Advanced Techniques in Diagnostic Microbiology Yi-Wei Tang Charles W. Stratton (cid:2) Editors Advanced Techniques in Diagnostic Microbiology Second Edition Editors Yi-Wei Tang Charles W. Stratton Department of Laboratory Medicine Departments of Pathology and Medicine Memorial Sloan-Kettering Cancer Center Vanderbilt University Medical Center New York, NY, USA Nashville, TN, USA ISBN 978-1-4614-3969-1 ISBN 978-1-4614-3970-7 (eBook) DOI 10.1007/978-1-4614-3970-7 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 201242474 © Springer Science+Business Media New York 2013 This work is subject to copyright. 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Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface In the United States, hospitals annually report over fi ve million cases of infectious- disease-related illnesses: clinical microbiology laboratories in these hospitals are engaged in detecting and identifying the pathogenic microorganisms in clinical specimens collected from patients with suspected infections. Clearly, the timely and accurate detection/identi fi cation of these microbial pathogens is critical for patient treatment decisions and outcomes for millions of patients each year. Despite an appreciation that the outcome of an infectious-disease-related illness is directly related to the time required to detect and identify a microbial pathogen, clinical microbiology laboratories in the United States as well as worldwide have long been hampered by traditional culture-based assays, which may require prolonged incuba- tion time for slowly growing microorganisms such as M ycobacterium tuberculosis . Moreover, traditional culture-based assays often require multiple steps with addi- tional time needed for discernment of species and/or detection of antimicrobial resistance. Finally, these traditional, slow multistep culture-based assays are labor- intensive and require skilled clinical microbiologists at the bench. Over the past several decades, advanced molecular techniques in diagnostic microbiology quietly have been revolutionizing the practice of clinical microbiol- ogy in the hospital setting. Indeed, molecular diagnostic testing in general and nucleic acid-based ampli fi cation methods in particular have been heralded as diag- nostic tools for the new millennium. There is no question that the development of rapid molecular techniques for nucleic acid ampli fi cation/characterization com- bined with automation and user-friendly software has greatly broadened the diag- nostic capabilities of the clinical microbiology laboratory. These technical advances in molecular microbiology over the fi rst decade of the twenty- fi rst century have profoundly in fl uenced the physical structure of clinical microbiology laboratories as well as their staf fi ng patterns, work fl ow, and turnaround time. These molecular microbiology advances have also resulted in the need for a revised and updated second edition of A dvanced Techniques in Diagnostic Microbiology . This second edition again provides an updated and comprehensive description of the ongoing v vi Preface evolution of molecular methods for the diagnosis of infectious diseases. In addition, many new chapters have been added, including a chapter on the clinical interpreta- tion and relevance of advanced technique results. The second edition, like the fi rst edition, includes both a “techniques” section describing the latest molecular tech- niques and an “applications” section describing how these advanced molecular techniques are being used in the clinical setting. Finally, the second edition, like the fi rst edition, utilizes a diverse team of authors who have compiled chapters that provide the reader with comprehensive and useable information on advanced molecular microbiology techniques. New York, NY, USA Yi-Wei Tang Nashville, TN, USA Charles W. Stratton Contents Part I Methods 1 Automated Blood Cultures .................................................................... 3 Xiang Y. Han 2 Breath Tests for Detection of Helicobacter pylori and Aspergillus fumigatus ...................................................................... 13 Sihe Wang, Wan-Ming Zhang, and Edmunds Reineks 3 Rapid Antigen Tests ............................................................................... 31 Sheldon Campbell and Marie L. Landry 4 Antibody Detection: Principles and Applications ............................... 53 Yun F. (Wayne) Wang and Miwako Kobayashi 5 Cytometry-Based Antimicrobial Resistance Techniques .................... 75 Vishnu Chaturvedi 6 Biochemical Profile-Based Microbial Identification Systems ............ 87 Nyasha O. Bullock and Jaber Aslanzadeh 7 Infectious Disease Biomarkers: Non-Antibody-Based Host Responses ....................................................................................... 