Infectious Disease - Pathogenesis, Prevention, and Case Studies PDF
Preview Infectious Disease - Pathogenesis, Prevention, and Case Studies
ID_1_A01.qxd 2/10/09 13:57 Page i Infectious Disease: Pathogenesis, Prevention, and Case Studies N. Shetty Department of Clinical Microbiology, University College London Hospitals J.W. Tang Division of Microbiology/Molecular Diagnostic Centre, Department of Laboratory Medicine, National University Hospital, Singapore J. Andrews Department of Clinical Microbiology, University College London A John Wiley & Sons, Ltd., Publication ID_1_A01.qxd 2/10/09 13:57 Page i Infectious Disease: Pathogenesis, Prevention, and Case Studies N. Shetty Department of Clinical Microbiology, University College London Hospitals J.W. Tang Division of Microbiology/Molecular Diagnostic Centre, Department of Laboratory Medicine, National University Hospital, Singapore J. Andrews Department of Clinical Microbiology, University College London A John Wiley & Sons, Ltd., Publication ID_1_A01.qxd 2/10/09 13:57 Page ii This edition first published 2009, © 2009 by N. Shetty, J.W. Tang and J. Andrews Blackwell Publishing was acquired by John Wiley & Sons in February 2007. Blackwell’s publishing program has been merged with Wiley’s global Scientific, Technical and Medical business to form Wiley-Blackwell. Registered office: John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK Editorial offices:9600 Garsington Road, Oxford, OX4 2DQ, UK The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK 111 River Street, Hoboken, NJ 07030-5774, USA For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com/wiley-blackwell The right of the author to be identified as the author of this work has been asserted in accordance with the Copyright, Designs and Patents Act 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books. Designations used by companies to distinguish their products are often claimed as trademarks. All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners. The publisher is not associated with any product or vendor mentioned in this book. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold on the understanding that the publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional should be sought. Library of Congress Cataloguing-in-Publication Data Shetty, N. (Nandini) Infectious disease : pathogenesis, prevention, and case studies / N. Shetty, J.W. Tang, J. Andrews. p. ; cm. Includes bibliographical references and index. ISBN 978-1-4051-3543-6 (hardcover : alk. paper) 1. Communicable diseases. I. Tang, J.W. (Julian W.) II. Andrews, J. (Julie) III. Title. [DNLM: 1. Communicable Diseases–etiology. 2. Communicable Disease Control–methods. WC 100 S554i 2009] RC111.S458 2009 616.9–dc22 2008042548 ISBN: 9781405135436 A catalogue record for this book is available from the British Library. Set in 11/13pt Bembo by Graphicraft Limited, Hong Kong Printed and bound in Malaysia 1 2009 ID_1_A01.qxd 2/10/09 13:57 Page iii Contents Editors and Contributors, iv Preface, v Glossary of abbreviated terms, vii PART 1 GENERAL PRINCIPLES OF INFECTIOUS DISEASES, 1 1 Microbial etiology of disease N. Shetty, E. Aarons, J. Andrews, 3 2 Structure and function of microbes N. Shetty, E. Aarons, J. Andrews, 15 3 Host defence versus microbial pathogenesis and the mechanisms of microbial escape N. Shetty, E. Aarons, J. Andrews, 41 4 Diagnosis of microbial infection N. Shetty, M. Wren, E. Aarons, J. Andrews, 85 5 General principles of antimicrobial chemotherapy N. Shetty, E. Aarons, J. Andrews, 124 6 Basic concepts of the epidemiology of infectious diseases N. Shetty, 157 PART 2 A SYSTEMS BASED APPROACH TO INFECTIOUS DISEASES, 177 7 Infections of the skin, soft tissue, bone, and joint N. Shetty, J.W. Tang, 179 8 Gastroenteritis N. Shetty, J.W. Tang, 212 9 Cardiac and respiratory tract infections N. Shetty, J.W. Tang, J. Andrews, 238 10 Infections of the central nervous system N. Shetty, J.W. Tang, 271 11 Infections of the genitourinary system N. Shetty, R. Smith, 294 PART 3 INFECTIONS IN SPECIAL GROUPS, 333 12 Obstetric, congenital and neonatal infections N. Shetty, J.W. Tang, J. Andrews, 335 13 Infections in the immunocompromised host D. Mack, N. Shetty, 363 14 Healthcare associated infections N. Shetty, 393 15 The fever and rash conundrum: rashes of childhood J.W. Tang, 414 PART 4 INFECTIONS OF GLOBAL IMPACT, 435 16 Tuberculosis S. Srivastava, N. Shetty, 437 17 Malaria D. Mack, 458 18 Human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS) J.W. Tang, 476 19 Viral hepatitis J.W. Tang, 491 20 Influenza J.W. Tang, P.K.S. Chan, 506 21 Infections in the returning