemer DF, Hagen RM. Increased detection of invasive enteropathogenic bacteria in pre-incubated blood culture materials by real-time PCR in comparison with automated incubation in Sub-Saharan Africa. Scan J Infect Dis 45, 616–622 (2013)

    Hagen RM , 'Increased detection of invasive enteropathogenic bacteria in pre-incubated blood culture materials by real-time PCR in comparison with automated incubation in Sub-Saharan Africa ' (2013 ) 45 Scan J Infect Dis : 616 -622 .

    • Search Google Scholar

  • Frickmann H, Schwarz NG, Wiemer DF, Fischer M, Tannich E, Scheid PL, Müller M, Schotte U, Bock W, Hagen RM: Food and drinking water hygiene and intestinal protozoa in deployed German soldiers. Eu J Microbiol Immunol (Bd.) 1, 53–60 (2013)

    Hagen RM , 'Food and drinking water hygiene and intestinal protozoa in deployed German soldiers ' (2013 ) 1 Eu J Microbiol Immunol (Bd.) : 53 -60 .

    • Search Google Scholar

  • Verweij JJ, Laeijendecker D, Brienen EAT, van Lieshout L, Polderman AM: Detection of Cyclospora cayetanensis in travellers returning from the tropics and subtropics using microscopy and real-time PCR. Int J Med Microbiol 293, 199–202 (2003)

    Polderman AM , 'Detection of Cyclospora cayetanensis in travellers returning from the tropics and subtropics using microscopy and real-time PCR ' (2003 ) 293 Int J Med Microbiol : 199 -202 .

    • Search Google Scholar

  • Verweij JJ, Blange RA, Templeton K, Schinkel J, Brienen EA, von Rooyen MA, van Lieshout L, Polderman AM: Simultaneous detection of Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum in fecal samples by using multiplex real-time PCR. J Clin Microbiol 42, 1220–1223 (2003)

    Polderman AM , 'Simultaneous detection of Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum in fecal samples by using multiplex real-time PCR ' (2003 ) 42 J Clin Microbiol : 1220 -1223 .

    • Search Google Scholar

  • Niesters HGM: Quantitation of viral load using real-time amplification techniques. Methods 25, 419–429 (2001)

    Niesters HGM , 'Quantitation of viral load using real-time amplification techniques ' (2001 ) 25 Methods : 419 -429 .

    • Search Google Scholar

  • Frickmann H, Tenner-Racz K, Eggert P, Schwarz NG, Poppert S, Tannich E, Hagen RM: Influence of parasite density and sample storage time on the reliability of Entamoeba histolytica-specific PCR from formalin-fixed and paraffin-embedded tissues. Diagn Mol Pathol 22, 236–244 (2013)

    Hagen RM , 'Influence of parasite density and sample storage time on the reliability of Entamoeba histolytica-specific PCR from formalin-fixed and paraffin-embedded tissues ' (2013 ) 22 Diagn Mol Pathol : 236 -244 .

    • Search Google Scholar
  • Collapse
  • Expand
Cover European Journal of Microbiology and Immunology
European Journal of Microbiology and Immunology
Print ISSN:
2062-509X
Online ISSN:
2062-8633

Senior editors

Editor(s)-in-Chief: Dunay, Ildiko Rita, Prof. Dr. Pharm, Dr. rer. nat., University of Magdeburg, Germany

Editor(s)-in-Chief: Heimesaat, Markus M., Prof. Dr. med., Charité - University Medicine Berlin, Germany

Editorial Board

  • Berit Bangoura, Dr. DVM. PhD,  University of Wyoming, USA
  • Stefan Bereswill, Prof. Dr. rer. nat., Charité - University Medicine Berlin, Germany
  • Dunja Bruder, Prof. Dr. rer. nat., University of Magdeburg, Germany
  • Jan Buer, Prof. Dr. med., University of Duisburg, Germany
  • Edit Buzas, Prof. Dr. med., Semmelweis University, Hungary
  • Renato Damatta, Prof. PhD, UENF, Brazil
  • Maria Deli, MD, PhD, DSc, Biological Research Center, HAS, Hungary
  • Olgica Djurković-Djaković, Prof. Phd, University of Belgrade, Serbia
  • Jean-Dennis Docquier, Prof. Dr. med., University of Siena, Italy
  • Zsuzsanna Fabry, Prof. Phd, University of Washington, USA
  • Ralf Ignatius, Prof. Dr. med., Charité - University Medicine Berlin, Germany
  • Achim Kaasch, Prof. Dr. med., Otto von Guericke University Magdeburg, Germany
  • Oliver Liesenfeld, Prof. Dr. med., Inflammatix, USA
  • Matyas Sandor, Prof. PhD, University of Wisconsin, USA
  • Ulrich Steinhoff, Prof. PhD, University of Marburg, Germany
  • Michal Toborek, Prof. PhD, University of Miami, USA
  • Susanne A. Wolf, PhD, MDC-Berlin, Germany

 

Dr. Dunay, Ildiko Rita
Magdeburg, Germany
E-mail: ildiko.dunay@med.ovgu.de

Indexing and Abstracting Services:

  • PubMed Central
  • Scopus
  • ESCI
  • CABI
  • CABELLS Journalytics

 

2023  
Web of Science  
Total Cites
WoS		 674
Journal Impact Factor 3.3
Rank by Impact Factor

Q2
Impact Factor
without
Journal Self Cites		 3.1
5 Year
Impact Factor		 3.2
Scimago  
Scimago
H-index		 15
Scimago
Journal Rank		 0.601
Scimago Quartile Score Microbiology (medical) (Q2)
Microbiology (Q3)
Immunology and Allergy (Q3)
Immunology (Q3)
Scopus  
Scopus
Cite Score		 5.0
Scopus
CIte Score Rank		 Microbiology (medical) Q2
Scopus
SNIP		 0.832

 

European Journal of Microbiology and Immunology
Publication Model Gold Open Access
Online only
Submission Fee none
Article Processing Charge 600 EUR/article
Regional discounts on country of the funding agency World Bank Lower-middle-income economies: 50%
World Bank Low-income economies: 100%
Further Discounts Editorial Board / Advisory Board members: 50%
Corresponding authors, affiliated to an EISZ member institution subscribing to the journal package of Akadémiai Kiadó: 100%
Subscription Information Gold Open Access
Purchase per Title  

European Journal of Microbiology and Immunology
Language English
Size A4
Year of
Foundation		 2011
Volumes
per Year		 1
Issues
per Year		 4
Founder Akadémiai Kiadó
Founder's
Address		 H-1117 Budapest, Hungary 1516 Budapest, PO Box 245.
Publisher Akadémiai Kiadó
Publisher's
Address		 H-1117 Budapest, Hungary 1516 Budapest, PO Box 245.
Responsible
Publisher		 Chief Executive Officer, Akadémiai Kiadó
ISSN 2062-509X (Print)
ISSN 2062-8633 (Online)

Monthly Content Usage

Abstract Views Full Text Views PDF Downloads
Apr 2024 0 29 4
May 2024 0 33 9
Jun 2024 0 48 10
Jul 2024 0 67 5
Aug 2024 0 67 19
Sep 2024 0 51 15
Oct 2024 0 27 8