Rapid Cycle Real-Time PCR — Methods and Applications: Microbiology and Food Analysis PDF
Preview Rapid Cycle Real-Time PCR — Methods and Applications: Microbiology and Food Analysis
.. U. REISCRL C. WITTWER F. COCKERILL (Eds.) Rapid Cycle Real-Time PCR - Methods and Applications Microbiology and Food Analysis .. Springer Berlin Heidelberg New York Barcelona Hong Kong London Milan Paris Tokyo lID U. Reischl C. Wittwer F. Cockerill (Eds.) Rapi eye e Real-Time peR - Methods and App ieat-ons Microbiology and Food Analysis With 76 Figures and 127 Tables , Springer .. Dr. Uno REISCHL Universitatsklinikum Regensburg Institut fUr Medizinische Mikrobiologie und Hygiene Franz-Josef-Strau6-Allee 11 93053 Regensburg, Germany Prof. Dr. CARL WITTWER University of Utah Medical School Department of Pathology Salt Lake City, UT 84132, USA Prof. Dr. FRANKLIN COCKERILL Division of Clinical Microbiology Mayo Clinic Rochester, Minnesota 55905, USA ISBN-13: 978-3-642-48353-0 Library of Congress applied for Die Deutsche Bibliothek - CIP-Einheitsaufnahme Rapid cycle real-time PCR : methods and applications; microbiology and food analysis 1 Udo Reischl ... (ed.). -Berlin; Heidelberg; New York; Barcelona; Hong Kong; London; Mailand ; Paris; Singapore; Tokyo: Springer, 2001 ISBN-13: 978-3-642-48353-0 e-lSBN-13: 978-3-642-48351-6 DOl: 10.1007/978-3-642-48351-6 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcas ting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer-Verlag. Violations are liable for prosecution under the German Copyright Law. Springer-Verlag Berlin Heidelberg New York a member of BertelsmannSpringer Science+ Business Media GmbH http://www.springer.de/medizin © Springer-Verlag Berlin Heidelberg 2002 Softcover reprint of the hardcover 1 st edition 2002 The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant pro tective laws and regulations and therefore free for general use. Product liability: The publisher cannot guarantee the accuracy of any information about dosage and application thereof contained in this book. In every individual case the user must check such infor mation by consulting the relevant literature. Cover Design: design & production, 69121 Heidelberg, Germany Production: ProEdit GmbH, 69126 Heidelberg, Germany Typesetting: TBS, 69207 Sandhausen, Germany Printed on acid free paper SPIN 10832920 18/3130 Re - 5432 1 0 • Table of Contents Introduction for Microbiology Volume of Rapid Cycle Real-Time PCR FRANKLIN COCKERILL Applications and Challenges of Real-Time PCR for the Clinical Microbiology Laboratory .. ............ ................. 3 FRANKLIN R. COCKERILL, III*, JAMES R. UHL Part I Bacteriology Rapid Detection and Simultaneous Differentiation of Bordetella pertussis and Bordetella parapertussis in Clinical Specimens by LightCycier PCR ........ 31 UDO REISCHL, KATRIN KOSTERS, BIRGIT LEPPMEIER, HANS-JORG LINDE, NORBERT LEHN Rapid Detection and Simultaneous Differentiation of Legionella spp. and L. pneumophila in Potable Water Samples and Respiratory Specimens by LightCycier PCR .......................... 45 NELE WELLINGHAUSEN, OLFERT LANDT, UDO REISCHL Homogeneous Assays for the Rapid PCR detection of Burkholderia pseudomallei 16s rRNA gene on a Real-Time Fluorometric Capillary Thermocycler .. .................... 59 ERIC P-H YAP, SOON-MENG ANG, SHIRLEY G-K SEAH, SENG-MENG PHANG Rapid Detection ofToxigenic Corynebacterium diphtheriae by LightCycier PCR ................................................. 71 UDO REISCHL, ELENA SAMOILOVICH, VALENTINA KOLODKINA, NORBERT LEHN, HANS-JORG LINDE Rapid Detection of Resistance Associated Mutations in Mycobacterium tuberculosis by LightCycier PCR .................... ... 