Bacterial Genomes and Infectious Diseases Edited by Voon L. Chan, PhD Philip M. Sherman, MD, FRCPC Billy Bourke, MD, FRCPI Bacterial Genomes and Infectious Diseases Bacterial Genomes and Infectious Diseases Edited by Voon L. Chan, PhD Department of Medical Genetics and Microbiology University of Toronto, Toronto, Ontario, Canada Philip M. Sherman, MD, FRCPC Department of Paediatrics Department of Laboratory Medicine and Pathobiology Hospital for Sick Children University of Toronto, Toronto, Ontario, Canada Billy Bourke, MD, FRCPI Children's Research Center, Our Lady's Hospital for Sick Children, School of Medicine and Medical Science, Conway Institute for Biomolecular and Biomedical Research, University College, Dublin, Ireland © 2006 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 www.humanapress.com All rights reserved. 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Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 1-59745-152-5 (e-book) Library of Congress Cataloging in Publication Data Bacterial genomes and infectious diseases / edited by Voon L. Chan, Philip M. Sherman, Billy Bourke. p. cm. Includes bibliographical references and index. ISBN 1-58829-496-X (alk. paper) 1. Bacterial genomes. 2. Communicable diseases--Pathogenesis. I. Chan, Voon L. II. Sherman, Philip M. III. Bourke, Billy. QH434.B334 2006 616.9'201--dc22 2005034347 Preface The first bacterial genome, Haemophilus influenzae, was completely sequenced, annotated, and published in 1995. Today, more than 200 prokaryotic (archaeal and bacterial) genomes have been completed and over 500 prokaryotic genomes are in vari- ous stages of completion. Seventeen eukaryotic genomes plus four eukaryotic chromo- somes have been completed. The concept of achieving better understanding of an organism through knowledge of the complete genomic sequence was first demonstrated in 1978 when the first bacteriophage genome, ΦX174, was sequenced. Complete genomic sequences of prokaryotes have led to a better understanding of the biology and evolution of the microbes, and, for pathogens, facilitated identification of new vaccine candidates, putative virulence genes, targets for antibiotics, new strategy for rapid diagnosis, and investigation of bacteria–host interactions and disease mecha- nisms. Recent increased interest in microbial pathogens and infectious diseases is largely attributed to the re-emergence of infectious diseases like tuberculosis, emergence of new infectious diseases like AIDS and severe acute respiratory syndrome, the problem of an increasing rate of emergence of antibiotic-resistant variants of pathogens, and the fear of bioterrorism. Microbes are highly diverse and abundant in the biosphere. Less than 1% of these morphologically identified microbes can be cultured in vitro using standard techniques and conditions. With such abundance of microbes in nature, we can expect to see new variants and new species evolve and a small number will emerge as pathogens to humans. In the first section of Bacterial Genomes and Infectious Diseases, some major gen- eral findings about bacterial genomes and their impact on strategy and approach for investigating mechanisms of pathogenesis of infectious diseases are discussed. Later chapters focus on the value and power of genomics, proteomics, glycomics, and bioinformatics as applied to selected specific bacterial pathogens. Bacterial Genomes and Infectious Diseases is designed to provide valuable reading for senior microbiology, pathobiology and genetics undergraduate and graduate stu- dents, medical students, clinician scientists, infectious diseases clinicians, and medical microbiologists. Voon L. Chan, PhD Philip M. Sherman, MD, FRCPC Billy Bourke, MD, FRCPI v Contents Preface .......................................................................................................................... v Contributors ................................................................................................................. ix Introduction.................................................................................................................. xi 1 Microbial Genomes Voon Loong Chan .................................................................................................. 1 2 Evolution and Origin of Virulence Isolates Voon Loong Chan, Philip M. Sherman, and Billy Bourke ................................... 21 3 Genomic Approach to Understanding Infectious Disease Mechanisms Voon Loong Chan, Philip M. Sherman, and Billy Bourke ................................... 31 4 Knockout and Disease Models in Toll-Like Receptor-Mediated Immunity Huey-Lan Huang and Wen-Chen Yeh ................................................................. 41 5 Campylobacter: From Glycome to Pathogenesis John Kelly, Jean-Robert Brisson, N. Martin Young, Harold C. Jarrell, and Christine M. Szymanski .............................................. 63 6 Genomics of Helicobacter Species Zhongming Ge and David B. Schauer................................................................. 91 7 The Organization of Leptospira at a Genomic Level Dieter M. Bulach, Torsten Seemann, Richard L. Zuerner, and Ben Adler ............................................................................................... 109 8 Listeria monocytogenes Keith Ireton ....................................................................................................... 125 9 Mycobacterial Genomes David C. Alexander and Jun Liu........................................................................ 151 10 Mycoplasma Yuko Sasaki ....................................................................................................... 175 11 Genome Comparisons of Diverse Staphylococcus aureus Strains Martin J. McGavin............................................................................................. 191 12 Type III Secretion Systems in Yersinia pestis and Yersinia pseudotuberculosis James B. Bliska, Michelle B. Ryndak, and Jens P. Grabenstein ................................................................................ 213 13 Genomics and the Evolution of Pathogenic Vibrio cholerae William S. Jermyn, Yvonne A. O’Shea, Anne Marie Quirke, and E. Fidelma Boyd .................................................... 227 vii viii Contents 14 Future Directions of Infectious Disease Research Philip M. Sherman, Billy Bourke, and Voon Loong Chan ................................. 255 Index ......................................................................................................................... 265 Contributors BEN ADLER • Australian Bacterial Pathogenesis Program and Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University Clayton, Victoria, Australia DAVID C. ALEXANDER • Montreal General Hospital Research Institute, McGill University Health Center, Montreal, Quebec, Canada JAMES B. BLISKA • Department of Molecular Genetics and Microbiology, Center for Infectious Diseases, State University of New York at Stony Brook, Stony Brook, NY E. FIDELMA BOYD • Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland BILLY BOURKE •Children's Research Center, Our Lady's Hospital for Sick Children, School of Medicine and Medical Science, Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Ireland JEAN-ROBERT BRISSON • Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada DIETER BULACH • Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University Clayton, Victoria, Australia VOON L. (RICKY) CHAN • Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada ZHONGMING GE • Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA JENS P. GRABENSTEIN • School of Medicine, New York University, New York, NY HUEY-LAN HUANG • The Campbell Family Institute for Breast Cancer Research, Ontario Cancer