Table Of Content

MICROBIAL BIOFILMS, SECOND EDITION Ghannoum MICROBIAL Parsek An examination of the research and translational applications Whiteley to prevent and treat biofilm-associated diseases Mukherjee In the decade since the first edition of Microbial Biofilms was published, the interest in this field has expanded, spurring breakthrough research that has advanced the treatment of biofilm-associated diseases. This second M BIOFILMS edition takes the reader on an exciting, extensive review of bacterial and fungal biofilms, ranging from basic molecular interactions to innovative therapies, with particular emphasis on the division of labor in biofilms, new approaches to combat the threat of microbial biofilms, and how biofilms evade the host defense. I Chapters written by established investigators cover recent findings, and contributions from investigators new to C the field provide unique and fresh insights. Specifically, Microbial Biofilms provides SECOND EDITION • state-of-the-art research in the field of bacterial and fungal biofilms R • detailed descriptions of the in vitro and in vivo models available to evaluate microbial biofilms • future areas of research and their translational and clinical applications O Microbial Biofilms is a useful reference for researchers and clinicians. It will also provide insight into the dynamic field of microbial biofilms for graduate and postgraduate students. B “ Biofilms influence human health and agriculture, and sustain diverse ecosystems. This second edition of Microbial Biofilms provides a masterful overview of critical topics central to fungal and bacterial I biofilms by celebrated experts in the field. It is a must read for any professional seeking basic or A advanced knowledge of microbial biofilms.” – David S. Perlin, Professor and Executive Director L Public Health Research Institute, New Jersey Medical School-Rutgers University B Mahmoud A. Ghannoum is a Professor in the De- Pranab Mukherjee is an Assistant Professor in the I partment of Dermatology at Case Western Reserve Department of Dermatology at Case Western Reserve O University and University Hospitals Case Medical Center University. Dr. Mukherjee has extensive experience in and Director of the Center for Medical Mycology. Dr. fungal pathogenesis and microbial biofilms, including Ghannoum’s investigations include the biology, patho- analyses of their biochemical and molecular pathways genesis, and resistance of clinically important fungi using systems biology approaches. He also studies the Candida, Aspergillus, and Cryptococcus, and his work human microbiome (bacteriome and mycobiome) in F has recently focused on the oral microbiome, fungal species, and human health and disease, including HIV-infection, corneal infections, inflammatory disease. He has published more than 300 peer-reviewed articles in the field bowel disease, eczema, and psoriasis. He advises pharmaceutical companies I Editors of biofilms, microbial pathogenesis, and preclinical in vitro and in vivo evalu- in antifungal drug development . L ations of antimicrobials. Marvin Whiteley is the Director of the Center for Matthew Parsek is a Professor of Microbiology at Infectious Disease and a fellow of the John Ring M Mahmoud Ghannoum the University of Washington, School of Medicine at LaMontagne Chair in Infectious Diseases and Global Seattle. Dr. Parsek’s research focuses on microbial Health at the University of Texas at Austin. Dr. Whiteley’s Matthew Parsek community behaviors and their relationship to disease. research focuses on understanding how microbes within infection sites cooperate to cause disease. S Marvin Whiteley Pranab K. Mukherjee SECOND EDITION ISBN 9781555817459 90000 > 9 781555 817459 MICROBIAL BIOFILMS SECOND EDITION MICROBIAL BIOFILMS SECOND EDITION Editors Mahmoud Ghannoum Matthew Parsek Marvin Whiteley Pranab