Oxford Textbook of Medical Mycology


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Oxford Textbook of
Medical Mycology

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Oxford Textbook of
Medical Mycology
Edited by
Christopher C. Kibbler
Centre for Medical Microbiology, University College London, UK
Richard Barton
Mycology Reference Centre, Leeds General Infirmary, UK
Neil A.R. Gow
Aberdeen Fungal Group, MRC Centre for Medical Mycology at the University of Aberdeen, UK
Susan Howell
Mycology Laboratory, St John’s Institute of Dermatology, Viapath, London, UK
Donna M. MacCallum
Aberdeen Fungal Group, MRC Centre for Medical Mycology at the University of Aberdeen, UK
Rohini J. Manuel
Public Health Laboratory, National Infection Service, Public Health England, London, UK
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Great Clarendon Street, Oxford, OX2 6DP, United Kingdom Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide. Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries © Oxford University Press 2018 The moral rights of the authors‌have been asserted First Edition published in 2018 Impression: 1 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, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, by licence or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this work in any other form and you must impose this same condition on any acquirer Published in the United States of America by Oxford University Press 198 Madison Avenue, New York, NY 10016, United States of America British Library Cataloguing in Publication Data Data available Library of Congress Control Number: 2017943525 ISBN 978–​0–​19–​875538–​8 Printed in Great Britain by Bell & Bain Ltd., Glasgow Oxford University Press makes no representation, express or implied, that the drug dosages in this book are correct. Readers must therefore always check the product information and clinical procedures with the most up-t​o-d​ ate published product information and data sheets provided by the manufacturers and the most recent codes of conduct and safety regulations. The authors and the publishers do not accept responsibility or legal liability for any errors in the text or for the misuse or misapplication of material in this work. Except where otherwise stated, drug dosages and recommendations are for the non-​pregnant adult who is not breast-​feeding Links to third party websites are provided by Oxford in good faith and for information only. Oxford disclaims any responsibility for the materials contained in any third party website referenced in this work.

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Foreword

I have a fondness for mycology because I have worked all my life on the fungus fission yeast, trying to uncover the mechanisms underlying the control of the eukaryotic cell cycle. Medical mycology is a specialty which has made great strides in recent years and is having increasing influence on the clinical outcomes of individuals with immunocompromising diseases such as leukaemia and AIDS. The mortality of some of their infections is still well over 70%. For example, there are around a million cases of cryptococcosis a year, of which more than 600,000 will result in death. Overall, infections due to fungi occur on a scale similar to malaria, and to many bacterial and viral diseases.
This is a timely comprehensive text on the subject, which has its roots in the British Society for Medical Mycology (BSMM) global Master’s programme, and is aimed at both scientists and clinicians. Advances in targeted chemotherapy can be marred by invasive fungal infections, and there is a real need to encourage young scientists and clinicians to fully engage with this specialty. In the last 50 years, we have gone from a time when there was just one broad-​spectrum antifungal agent for the treatment of serious invasive disease, to one

when there are around 20. Diagnostic methods have been refined and studied in clinical trials, antifungal susceptibility assays are internationally defined and tested, and our understanding of fungal taxonomy and epidemiology has been transformed by molecular biology. There is much to be optimistic about and there is a significant body of knowledge to be assimilated by those working in this area. I think that this Oxford Textbook will go a long way towards achieving this last aspiration.
The editors have recruited international experts to produce up-​ to-​date and detailed chapters aimed at a postgraduate readership. The scope of the book is broad and is divided into six sections, dealing in turn with the basics of mycology, the causative organisms, a systems approach to the mycoses, infections in special populations, diagnostics, and therapy. This book should be a companion for mycology courses and for many scientists and healthcare workers looking to further their knowledge of these topics.
Professor Sir Paul Nurse Director, The Francis Crick Institute, London

