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Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information Microbiology in Action Microbes play an important role in our everyday lives. As agents of infectious disease they cause untold human misery, yet their beneficial activities are manifold, ranging from the natural cycling of chemical elements through to the production of food, beverages and pharmaceuticals. In this introductory level text, the authors provide a clear and accessible account of the interactions between microbes, their environment and other organisms, using examples of both beneficial and adverse activities. The book begins by considering beneficial activities, focusing on environmental microbiology and manufacturing, and then moves on to consider some of the more adverse aspects, particularly the myriad of diseases to which we are susceptible and the treatments currently in use. This book is the companion volume to Introductory Microbiology, also published in this series. It provides essential reading for biological science and medical undergraduates, as well as being of interest to sixth form students and their teachers. is a Senior Lecturer in Microbiology at the University of Leeds where his research interests centre on the evolution and dissemination of antibiotic-resistance determinants in Gram-negative bacteria. He is a member of the UK Government Advisory Committee on Novel Foods and Processes. is Professor of Medical Mycology at the University of Leeds and Head of a UK Public Health Laboratory Service Mycology Reference Laboratory. His research interests concern aspects of epidemiology, serodiagnosis, treatment and pathogenesis of fungal infections. is a Senior Lecturer in Microbiology at the University of Leeds where his research focuses on biochemical and immunological aspects of herpesviruses, hepatitis C virus and rhinoviruses. © Cambridge University Press www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information The Institute of Biology aims to advance both the science and practice of biology. Besides providing the general editors for this series, the Institute publishes two journals Biologist and the Journal of Biological Education, conducts examinations, arranges national and local meetings and represents the views of its members to government and other bodies. The emphasis of the Studies in Biology will be on subjects covering major parts of first-year undergraduate courses. We will be publishing new editions of the ‘bestsellers’ as well as publishing additional new titles. Titles available in this series An Introduction to Genetic Engineering, D. S. T. Nicholl Photosynthesis, 6th edition, D. O. Hall and K. K. Rao Introductory Microbiology, J. Heritage, E. G. V. Evans and R. A. Killington Biotechnology, 3rd edition, J. E. Smith An Introduction to Parasitology, Bernard E. Matthews Essentials of Animal Behaviour, P. J. B. Slater Microbiology in Action, J. Heritage, E. G. V. Evans and R. A. Killington © Cambridge University Press www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information Microbiology in action J. Heritage, E. G. V. Evans and R. A. Killington Department of Microbiology, University of Leeds Published in association with the Institute of Biology © Cambridge University Press www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information The Pitt Building, Trumpington Street, Cambridge, United Kingdom The Edinburgh Building, Cambridge CB2 2RU, UK http://www.cup.cam.ac.uk 40 West 20th Street, New York, NY 10011-4211, USA http://www.cup.org 10 Stamford Road, Oakleigh, Melbourne 3166, Australia © Cambridge University Press 1999 This book is in copyright. Subject to statutory exception and to the provisions of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. First published 1999 Printed in the United Kingdom at the University Press, Cambridge Typeset in Monotype Garamond 11/13 in QuarkXPress™ [] A catalogue record for this book is available from the British Library Library of Congress Cataloguing in Publication data Heritage J. Microbiology in action / J. Heritage, E. G. V. Evans, and R. A. Killington. p. cm. Includes bibliographical references and index. ISBN 0 521 62111 9. – ISBN 0 521 62912 8 (pbk.) 1. Microbiology. I. Evans, E. G. V. (Emlyn Glyn Vaughn) II. Killington, R. A. III. Title. QR41.2.H463 1999 579–dc21 98-44695 CIP ISBN 0 521 62111 9 hardback ISBN 0 521 62912 8 paperback © Cambridge University Press www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information Contents Preface page xiii 1 The microbiology of soil and of nutrient cycling 1.1 What habitats are provided by soil? 1.2 How are microbes involved in nutrient cycling? 