Authors:
Sonja Obersteller University of Hamburg, Hamburg, Germany

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Heinrich Neubauer Federal Research Institute for Animal Health, Jena, Germany

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Ralf Matthias Hagen NATO Center of Excellence for Military Medicine (MilMedCOE), Munich, Germany

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Hagen Frickmann German Armed Forces Hospital of Hamburg, Bernhard Nocht street 74, 20359 Hamburg, Germany
German Armed Forces Hospital of Hamburg, Bernhard Nocht street 74, 20359 Hamburg, Germany

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Open access

The extraction and further processing of nucleic acids (NA) from formalin-fixed paraffin-embedded (FFPE) tissues for microbiological diagnostic polymerase chain reaction (PCR) approaches is challenging. Here, we assessed the effects of five different commercially available nucleic acid extraction kits on the results of real-time PCR.

FFPE samples from organs of Burkholderia pseudomallei-infected Swiss mice were subjected to processing with five different extraction kits from QIAGEN (FFPE DNA Tissue Kit, EZ1 DNA Tissue Kit, DNA Mini Kit, DNA Blood Mini Kit, and FlexiGene DNA Kit) in combination with three different real-time PCRs targeting B. pseudomallei-specific sequences of varying length after 16 years of storage.

The EZ1 DNA Tissue Kit and the DNA Mini Kit scored best regarding the numbers of successful PCR reactions. In case of positive PCR, differences regarding the cycle-threshold (Ct) values were marginal.

The impact of the applied extraction kits on the reliability of PCR from FFPE material seems to be low. Interfering factors like the quality of the dewaxing procedure or the sample age appear more important than the selection of specialized FFPE kits.

  • 1.

    Ludyga N , Grünwald B, Azimzadeh O, Englert S, Höfler H, Tapio Soile, Aubele M: Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses. Virchows Arch 460, 131140 (2012)

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  • 2.

    Dietrich D , Uhl B, Sailer V, Holmes E, Jung M, Meller S, Kristiansen G Improved PCR performance using template DNA from formalin-fixed and paraffin-embedded tissues by overcoming PCR inhibition. PLoS One 8, 110 (2013)

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  • 3.

    Huijsmans CJJ , Damen J, Linden JC, Van Der Savelkoul PHM, Hermans MHA: Comparative analysis of four methods to extract DNA from paraffin-embedded tissues: effect on downstream molecular applications. BMC Res Notes 3, 239 (2010)

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  • 4.

    Gauthier YP , Hagen RM, Brochier GS, Neubauer H, Splettstoesser WD, Finke E-J, Vidal DR: Study on the pathophysiology of experimental Burkholderia pseudomallei infection in mice. FEMS Immunol Med Microbiol 30, 5363 (2001)

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  • 5.

    Hagen RM , Gauthier YP, Sprague LD, Vidal DR, Zysk G, Finke E-J, Neubauer H: Strategies for PCR based detection of Burkholderia pseudomallei DNA in paraffin wax embedded tissues. Mol Pathol 55, 398400 (2002)

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  • 6.

    Benoit TJ , Blaney DD, Gee JE, Elrod MG, Hoffmaster AR, Doker TJ, Bower WA, Walke HT; Centers for Disease Control and Prevention (CDC): melioidosis cases and selected reports of occupational exposures to Burkholderia pseudomallei – United States, 2008–2013. MMWR Surveill Summ 64, 19 (2015)

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  • 7.

    Wuthiekanun V , Peacock SJ: Management of melioidosis. Expert Rev Anti Infect Ther 4, 445455 (2006)

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    Chambon L : Analyse serologique de l’antigene somatique de malleomyces pseudomallei. Ann Inst Pasteur 98, 405415 (1960)

  • 9.

    Niesters HGM : Quantitation of viral load using real-time amplification techniques. Methods 25, 419429 (2001)

  • 10.

    Tomaso H , Scholz HC, Al Dahouk S, Pitt TL, Treu TM, Neubauer H: Development of 5’ nuclease real-time PCR assays for the rapid identification of the Burkholderia mallei/ Burkholderia pseudomallei complex. Diagn Mol Pathol 13, 247253 (2004)

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  • 11.