K. Mukherjee Washington, DC Copyright © 2015 by ASM Press. ASM Press is a registered trademark of the American Society for Microbiology. All rights reserved. No part of this publication may be reproduced or transmitted in whole or in part or reutilized in any form or by any means, electronic or mechanical, including photocopying and recording, or by any information storage and retrieval system, without permission in writing from the publisher. Disclaimer: To the best of the publisher’s knowledge, this publication provides information concerning the subject matter covered that is accurate as of the date of publication. The publisher is not providing legal, medical, or other professional services. Any reference herein to any specifi c commercial products, procedures, or services by trade name, trademark, manufacturer, or otherwise does not constitute or imply endorsement, recommendation, or favored status by the American Society for Microbiology (ASM). The views and opinions of the author(s) expressed in this publication do not necessarily state or refl ect those of ASM, and they shall not be used to advertise or endorse any product. Library of Congress Cataloging-in-Publication Data Microbial biofi lms / editors, Mahmoud Ghannoum, Case Western University, Cleveland, OH; Matthew Parsek, University of Washington, Seattle, WA; Marvin Whiteley, University of Texas at Austin, Austin, TX; Pranab K. Mukherjee, Case Western University, Cleveland, OH. -- 2nd edition. pages cm Includes bibliographical references and index. ISBN 978-1-55581-745-9 (alk. paper) -- ISBN 978-1-55581-746-6 (alk. paper) 1. Biofi lms. I. Ghannoum, Mahmoud A. (Mahmoud Afi f), editor. II. Parsek, Matthew R., editor. III. Whiteley, Marvin, editor. IV. Mukherjee, Pranab K., editor. QR100.8.B55M5252 2015 579’.17--dc23 2015030735 ISBN 978-1-55581-745-9 e-ISBN 978-1-55581-746-6 doi:10.1128/9781555817466 Printed in the United States of America 10 9 8 7 6 5 4 3 2 1 Address editorial correspondence to: ASM Press, 1752 N St., N.W., Washington, DC 20036-2904, USA. Send orders to: ASM Press, P.O. Box 605, Herndon, VA 20172, USA. Phone: 800-546-2416; 703-661-1593. Fax: 703-661-1501. E-mail: [email protected] Online: http://estore.asm.org. Contents Contributors(cid:2)vii Preface(cid:2)xiii Acknowledgments(cid:2)xv 1 New Technologies for Studying Biofi lms(cid:3)1 Michael J. Franklin, Connie Chang, Tatsuya Akiyama, and Brian Bothner 2 Fungal Biofi lms: In Vivo Models for Discovery of Anti-Biofi lm Drugs(cid:3)33 Jeniel E. Nett and David R. Andes 3 Biofi lm Development(cid:3)51 Tim Tolker-Nielsen 4 Division of Labor in Biofi lms: the Ecology of Cell Diff erentiation(cid:3)67 Jordi van Gestel, Hera Vlamakis, and Roberto Kolter 5 Candida albicans Biofi lm Development and Its Genetic Control(cid:3)99 Jigar V. Desai and Aaron P. Mitchell 6 Candida Biofi lms: Development, Architecture, and Resistance(cid:3)115 Jyotsna Chandra and Pranab K. Mukherjee 7 Biofi lm Formation by Cryptococcus neoformans(cid:3)135 Luis R. Martinez and Arturo Casadevall 8 Aspergillus Biofi lm In Vitro and In Vivo(cid:3)149 Anne Beauvais and Jean-Paul Latgé 9 Adhesins Involved in Attachment to Abiotic Surfaces by Gram-Negative Bacteria(cid:3)163 Cécile Berne, Adrien Ducret, Gail G. Hardy, and Yves V. Brun 10 Biofi lm Matrix Proteins(cid:3)201 Jiunn N. C. Fong and Fitnat H. Yildiz 11 Bacterial Extracellular Polysaccharides in Biofi lm Formation and Function(cid:3)223 Dominique H. Limoli, Christopher J. Jones, and Daniel J. Wozniak 12 The Biology of the Escherichia coli Extracellular Matrix(cid:3)249 David A. Hufnagel, William H. DePas, and Matthew R. Chapman 13 Antimicrobial Tolerance in Biofi lms(cid:3)269 Philip S. Stewart 14 How Biofi lms Evade Host Defenses(cid:3)287 Emmanuel Roilides, Maria Simitsopoulou, Aspasia Katragkou, and Thomas J. Walsh v vi CONTENTS 15 c-di-GMP and its Eff ects on