Table Of ContentHuman Pathogenic Fungi
Molecular Biology and Pathogenic Mechanisms
Edited by
Derek J. Sullivan
and
Gary P. Moran
Caister Academic Press
Human Pathogenic Fungi
Molecular Biology and Pathogenic Mechanisms
Edited by
Derek J. Sullivan and Gary P. Moran
Division of Oral Biosciences
School of Dental Science and Dublin Dental University Hospital
Trinity College Dublin
Dublin
Ireland
Caister Academic Press
Copyright © 2014
Caister Academic Press
Norfolk, UK
www.caister.com
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library
ISBN: 978-1-908230-44-7 (hardback)
ISBN 978-1-908230-66-9 (ebook)
Description or mention of instrumentation, software, or other products in this book does
not imply endorsement by the author or publisher. The author and publisher do not assume
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book or for the consequences of their use.
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, without the prior permission of the publisher. No claim to original
U.S. Government works.
Cover design adapted from Figures 7.1 and 9.2
Contents
Contributors v
Preface ix
Part I Recent Advances in the Pathogenesis of Human Fungal Infections 1
1 Understanding Fungal Pathogenesis with High-throughput Sequencing 3
Vincent Bruno
2 Comparative Genomics and Evolutionary Analyses of Human
Fungal Pathogens 17
David A. Fitzpatrick
3 Data-driven Systems Biology of Fungal Infections 37
Fabian Horn, Vito Valiante, Reinhard Guthke and Axel A. Brakhage
4 Comparative Pathogenesis: Transcriptomic Analyses of Host
Cell–Fungus Interactions 61
Elaine Bignell
5 Animal Models of Human Fungal Infection 87
Donna M. MacCallum
6 Host Responses to Fungal Infection 117
David L. Moyes, Jonathan P. Richardson and Julian R. Naglik
Part II Pathogenic Mechanisms of Human Fungal Pathogens 141
7 A Molecular Update on the Pathogenesis of Candidiasis 143
Duncan Wilson and Bernhard Hube
8 Virulence Characteristics of Aspergillus fumigatus 165
Rebecca A. Owens, Grainne O’Keeffe, Karen A. O’Hanlon, Lorna Gallagher and
Sean Doyle
9 Cryptococcus 197
Rocío García-Rodas, Radames J.B. Cordero and Oscar Zaragoza
iv | Contents
10 Dermatophytes as Saprophytes and Pathogens 223
Michel Monod, Bernard Mignon and Peter Staib
11 Pathogenesis Mechanisms of Histoplasma capsulatum 253
Chad A. Rappleye
12 Blastomyces dermatitidis and Blastomycosis 273
Gregory M. Gauthier
13 New Insights into Pathogenesis of Pneumocystis Pneumonia 297
Jakrapun Pupaibool and Andrew H. Limper
14 Paracoccidioides Mechanisms of Pathogenesis and Virulence 317
Juliana Alves Parente, Clayton Luiz Borges, Maristela Pereira, Alexandre Melo
Bailão, Rosely Maria Zancopé Oliveira and Célia Maria de Almeida Soares
Index 339
Contributors
Célia Maria de Almeida Soares Axel A. Brakhage
Laboratório de Biologia Molecular Molecular and Applied Microbiology
Instituto de Ciências Biológicas Leibniz Institute for Natural Product Research and
Universidade Federal de Goiás Infection Biology
Goiânia, Goiás Hans Knöll Institute
Brazil Jena
Germany; and
[email protected]
Institute of Microbiology
Friedrich Schiller University
Alexandre M. Bailão
Jena
Laboratório de Biologia Molecular
Germany
Instituto de Ciências Biológicas
Universidade Federal de Goiás [email protected]
Goiânia, Goiás
Brazil Vincent Bruno
Department of Microbiology and Immunology
[email protected]
Institute for Genome Sciences
University of Maryland School of Medicine
Elaine Bignell
Baltimore, MD
Institute for Inflammation and Repair
USA
Manchester Fungal Infection Group
University of Manchester [email protected]
Manchester
UK Radames J.B. Cordero
Department of Microbiology and Immunology
[email protected]
Albert Einstein College of Medicine
Bronx, NY
Clayton L. Borges
USA
Laboratório de Biologia Molecular
Instituto de Ciências Biológicas [email protected]
Universidade Federal de Goiás
Goiânia, Goiás Sean Doyle
Brazil Department of Biology
National University of Ireland Maynooth
[email protected]
Maynooth
County Kildare
Ireland
[email protected]
vi | Contributors
David A. Fitzpatrick Bernhard Hube
Genome Evolution Laboratory Department of Microbial Pathogenicity Mechanisms
Department of Biology Leibniz Institute for Natural Product Research and
The National University of Ireland Maynooth Infection Biology
Maynooth Hans Knöll Institute
County Kildare Jena
Ireland Germany
[email protected] [email protected]
Lorna Gallagher Andrew H. Limper
Department of Biology Division of Pulmonary and Critical Care
National University of Ireland Maynooth Thoracic Diseases Research Unit
Maynooth Department of Internal Medicine
County Kildare Mayo Clinic College of Medicine
Ireland Mayo Clinic
Rochester, MN
[email protected]
USA
Rocío García-Rodas [email protected]
National Centre for Microbiology
Instituto de Salud Carlos III Donna M. MacCallum
Madrid Aberdeen Fungal Group
Spain School of Medical Sciences
Institute of Medical Sciences
[email protected]
University of Aberdeen
Aberdeen
Gregory M. Gauthier
UK
Department of Medicine
Division of Infectious Diseases [email protected]
University of Wisconsin-Madison
Madison, WI Bernard Mignon
USA Veterinary Mycology
Department of Infectious and Parasitic Diseases
[email protected]
Faculty of Veterinary Medicine
University of Liège
Reinhard Guthke
Liège
Systems Biology/Bioinformatics
Belgium
Leibniz Institute for Natural Product Research and
Infection Biology [email protected]