83 MARIA J. TORRES, ANTONIO CRIADO, JOSE C. PALOMARES, JAVIER AZNAR • Table of Contents Duplex LightCycier PCR Assay for the Rapid Detection of Methicillin-Resistant Staphylococcus aureus and Simultaneous Species Confirmation ............. 93 UDO REISCHL, HANS-JORG LINDE, BIRGIT LEPPMEIER, NORBERT LEHN Rapid Detection of Group BS treptococci Using the LightCycier Instrument 107 DANBING KE, CHRISTIAN MENARD, FRAN<;:OIS J. PICARD, MICHEL G. BERGERON Rapid Detection and Quantification of Chlamydia trachomatis in Clinical Specimens by LightCycier PCR ............................... ll5 HEIDI WOOD, UDO REISCHL, ROSANNA W. PEELING Quantification of Toxoplasma gondiiin Amniotic Fluid by Rapid Cycle Real-Time PCR ....................................... 133 FRAN<;:OIS DELHOMMEAU, FRAN<;:OIS FORESTIER Genospecies-Specific Melting Temperature of the recA PCR Product for the Detection of Borrelia burgdorferi sensu lato and Differentiation of Borrelia garinii from Borrelia afzelii and Borrelia burgdorferi sensu stricto 139 JOHANNA MAKINEN, QIUSHUI HE, MATTI K. VILJANEN Rapid and Specific Detection of Coxiella burnetiiby LightCycier PCR 149 MARKUS STEMMLER, HERMANN MEYER Molecular Identification of Campylobarter coli and Campylobarter jejuni Using Automated DNA Extraction and Real-Time PCR with Species-Specific TaqMan Probes ................ .................................. 155 LYNN A. COOPER, LUKE T. DAUM, ROBERT ROUDABUSH, KENTON 1. LOHMAN Rapid and Specific Detection of Plesiomonas shigelloides Directly from Stool by LightCycier PCR ....................................... 161 JIN PHANG LOH, ERIC PENG HUAT YAP Quantification of Thermostable Direct Hemolysin-Producing Vibrio parahaemolyticusfrom Foods Assumed to Cause Food Poisoning Using the LightCycier Instrument .................................... 171 YOSHITO IWADE, AKINORI YAMAUCHI, AKIRA SUGIYAMA, OSAMU NAKAYAMA, NORICHIKA H. KUMAZAWA Table of Contents go Part [J Detection of Fungal Pathogens Quantification and Speciation of Fungal DNA in Clinical Specimens Using the LightCycier Instrument ................................... . 179 JUERGEN LOEFFLER, HOLGER HEBART, NORBERT HENKE, KATHRIN SCHMIDT, HERMANN EINSELE Part III Virology Development, Implementation, and Optimization of LightCycier PCR Assays for Detection of Herpes Simplex Virus and Varicella-Zoster Virus from Clinical Specimens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 189 THOMAS F. SMITH, MARK J. Espy, ARLO D. WOLD Qualitative Detection of Herpes Simplex Virus DNA in the Routine Diagnostic Laboratory ................................. 201 HARALD H. KESSLER, GERHARD MUHLBAUER, EVELYN STELZL, EGON MARTH Use of Real-Time PCR to Monitor Human Herpesvirus 6 (HHV-6) Reactivation ... 211 JUNKO H. OHYASHIKI, KAZUMA OHYASHIKI, KOHTARO YAMAMOTO Simultaneous Identification of Five HCV Genotypes in a Single Reaction 217 OLFERT LANDT, ULRICH LASS, HEINZ-HuBERT FEUCHT Rapid Detection of West Nile Virus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 227 OLFERT LANDT, JASMIN DEHNHARDT, ANDREAS NITSCHE, GARY MILBURN, SHAWN D. CARVER Use of Rapid Cycle Real-Time PCR for the Detection of Rabies Virus ........... 235 LORRAINE McELHINNEY, JASON SAWYER, CHRISTOPHER J. FINNEGAN, JEMMA SMITH, ANTHONY R. FOOKS Development of One-Step RT -PCR for the Detection of an RNA Virus, Dengue, on the Capillary Real-Time Thermocycler .......... ................... .. 241 BOON-HuAN TAN, E'EIN SEE, ELIZABETH LIM, ERIC PENG-HUAT YAP mn Part IV Detection of Genetically Modified Organisms (GMO) Variation Analysis of Seven LightCycier Based Real-Time PCR Systems to Detect Genetically Modified Products (RRS, Btl 76, Btl 1, Mon81 0, T25, Lectin,lnvertase) ......... ... ................................... .. 