    Frickmann H , Chantratita N, Gauthier YP, Neubauer H, Hagen RM: Discrimination of Burkholderia mallei/pseudomallei from Burkholderia thailandensis by sequence comparison of a fragment of the ribosomal protein S21 (rpsU) gene. Eur, J Microbiol Immunol (Bp) 2, 148156 (2012)

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  • 12.

    Frickmann H , Neubauer H, Loderstaedt U, Derschum H, Hagen RM: rpsU-based discrimination within the genus Burkholderia. Eur, J Microbiol Immunol (Bp) 4, 106116 (2014)

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  • 13.

    Ostermann MF , Neubauer H, Frickmann H, Hagen RM: Correlation of rpsU gene sequence clusters and biochemical properties, GC–MS spectra and resistance profiles of clinical Burkholderia spp. isolates. Eur, J Microbiol Immunol (Bp) 6, 2539 (2016)

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  • 14.

    Zhang B , Wear D J, Kim H S, Weina P, Stojadinovic A, Izadjoo M: Development of hydrolysis probe-based realtime PCR for identification of virulent gene targets of Burk holderia pseudomallei and B. mallei – a retrospective study on archival cases of service members with melioidosis and glanders. Mil Med 177, 216221 (2012)

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  • 15.

    Perneger TV : What’s wrong with Bonferroni adjustments. BMJ 316, 12361238 (1998)

  • 16.

    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 paraffinembedded tissues. Diagn Mol Pathol 22, 236244 (2013)

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  • 17.

    Frickmann H , Loderstaedt U, Racz P, Tenner-Racz K, Eggert P, Haeupler A, Bialek R, Hagen RM: Detection of tropical fungi in formalin-fixed, paraffin-embedded tissue: still an indication for microscopy in times of sequencebased diagnosis? Biomed Res Int 2015, 93872 (2015)

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Senior editors

Editor(s)-in-Chief: Dunay, Ildiko Rita

Editor(s)-in-Chief: Heimesaat, Markus M.

Editorial Board

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

 

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

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2022  
Web of Science  
Total Cites
WoS
717
Journal Impact Factor 2.2
Rank by Impact Factor

n/a

Impact Factor
without
Journal Self Cites
2.2
5 Year
Impact Factor
2.8
Journal Citation Indicator 0.66
Rank by Journal Citation Indicator

Microbiology (Q2)

Scimago  
Scimago
H-index
11
Scimago
Journal Rank
0.614
Scimago Quartile Score Microbiology (Q3)
Microbiology (medical) (Q3)
Immunology and Allergy (Q3)
Immunology (Q3)
Scopus  
Scopus
Cite Score
8.3
Scopus
CIte Score Rank
Microbiology 33/163 (80th PCTL)
Microbiology (medical) 28/124 (77th PCTL)
Immunology and Allergy 63/211 (70th PCTL)
Immunology 69/217 (68th PCTL)
Scopus
SNIP
1.221

 

2021  
Web of Science  
Total Cites
WoS
790
Journal Impact Factor not applicable
Rank by Impact Factor not applicable
Impact Factor
without
Journal Self Cites
not applicable
5 Year
Impact Factor
not applicable
Journal Citation Indicator 0,64
Rank by Journal Citation Indicator Microbiology 81/157
Scimago  
Scimago
H-index
not indexed
Scimago
Journal Rank
not indexed
Scimago Quartile Score not indexed
Scopus  
Scopus
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not indexed
Scopus
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  not indexed
Scopus
SNIP
not indexed

2020  
CrossRef Documents 23
WoS Cites 708
Wos H-index 27
Days from submission to acceptance 219
Days from acceptance to publication 176
Acceptance Rate 70%

2019  
WoS
Cites
558
CrossRef
Documents
24
Acceptance
Rate
92%

 

European Journal of Microbiology and Immunology
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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.
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Publisher
Chief Executive Officer, Akadémiai Kiadó
ISSN 2062-509X (Print)
ISSN 2062-8633 (Online)

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