1.2.1 How is carbon cycled? 1.2.2 How is nitrogen cycled? 1.2.3 How is sulphur cycled? 2 Plant–microbe interactions 2.1 What are mycorrhizas? 2.2 What symbioses do cyanobacteria form? 2.3 What symbioses do other nitrogen-fixing bacteria form? 2.4 From what infections do plants suffer? 2.4.1 What plant diseases are caused by fungi? 2.4.2 What plant diseases are caused by bacteria? 2.4.3 What plant diseases are caused by viruses? 2.5 How are microbes used to control agricultural pests? 3 The microbiology of drinking water 3.1 What are water-borne diseases? 3.1.1 3.1.2 3.1.3 3.1.4 3.1.5 3.1.6 Cholera Enteric fever Bacilliary dysentry Water-borne campylobacter infections Water-borne virus infections Water-borne protozoal diseases © Cambridge University Press 1 1 6 8 8 13 16 16 19 21 22 23 28 29 32 36 36 36 38 39 40 41 42 www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information viii Contents 3.2 How is water examined to ensure that it is safe to drink? 3.3 How is water purified to ensure that it is safe to drink? 3.4 How is sewage treated to make it safe? 44 47 50 4 Microbial products 4.1 How did microbes contribute to the First World War effort? 4.2 What role do microbes play in the oil industry and in mining? 4.3 How are microbial enzymes exploited? 4.4 How do microbes help in the diagnosis of disease and related applications? 4.5 How do microbes contribute to the pharmaceutical industry? 4.6 How do microbes contribute to food technology? 54 55 56 61 5 Food microbiology 5.1 How do microbes affect food? 5.2 How are fungi used as food? 5.3 How are microbes involved in bread and alcohol production? 5.4 How are fermented vegetables and meats produced? 73 73 73 76 79 5.4.1 5.4.2 5.4.3 5.4.4 5.4.5 5.4.6 63 66 70 79 80 81 81 81 82 Sauerkraut Dill pickles Other fermented vegetable products Fermentation of meats Silage production Fermented dairy products 5.5 What role do microbes have in food spoilage and preservation? 86 86 88 5.5.1 How do microbes cause food spoilage? 5.5.2 How can food be preserved? 95 5.6 What causes food poisoning? 5.6.1 5.6.2 5.6.3 5.6.4 5.6.5 5.6.6 5.6.7 5.6.8 5.6.9 5.6.10 Chemical contamination of food Food poisoning associated with consumption of animal tissues Food poisoning associated with the consumption of plant material What are food-borne infections? What is bacterial food poisoning? What is bacterial intoxication? What food poisoning is associated with bacterial infection? What is the role of fungal toxins in food poisoning? What viruses cause food-borne illness? What are the pre-disposing factors in food poisoning incidents? 6 The human commensal flora 6.1 What constitutes the resident and transient flora of humans? 6.2 What constitutes the commensal flora of the human skin? 6.3 What constitutes the commensal flora of the human alimentary tract? © Cambridge University Press 96 97 98 99 101 101 106 113 116 117 119 119 121 122 www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information Contents ix 6.4 What constitutes the commensal flora of the human upper respitory tract? 6.5 What constitutes the commensal flora of the human genital tract? 6.6 What is the role of the human commensal flora? 6.7 What factors affect the human commensal flora? 6.8 Do viruses form part of the human commensal flora? 7 Microbial infections 7.1 How do microbes cause disease and how do we defend ourselves from infection? 7.2 What are urinary tract infections? 7.2.1 What causes urinary tract infections? 7.2.2 What are the symptoms of urinary tract infections? 7.2.3 How may the diagnostic laboratory assist in the diagnosis of urinary tract infections? 7.3 What causes sexually transmissible diseases? 7.3.1 7.3.2 7.3.3 7.3.4 7.3.5 7.3.6 7.3.7 7.3.8 7.3.9 Acquired immunodeficiency syndrome (AIDS) Syphilis Gonorrhoea Non-specific urethritis and other bacterial infections Candidosis (thrush) Trichomoniasis Genital herpes infections Genital warts Pubic lice and scabies 7.4 What causes infections of the central nervous system? 7.4.1 7.4.2 7.4.3 7.4.4 7.4.5 7.4.6 7.4.7 7.4.8 What causes meningitis? What causes encephalitis? What is rabies? What is progressive multifocal leukoencephalopathy? What are poliomyelitis and chronic fatigue syndrome? What are transmissible spongiform encephalopathies? What causes brain abscesses? What is tetanus and how is it related to botulism? 7.5 What causes infections of the circulatory system? 