Helicobacter Pylori
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Advanced Techniques in Diagnostic Microbiology Yi-Wei Tang Charles W. Stratton Advanced Techniques in Diagnostic Microbiology Yi-Wei Tang Charles W. Stratton Molecular Infectious Disease Laboratory Clinical Microbiology Laboratory Vanderbilt University Medical Center Vanderbilt University Medical Center Nashville, TN 37232-5310 Nashville, TN 37232-5310 USA USA [email protected] [email protected] Library of Congress Control Number: 2005935335 ISBN-10: 0-387-29741-3 e-ISBN 0-387-32892-0 ISBN-13: 978-0387-29741-5 Printed on acid-free paper. C 2006 Springer Science+Business Media, LLC. All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. 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(TB/EB) 987654321 springer.com Contributors Jaber Aslanzadeh Ali Danesh Division of Clinical Department of Experimental Microbiology Therapeutics Department of Pathology University Health Network Hartford Hospital and Clinical 200 Elizabeth Street Laboratory Partners Toronto, Ontario, Canada M5G 2C4 85 Seymour Street Hartford, CT 06102, USA Diane Dare Research Development Unit George Bolton Manchester Metropolitan BD Biosciences University 10975 Torreyana Road St. Augustine’s Lower Chatham San Diego, CA 92121, USA Street Manchester, UK MI5 5HA Mark J. Cameron Department of Experimental Therapeutics Phyllis Della-Latta University Health Network Clinical Microbiology Services 200 Elizabeth Street Department of Pathology Toronto, Ontario, Canada M5G Columbia University Medical 2C4 Center New York Presbyterian Hospital 622 West 168th Street Sheldon Campbell Pathology and Laboratory Medicine New York, NY 10032, USA Service VA Connecticut Helen Deng West Haven, CT and Public Health Laboratory Department of Laboratory Medicine Arkansas Department of Health Yale University School of Medicine 4815 West Markham Street New Haven, CT 06520-8035, USA Little Rock, AR 72205, USA v vi Contributors Wonder Drake University of Alabama in Huntsville Department of Medicine 2707 Artie Street Division of Infectious Diseases Huntsville, AL 35805, USA Vanderbilt University School of Medicine Xiang Y. Han 1161 21st Ave. South Department of Laboratory Medicine Nashville, TN 37232-2605, USA The University of Texas M.D. Anderson Cancer Center David Ernst 1515 Holcombe Blvd. BD Biosciences Houston, TX 77030, USA 10975 Torreyana Road San Diego, CA 92121, USA Randall T. Hayden Department of Pathology Tao Feng St. Jude Children’s Research Hospital Molecular Pathology Laboratory 332 N. Lauderdale Street Department of Pathology Memphis, TN 38105-2794, USA Mount Sinai School of Medicine, Box 1122 Mimi Healy One Gustave Levy Place Bacterial Barcodes, Inc. New York, NY 10029, USA 8080 N. Stadium Drive Houston, TX 77054, USA Patrice Francois Department of Internal Medicine Irvin Hirshfield Geneva University Hospital Department of Biological Sciences 21 rue Micheli-du-Crest St. John’s University Geneva 14, 1211, Switzerland 8000 Utopia Parkway Jamaica, NY 11439, USA Stacie R. Frye Bacterial Barcodes, Inc. Tao Hong 8080 N. Stadium Drive Department of Pathology Houston, TX 77054, USA Clinical Microbiology Laboratory Hackensack University Medical Center Amitabh Gaur 30 Prospect Ave. BD Biosciences Hackensack, NJ 07601, USA 10975 Torreyana Road San Diego, CA 92121, USA Yuan Hu Terry J. Gentry U.S. Food and Drug Administration Environmental Sciences Division Northeast Regional Laboratory Oak Ridge National Laboratory 158-15 Liberty Avenue 1 Bethel Valley Road Jamaica, NY 11433, USA Oak Ridge, TN 37831, USA Kai Man Kam Jian Han Public Health Laboratory Centre Genaco 382 Nam Cheong Street, Shek Kip Mei Department of Pathology Kowloon, Hong Kong Contributors vii David J. Kelvin Elizabeth M. Marlowe Department of Experimental Gen-Probe Therapeutics 10210 Genetic Center Drive University Health Network San Diego, CA 92121-4362, 200 Elizabeth Street USA Toronto, Ontario, Canada M5G 2C4 Michael L. Pendrak National Institutes of Health Abdullah Kilic Bethesda, MD 20892, USA Department of Microbiology Gulhane Military Medical Desmond Persad Academy Department of Experimental Ankara 06018, Turkey Therapeutics University Health Network Marie L. Landry 200 Elizabeth Street Department of Laboratory Medicine Toronto, Ontario, Canada M5G Yale University School of Medicine 2C4 P.O. Box 802035 New Haven, CT 06520-8035, USA Raymond P. Podzorski Department of Pathology Ivy Lee Waukesha Memorial Hospital Molecular Pathology