traveler N. Shetty, 521 PART 5 EMERGING AND RESURGENT INFECTIONS, 551 22 Viral hemorrhagic fevers J.W. Tang, 553 23 Emerging infections I (human monkeypox, hantaviruses, Nipah virus, Japanese encephalitis, chikungunya) J.W. Tang, 567 24 Emerging infections II (West Nile virus, dengue, severe acute respiratory syndrome-associated coronavirus) J.W. Tang, P.K.S. Chan, 583 25 Diphtheria N. Shetty, 599 26 Agents of bioterrorism J.W. Tang, 607 Answers to test yourself questions, 627 Index, 647 ID_1_A01.qxd 2/10/09 13:57 Page iv Editors and Contributors N. Shetty Consultant Microbiologist and Honorary Senior Lecturer, Department of Clinical Microbiology, University College London Hospitals J.W. Tang Consultant Virologist, Division of Microbiology/Molecular Diagnostic Centre, Department of Laboratory Medicine, National University Hospital, Singapore J. Andrews Consultant Microbiologist, Department of Clinical Microbiology, University College London E. Aarons Consultant Virologist, University College London, UK P.K.S. Chan Professor, Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong D. Mack Consultant Microbiologist, Barnet & Chase Farm Hospitals, London, UK R. Smith Consultant Microbiologist, The Royal Free Hospital, London, UK S. Srivastava Specialist Registrar in Microbiology, Royal Devon and Exeter Hospitals, Exeter, Devon, UK M. Wren Consultant Biomedical Scientist, University College London Hospitals, UK ID_1_A01.qxd 2/10/09 13:57 Page v Preface Infectious Disease: Pathogenesis, Prevention, and Case Studies is a new textbook written in the modern era of widespread and ready access to internet resources. The book is aimed at university students with interest in infectious diseases. The level of the text is at an intermediate to senior undergraduate college level and will give the student a sense of the many areas of infectious disease in which he/she may want to specialize further, e.g. an infectious disease clinician, a public health physician, a basic science researcher, or perhaps even a medical journalist specializing in infectious diseases. Topics covered include hospital-acquired infections, emerging and re-emerging infections, infections in the immunocompromised, in pregnancy and in children. The multidisciplinary text makes it suitable for clinical (and perhaps some more basic) microbiology, public health and infectious disease epidemiology courses. A special feature is the extensive use of illustrative clinical cases (many of them based on real cases seen by the authors), which have been included to reinforce some of the concepts touched upon in that chapter. The text is organized into chapters on infections of specific organ systems as well as chapters on specific organisms. This has been done to allow the text to be used on a wide variety of different courses, as well as by different student learning strategies. The style as well as the detail of the text varies from chapter to chapter, reflecting the specialties of the individual authors, but also includes standard items, i.e. sections on epidemiology, pathogenesis, clinical features, diagnosis and treatment, as well as Q&A sections (with answers in the back) and boxes describing specific areas of interest and relevance in each chapter theme. Other boxes are designed to encourage students to think about certain issues, and here, answers are not provided and the student is encouraged to read further. The textbook is sufficient for a complete course in infectious diseases, covering all the major pathogen groups (i.e. bacteria, fungi, parasites, and viruses). It can also be used in specialist modules that may last only one or two semesters, e.g. on hospital-acquired infections, emerging infections, infections of childhood, pregnancy, returning travelers, or the immunocompromised. Teaching can be organized at an organ system level, with specialist modules on specific organisms, e.g. respiratory infections with further detail in a chapter on influenza or infections of the immunocompromised with a specialist chapter on HIV. Although there is extensive cross-referencing between the chapters, each chapter has been written to also stand alone, and the book does not necessarily need to be read in the order in which the chapters are presented. Since the worldwide severe acute respiratory syndrome (SARS) outbreaks of 2003, the ongoing HIV/AIDS pandemic, and the more recent preparedness for a possibly approaching influenza pandemic, internet resources for infectious diseases have become invaluable for tracking and updating information on infectious diseases worldwide. These include comprehensive, easily