7.5.1 7.5.2 7.5.3 7.5.4 7.5.5 A problem with terminology What is plague? What causes septicaemia? What are the symptoms and consequences of septicaemia? How is septicaemia diagnosed in the diagnostic microbiology laboratory? 7.5.6 What is endocarditis and how does it develop? 7.6 What causes oral cavity and respitory infections? 7.6.1 What causes infections of the oral cavity? 7.6.2 What causes dental caries? © Cambridge University Press 124 125 125 127 128 130 130 139 140 143 143 146 148 152 156 158 160 160 161 161 162 162 163 169 171 172 172 174 176 176 177 178 178 180 180 183 185 187 187 187 www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information x Contents 7.6.3 7.6.4 7.6.5 7.6.6 7.6.7 7.6.8 7.6.9 7.6.10 7.6.11 7.6.12 7.6.13 7.6.14 7.6.15 7.6.16 7.6.17 7.6.18 7.6.19 7.6.20 189 189 190 190 190 191 192 193 194 195 196 197 197 197 201 202 204 205 What is periodontal disease? What is actinomycosis? What is oral thrush? What causes cold sores? What are upper respitory tract infections? What causes sore throats and glandular fever? What causes tonsillitis? What is mumps? What is diptheria? What is acute epiglottitis? What causes middle ear infections? What are lower respitory tract infections? What causes chronic bronchitis? What causes pneumonia? What is Legionnaire’s disease? What is tuberculosis? What causes whooping cough? What is aspergillosis? 206 7.7 What causes gastrointestinal infections? 7.7.1 7.7.2 7.7.3 7.7.4 7.7.5 206 207 209 210 212 What is pseudomembranous colitis? How are faecal samples examined for pathogens? What viruses are associated with gastroenteritis? What causes hepatitis? What is peritonitis 7.8 What causes infections of skin, bone and soft tissues? 7.8.1 7.8.2 7.8.3 7.8.4 7.8.5 What bacteria cause skin and muscle infections? What viruses cause skin lesions? What causes eye infections? What animal-associated pathogens cause soft tissue infections? What infections affect bone and joints? 7.9 What causes perinatal infections? 7.10 What infection do fungi cause? 7.10.1 How are mycoses diagnosed in the laboratory? 7.11 How do we recognise clinically important bacteria? 7.11.1 7.11.2 7.11.3 7.11.4 7.11.5 Gram-positive cocci Gram-positive bacilli Mycobacteria Gram-negative cocci Gram-negative bacilli 8 Chemotherapy and antibiotic resistance 8.1 What inhibits bacterial cell wall synthesis? 8.1.1 8.1.2 8.1.3 8.1.4 8.1.5 8.1.6 Fosfomycin Cycloserine Bacitracin Vancomycin Beta-lactams Isoniazad © Cambridge University Press 213 213 219 221 222 226 227 230 234 237 240 243 245 245 245 249 251 251 251 252 252 252 254 www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information Contents xi 8.2 Which antibacterial agents affect bacterial cell membrane function? 8.3 Which antibacterial agents are inhibitors of nucleic acid metabolism? 8.3.1 Sulphonamides and trimethoprim 8.3.2 Quinolones 254 254 254 255 8.4 Which antibacterial agents are inhibitors of RNA metabolism? 255 8.5 Which antibacterial agents are inhibitors of protein synthesis? 256 8.5.1 8.5.2 8.5.3 8.5.4 8.5.5 8.5.6 Aminoglycosides Tetracyclines Chloramphenicol Macrolides Fusidic acid Mupirocin 8.6 What drugs act as antifugal agents? 8.6.1 8.6.2 8.6.3 8.6.4 8.6.4 Polyene antibiotics Azoles Griseofulvin Flucytosine Allylamines and benzylamines 8.7 What drugs can be used to treat virus infections? 8.7.1 8.7.2 8.7.3 8.7.4 Aciclovir and ganciclovir Amantidine Ribavirin Zidovudine 8.8 What causes antibiotic resistance in bacteria? Further reading Glossary Index © Cambridge University Press 256 256 256 257 257 258 258 258 259 259 260 260 260 261 261 262 262 262 267 269 281 www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information Preface When we wrote Introductory Microbiology some very hard decisions had to be made concerning the contents of the book. We were constrained by the style of the Studies in Biology series to write a book of no more than 200 pages. In the end, we decided that students needed a description of what microorganisms were and how they can be safely manipulated before appreciating what they can do. We therefore took the decision to base our first book on these fundamental aspects of the subject. We were convinced at the time, however, that we could fill a second book with the material that we had omitted from the first. All we had to do was to persuade a publisher that students need to know about much more than we could include in that book. Tim Benton, who edited our Introductory Microbiology, was so pleased with our proposal that he accepted our ideas and then promptly left Cambridge University