Laboratory 725 American Ave. Department of Pathology Waukesha, WI 53188, USA Mount Sinai School of Medicine, Box 1122 Chao Qi One Gustave Levy Place Department of Pathology New York, NY 10029, USA Northwestern University Memorial Haijing Li Hospital Division of Infectious Diseases 251 East Huron Street Vanderbilt University School of Chicago, IL 60611-2908, USA Medicine 1161 21st Ave. South Xuan Qin Nashville, TN 37232-2605, USA Department of Laboratories and Pathology Angus C.T. Lo Children’s Hospital and Regional Public Health Laboratory Services Medical Center Branch University of Washington School of Centre for Health Protection Medicine Department of Health 4800 Sand Point Way, N.E. Kowloon, Hong Kong Seattle, WA 98105, USA Michael Loeffelholz Diether Recktenwald ViroMed Laboratories/LabCorp BD Biosciences 6101 Blue Circle Drive 2350 Qume Drive Minnetonka, MN 55343, USA San Jose, CA 95131, USA viii Contributors Jacques Schrenzel Donna M. Wolk Department of Internal Medicine Department of Clinical Pathology and Clinical Microbiology Laboratory Medicine Geneva University Hospital University of Arizona 21 rue Micheli-du-Crest Department of Pathology and Geneva 14, 1211, Switzerland Laboratory Medicine South Arizona VA Health Care System Susan Sefers 3601 South 6th Ave. Molecular Infectious Diseases Tucson, AZ 85723, USA Laboratory Departments of Pathology Fann Wu Vanderbilt University School of Clinical Microbiology Services Medicine Department of Pathology 1161 21st Avenue South Columbia University Medical Center Nashville, TN 37232-5310, USA New York Presbyterian Hospital 622 West 168th Street Charles W. Stratton New York, NY 10032, USA Departments of Pathology and Medicine Josephine Wu Vanderbilt University School of Molecular Pathology Laboratory Medicine Department of Pathology 1161 21st Avenue South Mount Sinai School of Medicine, Box Nashville, TN 37232-5310, USA 1122 One Gustave Levy Place Yi-Wei Tang New York, NY 10029, USA Departments of Medicine and Pathology S. Steve Yan Vanderbilt University School of Food and Drug Administration Medicine Rockville, MD 20855, USA 1161 21st Avenue South Nashville, TN 37232-5310, USA Fei Ye Molecular Pathology Laboratory Sihe Wang Department of Pathology Northwestern University Mount Sinai School of Medicine, Box The Feinberg School of Medicine 1122 Children’s Memorial Hospital One Gustave Levy Place 2300 Children’s Plaza New York, NY 10029, USA Chicago, IL 60614, USA Bingjiao Yin Yun F. (Wayne) Wang Molecular Pathology Laboratory Department of Pathology Department of Pathology Emory University School of Medicine Mount Sinai School of Medicine, Grady Memorial Hospital Box 1122 80 Jesse Hill Dr., S.E. One Gustave Levy Place Atlanta, GA 30303, USA New York, NY 10029, USA Contributors ix David Zhang Children’s Memorial Hospital Molecular Pathology Laboratory 2300 Children’s Plaza Department of Pathology Chicago, IL 60614, USA Mount Sinai School of Medicine, Box 1122 Jizhong Zhou One Gustave Levy Place Environmental Sciences New York, NY 10029, USA Division Oak Ridge National Xiaotian Zheng Laboratory Northwestern University 1 Bethel Valley Road The Feinberg School of Medicine Oak Ridge, TN 37831, USA Preface Clinical microbiologists are engaged in the field of diagnostic microbiology to determine whether pathogenic microorganisms are present in clinical specimens collected from patients with suspected infections. If microorganisms are found, these are identified and susceptibility profiles, when indicated, are determined. During the past two decades, technical advances in the field of diagnostic micro- biology have made constant and enormous progress in various areas, including bacteriology, mycology, mycobacteriology, parasitology, and virology. The diag- nostic capabilities of modern clinical microbiology laboratories have improved rapidly and have expanded greatly due to a technological revolution in molecu- lar aspects of microbiology and immunology. In particular, rapid techniques for nucleic acid amplification and characterization combined with automation and user-friendly software have significantly broadened the diagnostic arsenal for the clinical microbiologist. The conventional diagnostic model for clinical microbi- ology has been labor-intensive and frequently required days to weeks before test results were available. Moreover, due to the complexity and length of such testing, this service was usually directed at the hospitalized patient population. The phys- ical