Hans Knöll Institute
Jena Michel Monod
Germany Department of Dermatology
Centre Hospitalier Universitaire Vaudois
[email protected]
Lausanne
Switzerland
Fabian Horn
Systems Biology/Bioinformatics [email protected]
Leibniz Institute for Natural Product Research and
Infection Biology
Hans Knöll Institute
Jena
Germany
[email protected]
Contributors | vii
David L. Moyes Juliana A. Parente
Department of Oral Immunology Laboratório de Biologia Molecular
Clinical and Diagnostic Science Group Instituto de Ciências Biológicas
King’s College London Dental Institute Universidade Federal de Goiás
King’s College Goiânia, Goiás
London Brazil
UK
[email protected]
[email protected]
Maristela Pereira
Julian R. Naglik Laboratório de Biologia Molecular
Department of Oral Immunology Instituto de Ciências Biológicas
Clinical and Diagnostic Science Group Universidade Federal de Goiás
King’s College London Dental Institute Goiânia, Goiás
King’s College Brazil
London
[email protected]
UK
[email protected] Jakrapun Pupaibool
Division of Infectious Diseases
Karen A. O’Hanlon Mayo Clinic College of Medicine
Department of Biology Rochester, MN
National University of Ireland Maynooth USA
Maynooth
[email protected]
County Kildare
Ireland
Chad A. Rappleye
[email protected] Department of Microbiology
Department of Microbial Infection and Immunity
Grainne O’Keeffe Ohio State University
Department of Biology Columbus, OH
National University of Ireland Maynooth USA
Maynooth
[email protected]
County Kildare
Ireland
Jonathan P. Richardson
[email protected] Department of Oral Immunology
Clinical and Diagnostic Science Group
Rosely Maria Zancopé Oliveira King’s College London Dental Institute
Laboratório de Micologia King’s College
Instituto de Pesquisa Clínica Evandro Chagas London
Fundação Oswaldo Cruz UK
Manguinhos, Rio de Janeiro
[email protected]
Brazil
[email protected] Peter Staib
Department of Research and Development
Rebecca A. Owens Kneipp-Werke
Department of Biology Würzburg
National University of Ireland Maynooth Germany
Maynooth
[email protected]
County Kildare
Ireland
[email protected]
viii | Contributors
Vito Valiante Duncan Wilson
Molecular and Applied Microbiology Department of Microbial Pathogenicity Mechanisms
Leibniz Institute for Natural Product Research and Leibniz Institute for Natural Product Research and
Infection Biology Infection Biology
Hans Knöll Institute Hans Knöll Institute
Jena Jena
Germany Germany
[email protected] [email protected]
Oscar Zaragoza
National Centre for Microbiology
Instituto de Salud Carlos III
Madrid
Spain
[email protected]
Preface
Human Pathogenic Fungi: New Technologies
and New Insights into Pathogenesis
Infections caused by fungi are a significant con- techniques are revolutionizing our understanding
tributor to morbidity and mortality in humans. of how fungi cause disease. Meanwhile, Chapter
These infections range from comparatively 2 describes how these same techniques have led
innocuous superficial skin diseases caused by to the sequencing of over 100 fungal genomes,
dermatophytes to invasive life-threatening infec- including those of the most important human
tions caused by species such as Candida albicans, pathogens, and how these data are being used to
Cryptococcus neoformans and Aspergillus fumiga- elucidate the evolution of fungal virulence. How
tus, amongst others. Since many of the diseases the application of high throughput data-driven
caused by fungi are opportunistic in nature, the systems biology can impact on our understand-
pathogenesis of fungal infections is complex and ing of fungal–host interactions is discussed in
our understanding of how these microorgan- Chapter 3, while Chapter 4 examines specifically
isms cause disease has lagged behind bacterial what comparative transcriptomics can tell us
and viral pathogens. However, the application of about how the fungus and host cells interact and
new genomic and other molecular techniques in respond during infection. Chapter 5 describes the
recent years has revolutionized the field of fungal fungal infection models currently in use and how
pathogenesis. This has resulted in a dramatic these have helped enhance our understanding of
improvement in our understanding of how fungi the processes involved in human disease while
cause disease in humans and the aim of this book Chapter 6 provides an overview of our current
is to summarize recent developments in this rap- understanding of how the host recognizes colo-
idly evolving area. nizing and infecting fungi and how host immune
The book is divided into two sections; the first defences prevent and resolve infections. The
includes chapters detailing the state of the art tools second section includes chapters (Chapters 7–14)
and approaches currently in use at the forefront of that specifically provide a self-contained and
comparative biology of pathogenic fungi; and the detailed analysis of recent advances in the study
second an in-depth analysis of the current under- of the pathogenesis of the major fungal patho-
standing of the pathogenic mechanisms of specific gens of humans, including Candida, Aspergillus,
fungal pathogens. Each chapter has been written Cryptococcus, Dermatophytes, Histoplasma,
by a high profile author(s) who is a recognized Blastomyces, Pneumocystis and Paracoccidioides.
leader in their field. In the first section, Chapter
1 summarizes how next generation sequencing