Biofi lm Formation and Dispersion: a Pseudomonas Aeruginosa Review(cid:3)301 Dae-Gon Ha and George A. O’Toole 16 Mechanisms of Competition in Biofi lm Communities(cid:3)319 Olaya Rendueles and Jean-Marc Ghigo 17 Dispersal from Microbial Biofi lms(cid:3)343 Nicolas Barraud, Staff an Kjelleberg, and Scott A. Rice 18 Chemical Biology Strategies for Biofi lm Control(cid:3)363 Liang Yang and Michael Givskov 19 From Biology to Drug Development: New Approaches to Combat the Threat of Fungal Biofi lms(cid:3)373 Christopher G. Pierce, Anand Srinivasan, Anand K. Ramasubramanian, and José L. López-Ribot Index(cid:2)389 Contributors Tatsuya Akiyama Center for Biofi lm Engineering Department of Microbiology and Immunology Montana State University-Bozeman Bozeman, MT 59717 David R. Andes Department of Medicine and Department of Medical Microbiology and Immunology University of Wisconsin Madison, WI 53706 Nicolas Barraud Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney, NSW 2052, Australia Anne Beauvais Unité des Aspergillus Institut Pasteur 75015 Paris, France Cécile Berne Department of Biology Jordan Hall JH142 Indiana University Bloomington, IN 47405 Brian Bothner Center for Biofi lm Engineering Department of Chemistry and Biochemistry Montana State University-Bozeman Bozeman, MT 59717 Yves V. Brun Department of Biology Jordan Hall JH142 Indiana University Bloomington, IN 47405 vii viii CONTRIBUTORS Arturo Casadevall Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health Baltimore, MD 21205 Jyotsna Chandra Center for Medical Mycology and Mycology Reference Laboratory Department of Dermatology University Hospitals of Cleveland and Case Western Reserve University Cleveland, OH 44106 Connie Chang Center for Biofi lm Engineering Department of Chemical and Biological Engineering Montana State University-Bozeman Bozeman, MT 59717 Matthew R. Chapman Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor, MI 48109 William H. DePas Department of Microbiology and Immunology University of Michigan Ann Arbor, MI 48109 Jigar V. Desai Department of Biological Sciences Carnegie Mellon University Pittsburgh, PA 15213 Adrien Ducret Department of Biology Jordan Hall JH142 Indiana University Bloomington, IN 47405 Jiunn N. C. Fong Department of Microbiology and Environmental Toxicology University of California, Santa Cruz Santa Cruz, CA 95064 Michael J. Franklin Center for Biofi lm Engineering Department of Microbiology and Immunology Montana State University-Bozeman Bozeman, MT 59717 Jean-Marc Ghigo Institut Pasteur Unité de Génétique des Biofi lms Département de Microbiologie F-75015 Paris, France CONTRIBUTORS ix Michael Givskov Singapore Centre on Environmental Life Sciences Engineering Nanyang Technological University Singapore Costerton Biofi lm Center Department of International Health, Immunology, and Microbiology University of Copenhagen 2200 København N, Denmark Dae-Gon Ha Departments of Microbiology and Immunology Geisel School of Medicine at Dartmouth Hanover, NH 03755 Gail G. Hardy Department of Biology Jordan Hall JH142 Indiana University Bloomington, IN 47405 David A. Hufnagel Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor, MI 48109 Christopher J. Jones Department of Microbiology and Environmental Toxicology University of California, Santa Cruz Santa Cruz, CA 95064 Aspasia Katragkou Infectious Diseases Unit 3rd Department of Pediatrics Faculty of Medicine Aristotle University School of Health Sciences Hippokration Hospital 54642 Thessaloniki, Greece Transplantation-Oncology Infectious Diseases Program Weill Cornell Medical Center of Cornell University New York, NY 14850 Staff an Kjelleberg Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney, NSW 2052, Australia Singapore Centre on Environmental Life Sciences Engineering, and the School of Biological Sciences Nanyang Technological University Singapore 639798