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Preface

This book had its genesis in the British Society for Medical Mycology (BSMM) Master’s programme. The editors are tutors on this programme and came together with the express idea of producing a suitable textbook to accompany the courses. Hence, the structure of the book is loosely based on the course structure, expanding content in areas of focused study and bringing together recently acquired knowledge in one place.
However, it was apparent that such a book could be a companion for other courses and, indeed, for scientists and clinicians looking to further their knowledge of medical mycology in topics as diverse as cell function, epidemiology, and advanced diagnostics, through to therapeutic drug monitoring in the management of mycoses. As a consequence, the scope of the book is broader and deeper than originally planned and its readership is expected to be much wider. We have, therefore, divided the book into more sections than originally considered, dealing in turn with the basics of mycology (cell function, taxonomy, pathogenesis, immunology, and so on), the causative organisms, a systems approach to the mycoses, infections

in special populations, diagnostics, and therapy. To take advantage of this broad remit, the reader should make use of all the different sections. For example, whilst the general principles of therapy are dealt with in the clinical sections, the reader will find more details of the individual drugs and strategies in the therapy section, and more about the causative fungi in the mycology section.
We have recruited a faculty of international experts, many of whom are lecturers on the BSMM programme, to produce up-​to-​ date and detailed chapters aimed at a postgraduate readership, and we are very grateful to them for the time and care they have put into their efforts on your behalf. In addition, I would like to thank my fellow editors and everyone who has been involved with the BSMM course. This Oxford Textbook of Medical Mycology is dedicated to them and to the current and former students scattered around the world.
Professor Chris Kibbler London, January 2018

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Contents

List of Abbreviations  xi List of Contributors  xv
SECTION 1 The principles of medical mycology  1
1 Introduction to medical mycology  3 David W. Warnock
2 Fungal taxonomy and nomenclature  8 Andrew M. Borman
3 Physiology and metabolism of fungal pathogens  17 Neil A.R. Gow and Alistair J.P. Brown
4 Fungal cell structure and organization  23 Nick D. Read
5 Fungal genetics  35 Paul S. Dyer, Carol A. Munro, and Rosie E. Bradshaw
6 Fungal genomics and transcriptomics  43 Carol A. Munro and Duncan Wilson
7 Epidemiology of fungal disease  50 Rajal K. Mody, Angela Ahlquist Cleveland, Shawn R. Lockhart, and Mary E. Brandt
8 Pathogenesis of fungal disease  56 Frank C. Odds
9 Immunology of fungal disease  62 Ivy M. Dambuza, Jeanette Wagener, Gordon D. Brown, and Neil A.R. Gow
SECTION 2 Medically important fungi  71
10 Aspergillus species  73 Stephanie J. Smith, Rohini J. Manuel, and Christopher C. Kibbler

11 Candida species  77 Bernhard Hube and Oliver Kurzai
12 Cryptococcus species  80 Catriona L. Halliday and Sarah E. Kidd
13 Other yeasts  83 Chris Linton and Susan Howell
14 Dematiaceous fungi  88 Sarah E. Kidd and Catriona L. Halliday
15 The dermatophytes  93 Susan Howell
16 Endemic dimorphic fungi  98 Angela Restrepo, Angel González, and Beatriz L. Gómez
17 Hyaline moulds  107 Elizabeth M. Johnson
18 Mucoraceous moulds  111 Thomas R. Rogers and Elizabeth M. Johnson
19 Pneumocystis jirovecii  116 Stuart Flanagan
SECTION 3 Fungal diseases  119
20 Fungal bone and joint infections  121 Damien Mack, Simon Warren, Shara Palanivel, and Christopher P. Conlon
21 Fungal cardiovascular infections  128 Sarah Drake and Jonathan Sandoe
22 Fungal central nervous system infections  135 Tihana Bicanic and Thomas S. Harrison
23 Fungal infections of the skin and subcutaneous tissue  145 Roderick J. Hay

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Oxford Textbook of Medical Mycology