Gene Probes for Bacteria Edited by Alberto J. L. Macario Everly Conway de Macario Wadsworth Center for Laboratories and Research New York State Department of Health and School of Public Health State University of New York Albany, New York ACADEMIC PRESS, INC. Harcourt Brace Jovanovich, Publishers San Diego New York Berkeley Boston London Sydney Tokyo Toronto This book is printed on acid-free paper. @ Copyright © 1990 by Academic Press, Inc. All Rights Reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Academic Press, Inc. San Diego, California 92101 United Kingdom Edition published by Academic Press Limited 24-28 Oval Road, London NW1 7DX Library of Congress Cataloging-in-Publication Data Gene probes for bacteria / edited by Alberto J. L. Macario, Everly Conway de Macario. p. cm. Includes bibliographical references. ISBN 0-12-463000-6 (alk. paper) 1. Diagnostic bacteriology-Technique. 2. DNA probes—Diagnostic use. I. Macario, Alberto J. L. II. Conway de Macario, Everly. [DNLM: 1. Bacteria—isolation & purification. 2. Nucleic Acid Probes. 3. Nucleic Acids-diagnostic use. QU 58 G326] QR67.2.G46~dc20 DNLM/DLC for Library of Congress 89-17733 CIP Printed in the United States of America 90 91 92 93 9 8 7 6 5 4 3 2 1 To our collaborators, assistants, α Aid students of sundry places and times. Contributors Numbers in parentheses indicate the pages on which the authors' contributions begin. Peter W. Andrew (179), Department of Microbiology, University of Leicester, Medical Sciences Building, Leicester LEI 9HN, England G. T. Attwood (389), Department of Animal Sciences, Waite Agriculture Research Institute, Glen Osmond, South Australia 5064, Australia Christiane Bebear (45), Laboratoire de Bacteriologie, Hopital Pellegrin, 33076 Bordeaux, France Lawrence H. Bopp (69), Laboratories for Bacteriology, Wadsworth Cen ter for Laboratories and Research, New York State Department of Health, Albany, New York 12201-0509 Graham J. Boulnois (179), Department of Microbiology, University of Leicester, Medical Sciences Building, Leicester LEI 9HN, England J. D. Brooker (389), Department of Animal Sciences, Waite Agriculture Research Institute, Glen Osmond, South Australia 5064, Australia Arunsri Chatkaeomorakot (95), Armed Forces Research Institute of Medi cal Sciences, Bangkok 10400, Thailand Everly Conway de Macario (485), Wadsworth Center for Laboratories and Research, New York State Department of Health, and School of Public Health, State University of New York, Albany, New York 12201-0509 Hirofumi Danbara (167), Department of Bacteriology, The Kitasato Insti tute, Minato-ku, Tokyo 108, Japan James J. Donegan (1), Enzo Biochem, Inc., New York, New York 10013 Ram Dular (417), Ontario Ministry of Health, Regional Public Health Laboratory, Ottawa, Ontario K2A 1S8, Canada xiii xiv Contributors Brigitte Dutilh1 (45), Laboratoire de Bacteriologie, Hopital Pellegrin, 33076 Bordeaux, France Peter Echeverria (95), Armed Forces Research Institute of Medical Sci ences, Bangkok 10400, Thailand Sherry P. Goltz (1), Enzo Biochem, Inc., New York, New York 10013 Patrick A. D. Grimont (45), Unite des Enterobacteries, Unite 199 INSERM, Institut Pasteur, 75724 Paris, France Roy Gross (205), Sclavo Research Center, 53100 Siena, Italy David J. Groves (233), Department of Pathology, McMaster University, and Department of Laboratory Medicine, St. Joseph's Hospital, Hamilton, Ontario L8N 4A6, Canada Alan M. Johnson (255), Department of Clinical Microbiology, School of Medicine, Flinders University and Flinders Medical Center, Bedford Park, South Australia 5042, Australia Robert J. Jovell (485), Wadsworth Center for Laboratories and Research, New York State Department of Health, and School of Public Health, State University of New York, Albany, New York 12201-0509 Norman Kelker (1), Enzo Biochem, Inc., New York, New York 10013 R. A. Lockington (389), Department of Animal Sciences, Waite Agricul ture Research Institute, Glen Osmond, South Australia 5064, Aus tralia Alberto J. L. Macario (485), Wadsworth Center for Laboratories and Research, New York State Department of Health, and School of Public Health, State University of New York, Albany, New York 12201-0509 S. Miller (389), Department of Animal Sciences, Waite Agriculture Re search Institute, Glen Osmond, South Australia 5064, Australia Margarita M. Molina (1), Enzo Biochem, Inc., New York, New York 10013 S. Notermans (353), Laboratory of Water and Food Microbiology, Na tional Institute of Public Health and Environmental Protection, 3720 BA Bilthoven, The Netherlands Linda M. Parsons (69), Laboratories for Bacteriology, Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, New York 12201-0509 Marjorie Pollice (1), Enzo