251 ISABELLE DAHINDEN, ANDREAS ZIMMERMANN, MARIANNE LINIGER, URS PAULI lEt Abbreviations Bp Base pair EDTA Ethylenediamine Tetraacetic Acid F Fluorescein LCRed640 LightCycler Red 640 Fluorescent Dye LCRed705 LightCycler Red 705 Fluorescent Dye Nt Nucleotide( s) P Phosphate PBS Phosphate Buffered Saline SDS Sodium Dodecylsulfate TE 1xTE Buffer Contains 0.01 M Tris, 0.001 M EDTA, pH 8.0 TE' 1xTE' Buffer Contains 0.01 M Tris, 0.0001 M EDTA, pH 8.0 TEN (=STE) 1xTEN Buffer Contains 0.01 M Tris (pH 8.0), 150 mM NaCI, 0.05% Tween 20 Tm(°C) Melting Temperature n-n nearest neighbor FRET Fluorescence Resonance Energy Transfer ~H Enthalpy ~S Entropy ~G Free Energy TPMT Thiopurine Methyltransferase XO Xanthine Oxidase AA Amino Acid ORF Open Reading Frame LightCycler is a trademark of a member of the Roche Group MagNA Pure LC is a trademark of a member of the Roche Group ., Introduction for Microbiology Volume of Rapid Cycle Real-Time PCR Several commercial testing platforms have become available or soon will be avail able which combine rapid cycle polymerase chain reaction with fluorescent probe detection of amplified target nucleic acid in the same closed vessel. This technol ogy is referred to as rapid cycle real-time PCR. One testing platform which exploits this technology, the LightCycler instru ment (Roche Diagnostics Corporation), has become particularly popular. The LightCycler system was the first system available that permitted the operator to evaluate target amplification after each PCR cycle. Recently an automated nucle ic acid extraction system, the MagNA Pure LC (Roche Diagnostics Corporation), has been developed to complement the LightCycler system. The combination of the MagNA Pure LC and LightCycler system now permits complete automation of extraction, purification, concentration, amplification and detection of target nucleic acid from patient samples. Although the LightCycler system was initially intended for research purposes, it became quickly obvious to many microbiologists, that the system had immense potential for diagnostic microbiology testing. The LightCycler-MagNA Pure LC system could not only replace cumbersome and work intense procedures required for conventional, "home-brewed" PCR assays, but as well could replace standard antigen or culture-based assays. As an example, the accepted diagnostic approach for detecting Group A Streptococcus (Streptococcus pyogenes) from throat swabs is to screen for group A streptococcal antigens using a commercial direct immunoassay. If the result for this "rapid antigen" assay is negative, a cul ture is performed. This two-step procedure follows guidelines provided by the Infectious Diseases Society of America and other professional organizations and is required because current rapid antigen assays lack sensitivity. We have devel oped a LightCycler assay which is -10% more sensitive and approximately half the cost ($1-$2 vs $2-$3) and requires much less time to perform « 1 hr vs up to 48 h) than the combined antigen-culture assay. In addition to accuracy, speed and cost issues, the LightCycler system and other rapid cycle real-time PCR platforms have other advantages over conventional PCR methods. These include decreased risk for contamination (specimen or amplicon) and adaptability for a wide range of testing. The containment of the PCR reaction and amplicon detection in the same closed vessel, as is possible with the LightCycler system, lessens the possi bility of amplicon contamination including amplicon "carryover" from previous assay runs. As well, the possibility of specimen to specimen contamination is essentially eliminated. The versatility for testing is exemplified by applications
The list of books you might like