123 Audrey N. Schuetz 8 Functional Assessment of Microbial and Viral Infections by Real-Time Cellular Analysis System ............................................... 151 Xiao Xu and Min Zheng 9 Cellular Fatty Acid-Based Microbial Identification and Antimicrobial Susceptibility Testing ............................................. 177 Nicole Parrish and Stefan Riedel vii viii Contents 10 MALDI-TOF Mass Spectrometry-Based Microbial Identification ......................................................................... 187 Alexander Mellmann and Johannes Müthing 11 Nucleic Acid Extraction Techniques ..................................................... 209 Jeong Hwan Shin 12 Nonamplified Probe-Based Microbial Detection and Identification ................................................................................... 227 Fann Wu, Tao Hong, and Phyllis Della-Latta 13 Molecular Typing Techniques: State of the Art ................................... 239 Richard V. Goering 14 An Introduction to In Vitro Nucleic Acid Amplification Techniques ...................................................................... 263 Haijing Li and Yi-Wei Tang 15 PCR and Its Variations .......................................................................... 273 Michael Loeffelholz and Jianli Dong 16 Non-PCR Target Amplification Techniques......................................... 293 Rosemary C. She and Elizabeth M. Marlowe 17 Probe Amplification Technologies ........................................................ 307 Fei Ye, Miao Cui, Tao Feng, Ivy Lee, Josephine Wu, Bingjiao Yin, and David Zhang 18 Signal Amplification Technologies ........................................................ 327 Ted E. Schutzbank 19 Real-Time Nucleic Acid Quantification................................................ 345 Nima Mosammaparast and Alexander J. McAdam 20 An Introduction to Amplification–Production– Detection Techniques ............................................................................. 355 Criziel Quinn, Charles W. Stratton, and Yi-Wei Tang 21 Gel Electrophoresis, Southern Blot, and Colorimetric Microwell Plate-Based System .............................................................. 367 Jie He, Michael J. Loeffelholz, and Jiang Fan 22 Direct Nucleotide Sequencing for Amplification Product Identification ............................................................................ 383 Tao Hong 23 Microarray-Based Amplification Product Detection and Identification ................................................................................... 397 Joy D. Van Nostrand, Terry J. Gentry, and Jizhong Zhou 24 Real-Time Detection of Amplification Products Through Fluorescence Quenching or Energy Transfer ...................................... 413 Shihai Huang Contents ix 25 Microbial Identification by PCR/Electrospray Ionization-Mass Spectrometry .............................................................. 441 David Metzgar, Rangarajan Sampath, Lawrence B. Blyn, Christian Massire, and David J. Ecker 26 Amplification Product Inactivation ...................................................... 467 Susan Sefers, Charles W. Stratton, and Yi-Wei Tang Part II Applications 27 Bacterial Identification Based on Universal Gene Amplification and Sequencing .............................................................. 483 Susanna K.P. Lau, Jade L.L. Teng, and Patrick C.Y. Woo 28 Molecular Techniques for Blood and Blood Product Screening .................................................................................. 511 Yuan Hu 29 Molecular Diagnostics of Sexually Transmitted Diseases ................... 535 Angus C.T. Lo and Kai Man Kam 30 Advances in the Diagnosis of Mycobacterium tuberculosis and Detection of Drug Resistance ......................................................... 557 Abdullah Kilic 31 Rapid Screening and Identification of Methicillin-Resistant Staphylococcus aureus ............................................................................ 587 Patrice Francois and Jacques Schrenzel 32 Advanced Methods for Detection of Foodborne Pathogens ............... 605 Heather Harbottle and Michael Pendrak 33 Technical and Clinical Niches for Point of Care Molecular Devices .................................................................................. 619 Ellen Jo Baron and Sheldon Campbell 34 Multiplex PCR in Molecular Differential Diagnosis of Microbial Infections: Methods, Utility, and Platforms .................. 627 Jian Han 35 Technical Advances in Veterinary Diagnostic Microbiology .............. 647 Dongyou Liu 36 Recent Advances in Veterinary Diagnostic Virology: Report from a Collaborating Centre of the World Organization for Animal Health (OIE) ................................................ 661 Sándor Belák and Lihong Liu 37 Deep Sequencing: Technical Advances and Clinical Microbiology Applications .................................................................... 679 Chunlin Wang