Biochem, Inc., New York, New York 10013 Rino Rappuoli (205), Sclavo Research Center, 53100 Siena, Italy Fran A. Rubin (323), Department of Bacterial Immunology, Walter Reed Army Institute of Research, Washington, D.C. 20307-5100 J. ter Schegget (295), Department of Medical Microbiology, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands 1 Present address: Laboratoire d'Analyses Ntedicales, 218, rue Mandron, 33000 Bor deaux, France. Contributors XV G. J. Schoone (295), Department of Tropical Hygiene, Royal Tropical Institute, 1105 AZ Amsterdam, The Netherlands Jitvimol Seriwatana (95), Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand Orntipa Sethabutr (95), Armed Forces Research Institute of Medical Sci ences, Bangkok 10400, Thailand Mehdi Shayegani (69), Laboratories for Bacteriology, Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, New York 12201-0509 W. J. Terpstra (295), Department of Tropical Hygiene, Royal Tropical Institute, 1105 AZ Amsterdam, The Netherlands John A. Todd (1), Enzo Biochem, Inc., New York, New York 10013 Kevin J. Towner (459), Department of Microbiology and PHLS Labora tory, University Hospital, Nottingham NG7 2UH, England Jacob Victor (1), Enzo Biochem, Inc., New York, New York 10013 Alfred L. Waring (69), Laboratories for Bacteriology, Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, New York 12201-0509 K. Wernars (353), Laboratory of Water and Food Microbiology, National Institute of Public Health and Environmental Protection, 3720 BA Bilthoven, The Netherlands Bruce L. Wetherall (255), Department of Clinical Microbiology, Flinders Medical Center, Bedford Park, South Australia 5042, Australia Peter H. Williams (143), Department of Genetics, University of Leicester, Leicester LEI 7RH, England Huey-Lang Yang (1), Enzo Biochem, Inc., New York, New York 10013 Preface Molecular genetics has advanced enormously in the past decade. It is changing our views of physiological and pathological phenomena and, consequently, our strategies to study and control them. The construction of gene probes to analyze microbes is one example of these contemporary trends. Clinical and epidemiological applications of nucleic acid probes for bacteria have just begun. This book attempts to furnish a comprehensive account of the state of the art of this new area. It complements the treatise on antibacterial monoclonal antibodies published earlier (see Introduc tion). Both present extensive reviews of probes for bacteria. The earlier work dealt with immunologic probes and methods; this one covers molec ular genetics and nucleic acids, emphasizing diagnosis. The preparation and use of nucleic acid probes for identifying bacteria in clinical specimens and in other samples of practical or scientific interest are described. The contributors are pioneers in their fields of expertise. They are affiliated with academe, government, or industry, thus representing all major interest groups. Their chapters—particularly their methods, conclu sions, and suggestions for the future—should be of great use to profes sionals, technicians, and R&D directors in universities, in federal and state-dependent service and research institutes, and in private (e.g., hospi tal) and industrial laboratories. The probes and procedures described are applicable to a variety of areas pertinent to medicine, veterinary sciences, environmental (sanitary) engi neering, agronomy, zoology, and to other branches of science and bio technology dealing with microbes. These probes and procedures have been standardized for detecting the presence of bacteria and for identifying xvii xviii Preface and classifying them in clinical specimens, environmental samples, labora tory cultures, etc. The probes are for pathogens affecting the oral cavity, nasopharynx, gastrointestinal and genitourinary tracts (including those causing venereal diseases), eyes, blood and meninges, the cardiovascular, respiratory, and immune systems, and for bacteria found in water and foods, tissue cultures, and other ecosystems of importance. Salient features of the book are highlighted in the Introduction. It calls the reader's attention to chapter sections covering laboratory applications and identifies other sections of general interest. To enhance the book's utility, the Introduction also comprises a bibliographic update. We would like to thank our teachers, assistants, collaborators, and students for their continual support and for their help in the many tasks that directly or indirectly culminated in this book. We would also like to thank the contributors for their excellent manuscripts and the staff of Academic Press for expert advice, unfailing support, and encouragement. Alberto /. L. Macario Everly Conway de Macario Introduction: Molecular Genetics in Diagnostic Bacteriology Molecular genetics, including genetic engineering, has revolutionized biology. Genes have been and are being isolated and characterized. Cur rently, studies on how genes function and are regulated are progressing rapidly. Techniques for manipulating and modifying genes are becoming widespread. These advances have permeated into virtually all branches of biology. Examining how cells and organisms work can now be done from the vantage point of molecular genetics. One of the many outcomes of these innovative ideas and techniques has been the generation of nucleic acid probes for identifying microbes. Thus, diagnostic microbiology has been endowed with new means to accomplish its primary goals, namely, to detect and identify viruses, bacteria, and other microorganisms in samples of scientific or practical interest. Diagnostic bacteriology, the central theme of this volume, is entering a new era marked by the application of gene probes in addition to other classical identification methods, such as culture-isolation and immunoas says, based on polyclonal or monoclonal antibodies. This book was con ceived along the lines of its predecessor "Monoclonal Antibodies against Bacteria" (Volumes I-III, 1985-1986. A. J. L. Macario and E. Conway de Macario, editors. Academic Press, Inc.). The main objective was to pro vide a comprehensive report on the current status of gene probes for bacteria useful in diagnostics. Which nucleic acid probes are available, how and when to utilize them, what to expect in terms of results obtained with their use, and how to prepare new probes are all questions addressed in the various chapters. xix XX Introduction The contributors were asked to prepare comprehensive manuscripts covering the microorganisms of their expertise. A few bacterial species are treated in more than one chapter in order to provide a multidimensional picture of important microbes and to compile the knowledge gained from different laboratories using the same or different (e.g., radioactive vs. nonradioactive) probes or methods. To maintain unity of format and en sure full coverage, the chapters include a uniform series of sections. Sections I, "Introduction," and II, "Background," present the main theme of the chapter, its origins, and pertinent problems and questions. A brief historical overview is included in Section II, with descriptions of microorganisms and diseases dealt with in the chapter. The purpose of this introductory material is to familiarize the nonspecialist with topics that need to be known to understand the subsequent sections, particularly Section III, "Results and Discussion," in which the expertise of the authors is displayed. Data are reported and analyzed to illustrate prepara tion and/or use of nucleic acid probes. A critical examination of the results leads to inferences and speculations which are summarized in Section IV, "Conclusions." The advantages and disadvantages of nucleic acid probes as opposed to antisera and monoclonal antibodies are discussed in Section V, "Gene Probes versus Antisera and Monoclonal Antibodies." Here the bibliography serves as a starting point in the search for additional informa tion regarding modern serology and immunoassays based on monoclonal antibodies. As such, Section V may help those unfamiliar with immunoas says to venture into the advanced field of immunology and immunochemis- try that originated only a few years ago with the widespread application of the hybridoma technology. Section VI, "Prospects for the Future," contains opinions, specula tions, and suggestions by the authors based on their invaluable experience. Suggestions relate to a variety of problems (methodological, biological, pathological, environmental, biotechnological) the authors deem impor tant for research in the near future. Section VII is a synopsis of the chapter's content. It leads the reader into Section VIII, "Materials and Methods," which is very important since it gives detailed instructions for the preparation and/or utilization of the nucleic acid probes specifically treated in the chapter. Procedures already published in manuals available in virtually all laboratories working with nucleic acids are only briefly mentioned or not described at all, unless modifications have been introduced. These modifications are given in detail and represent the authors' contribution to a field burgeoning with innovations. Some are improvements on the original methods; others are adaptations required to deal with unique technical difficulties posed by special characteristics of some microorganisms. Section VIII should be