Press to take up an academic career. We are not suggesting that this career change has any bearing on Tim’s ability to make rational decisions or on the viability of our proposals. The project was handed on to Barnaby Willitts. He was very supportive throughout the writing of this book. As the deadline for submission arose, however, Barnaby left the press (and the country). The project was then handed to Maria Murphy. We owe all those who played a part in producing this book a debt of thanks. The title chosen for this book is Microbes in Action. This implies that microbes have an active impact on our lives. We have framed the text around a series of questions. The answers to these questions illustrate the effects microbes have on humans. In planning this book, we hope to show that microorganisms are more than just the agents of infectious diseases. Without the activities of microbes, for example in the biological cycling of chemical © Cambridge University Press www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information xiv Preface elements, life as we know it would very soon become extinct. To indicate the importance of such beneficial processes, environmental microbiology and the role of microbes in manufacturing have been placed at the beginning of the book. Microbes do, however, cause untold human misery as well as bringing unnoticed benefits. Very early on we reveal how microbes nearly caused the downfall of Winchester Cathedral. This fulfils the promise we made in the preface to Introductory Microbiology, even if we mistook the wood used to build its raft. The cathedral was built on a beech raft, not one of oak. Furthermore, all three authors have research interests that lie within the sphere of medical microbiology. It is for these reasons that the majority of the text describes how microbes harm humans and how we can control them. We trust that our readers will forgive our bias in that direction. We complained in the preface to Introductory Microbiology that there was insufficient room to cover all of microbiology in a text of that size. We have again failed to include everything of interest that we had to omit from our first book. It would be churlish to complain again about the lack of space. We have, however, left uncovered those things which we ought to have covered . . . And there is no health in us. To get around this problem we have included a list of texts through which interested readers may extend their knowledge. We hope that this provides recompense for our manifold sins and wickedness. Constraints of space have beaten us once again. We have concentrated on the areas covered by our research interests. This is why the book is largely devoted to bacteria, fungi and viruses. We have had to omit important material on parasites, for example, although books listed in the Further reading section should cover the material that we have left out. If readers are wondering about the differences between bacteria, fungi and viruses, or how prokaryotic cells differs from eukaryotic cells, then we can do no better than recommend Introductory Microbiology. Alternatively, the reader could always refer to the glossary at the back of this book. During the production of this book, my wife took our children to visit her mother for two weeks while the writing was at its most difficult. This was a time when too much of the book had been written to cancel the project and not enough had been assembled to allow sight of the end of the writing. I am truly grateful to my family for the break this gave me to write uninterrupted. Without this gesture it is doubtful that you would now be holding this book in your hand. I owe a huge debt to my family. They showed great patience during the writing of this book. Again, this book would not have been possible without the assistance of colleagues who have advised on different aspects of the project. Our thanks © Cambridge University Press www.cambridge.org Cambridge University Press 0521621119 - Microbiology in Action J. Heritage, E. G. V. Evans and R. A. Killington Frontmatter More information Preface xv are extended to those who have participated in the production of this book but the mistakes that are left remain our responsibility. We were pleased with the success of Introductory Microbiology: Cambridge University Press must have been similarly pleased to allow us to finish this project. We are grateful for that trust and hope that you will enjoy this book as much as its predecessor. JH York © Cambridge University Press www.cambridge.org