navigated websites at the Center for Disease Control and Prevention (CDC: http://www.cdc.gov/), the World Health Organization (WHO: http://www.who.int/), and email alert systems like ProMED (http://www.promedmail.org/). In addition, there are now excellent online medical resources, such as eMedicine (www.emedicine.com/) and Medscape (www.medscape.com/). This text incorporates some of these online resources as part of the recommended ‘Further Reading’ in many of the chapters, as it is understood by the authors that the reference journal articles and textbooks, which are also listed, may be less accessible to many readers. In addition, many of the images used in the book are from freely available online resources, particularly the CDC Public Health Image Library (http://phil.cdc.gov/phil/home.asp), which allows students to download such images (after having been directed to them by the main text) for their own use, either as revision and aidé-memoirs, or for their own presentations. A CD is also included containing other images created specially for this book for similar purposes. ID_1_A01.qxd 2/10/09 13:57 Page vi vi Preface This text has been reviewed by teaching staff at many universities. The authors have taken the feedback/comments seriously and made appropriate amendments to the text to enhance its quality for both accuracy and student teaching. Nandini Shetty, Julie Andrews (University College London) Julian Tang (National University Hospital, Singapore) ID_1_A01.qxd 2/10/09 13:57 Page vii Glossary of abbreviated terms AAC N-acetyltransferases AAD antibiotic associated diarrhea Ab antibody ADCC antibody-dependent cellular cytotoxicity ADE antibody-dependent enhancement ADEM acute disseminated encephalomyelitis ADPR adenine diphosphate ribose AIDS acquired immune deficiency syndrome ALT alanine amino transferase ANT O-adenyltransferases APC antigen presenting cell APH O-phosphotransferases ARDS acute respiratory distress syndrome ART antiretroviral therapy ASP amnesic shellfish poisoning ATP adenosine triphosphate ATS American Thoracic Society AZT azidothymidine BAL bronchoalveolar lavage BBB blood–brain barrier BCG Bacille Calmette Guerin BCYE buffered charcoal yeast extract BL Biosafety Level BOOP bronchiolitis obliterans organizing pneumonia BSAC British Society for Antimicrobial Chemotherapy BSE bovine spongiform encephalopathy BSI bloodstream infections BTWC Biological and Toxin Weapons Convention BV bacterial vaginosis CAP community acquired pneumonia CCHF Crimean-Congo hemorrhagic fever CDC Centers for Disease Control and Prevention CF cystic fibrosis CFA colonizing factor antigen CGD chronic granulomatous disease CLSI Clinical and Laboratory Standards Institute CMV cytomegalovirus CNS central nervous system CoNS coagulase negative staphylococci COPD chronic obstructive pulmonary disease CoV coronaviruses CPE cytopathic effect CRC congenital rubella syndrome CRF circulating recombinant forms CRP C reactive protein ID_1_A01.qxd 2/10/09 13:57 Page viii viii Glossary of abbreviated terms CSF cerebrospinal fluid CSF colony-stimulating factor CT computed tomography CTL cytotoxic T lymphocytes CVS congenital varicella syndrome CWD chronic wasting disease d4T stavudine DAP diaminopimelic acid DDC zalcitabine DDI didanosine DDT dichloro-diphenyl-trichloroethane DFA direct fluorescent assay DHF dengue hemorrhagic fever DHF dihydrofolate DIC disseminated intravascular coagulation DIN Deutsches Institut für Normung (English: the German Institute for Standardization) DNA deoxyribonucleic acid DSP diarrheic shellfish poisoning dsRNA double-stranded ribonucleic acid DSS dengue shock syndrome DTH delayed-type hypersensitivity EAEC entero-aggregative E. coli EB elementary body EBV Epstein–Barr virus ECL electrochemiluminescence EEG electroencephalography EF elongation factor EGD esophagogastroduodenoscopy EHEC enterohemorrhagic E. coli EIA enzyme-linked immunoassay EIEC enteroinvasive E. coli EKG electrocardiogram ELISA enzyme-linked immunosorbent assay ELONA enzyme-linked oligonucleotide assay EM electron microscopy EPEC entero-pathogenic E. coli EPP exposure-prone procedures ER emergency room ESBL extended spectrum beta-lactamase ET exfoliatin toxin ETEC entero-toxigenic E. coli EV enterovirus FDA Food and Drug Administration FPA fluorescence polarization assay FRET fluorescence (or Forster) resonance energy transfer G6PD glucose-6-phosphate dehydrogenase deficiency GABHS group A beta-hemolytic streptococci GBS group B beta-hemolytic streptococci G-CSF granulocyte-colony stimulating factor GE gastroenteritis
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