Genomes of Foodborne and Waterborne Pathogens

382 Pages·2010·20.336 MB·English

by  Pina Fratamico, Yanhong Liu, Sophia Kathariou

Genomes of Foodborne
and Waterborne Pathogens
This page intentionally left blank
Genomes of Foodborne
and Waterborne Pathogens
edited by
Pina Fratamico
Eastern Regional Research Center
Agricultural Research Service
U.S. Department of Agriculture
Wyndmoor, Pennsylvania
Yanhong Liu
Eastern Regional Research Center
Agricultural Research Service
U.S. Department of Agriculture
Wyndmoor, Pennsylvania
Sophia Kathariou
Department of Food, Bioprocessing and Nutrition Sciences
North Carolina State University
Raleigh, North Carolina
W A S H I N G T O N , D C
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Library of Congress Cataloging-in-Publication Data
Genomes of foodborne and waterborne pathogens / edited by Pina Fratamico, Yanhong Liu, Sophia Kathariou.
p. ; cm.
Includes bibliographical references and index.
ISBN 978-1-55581-457-1 (hardcover)
1. Food—Microbiology. 2. Water—Microbiology. 3. Microbial genetics. I. Fratamico, Pina M.
II. Liu, Yanhong, 1965 May 1- III. Kathariou, Sophia. IV. American Society for Microbiology.
[DNLM: 1. Food Microbiology. 2. Gram-Negative Bacteria—genetics. 3. Gram-Negative
Bacteria—pathogenicity. 4. Gram-Positive Bacteria—genetics. 5. Gram-Positive Bacteria—pathogenicity.
6. Water Microbiology. QW 85]
QR115.G46 2011
664.001'579—dc22
2010035116
10 9 8 7 6 5 4 3 2 1
All Rights Reserved
Printed in the United States of America
CONTENTS
Contributors • vii 8. Genomics of the Enteropathogenic
Preface • xi Yersiniae • 101
Alan McNally, Nicholas R. Thomson,
and Brendan W. Wren
1. Insights from Genomic Studies of the
Foodborne and Waterborne Pathogen 9. Staphylococcus aureus • 113
Escherichia coli O157:H7 • 1 Scott Weese, Jinzhe Mao, and David M. Donovan
Victor P. J. Gannon, Chad R. Laing,
and Yongxiang Zhang 10. Genomics of Listeria monocytogenes and
Other Members of the Genus Listeria • 125
2. Shigella Genomes: a Tale of Convergent Carmen Buchrieser and Philippe Glaser
Evolution and Specialization through IS Expansion
and Genome Reduction • 23 11. Bacillus cereus • 147
Jian Yang, Vartul Sangal, Qi Jin, and Jun Yu Monika Ehling-Schulz, Rickard Knutsson,
and Siegfried Scherer
3. Genome Rearrangements in Salmonella
• 41 12. Bacillus anthracis • 165
Jean F. Challacombe, Richard T. Okinaka,
T. David Matthews and Stanley Maloy
A. Christine Munk, Thomas S. Brettin, and Paul Keim
4. Campylobacter and Arcobacter • 49
13. Clostridium botulinum • 185
William G. Miller and Craig T. Parker
Holger Brüggemann, Antje Woltherr,
Christelle Mazuet, and Michel R. Popoff
5. Comparative Genomics of Vibrio vulnificus:
Biology and Applications • 67 14. Clostridium perfringens • 213
Lien-I Hor, Hung-Yu Shu, Keh-Ming Wu,
Karl A. Hassan and Ian T. Paulsen
and Shih-Feng Tsai
15. Mycobacterium avium Subspecies
6. Vibrio parahaemolyticus • 77 paratuberculosis • 223
Kaori Izutsu and Tetsuya Iida John P. Bannantine, Yung-Fu Chang, and Vivek Kapur
7. How Genomics Has Shaped Our Understanding 16. Foodborne Noroviruses • 237
of the Evolution and Emergence of Pathogenic David H. Kingsley
Vibrio cholerae • 85
Salvador Almagro-Moreno, Ronan A. Murphy, 17. Hepatitis A and E Viruses • 247
and E. Fidelma Boyd Albert Bosch and Rosa M. Pintó
v
vi CONTENTS
18. Genomics of Aspergillus flavus 22. Impact of the Toxoplasma gondii
Mycotoxin Production • 259 Genome Project • 309
Gary A. Payne, D. Ryan Georgianna, Jiujiang Yu, Benjamin M. Rosenthal
Ken Ehrlich, Greg OBrian, and Deepak Bhatnagar
23. Genomic and Postgenomic Approaches
19. Cryptosporidium Species • 271 to Understanding the Pathogenesis of the
Guan Zhu and Lihua Xiao Enteric Protozoan Parasite Entamoeba
histolytica • 321
20. Giardia lamblia: Molecular Studies of an Kumiko Nakada-Tsukui and
Early Branching Eukaryote • 287 Tomoyoshi Nozaki
Mark C. Jenkins and Katarzyna Miska
21. Cyclospora cayetanensis: a Review Index • 343
of the Genome • 299
Joan M. Shields
CONTRIBUTORS
Salvador Almagro-Moreno Jean F. Challacombe
Department of Biological Sciences, University of Bioscience Division and DOE Joint Genome Institute,
Delaware, Newark, Delaware 19716 Los Alamos National Laboratory, Los Alamos,
NM 87545
John P. Bannantine
National Animal Disease Center, Bacterial Diseases Yung-Fu Chang
of Livestock Research Unit, USDA-Agricultural Cornell University, College of Veterinary Medicine,
Research Service, Ames, IA 50010 Ithaca, NY 14853
David M. Donovan
Deepak Bhatnagar
U.S. Department of Agriculture, Agricultural Research
United States Department of Agriculture,
Service, Beltsville Agricultural Research Center,
Agricultural Research Service, Southern Regional
Beltsville, MD 20705
Research Center, New Orleans, LA 70124
Monika Ehling-Schulz
Albert Bosch
Food Microbiology Unit, Clinic of Ruminants,
Enteric Virus Laboratory, Department of
Department for Farm Animals and Veterinary Public
Microbiology, School of Biology and Institute of
Health, University of Veterinary Medicine Vienna,
Nutrition and Food Safety, University of Barcelona,
Austria
Barcelona, Spain
Ken Ehrlich
E. Fidelma Boyd
United States Department of Agriculture,
Department of Biological Sciences, University of
Agricultural Research Service, Southern Regional
Delaware, Newark, DE 19716
Research Center, New Orleans, LA 70124
Thomas S. Brettin
Victor P. J. Gannon
Bioscience Division and DOE Joint Genome Institute,
Laboratory for Foodborne Zoonoses, Public Health
Los Alamos National Laboratory, Los Alamos,
Agency of Canada, Lethbridge, Alberta, Canada
NM 87545
D. Ryan Georgianna
Holger Brüggemann Duke Department of Molecular Genetics and
Department of Molecular Biology, Max Planck Microbiology, Duke University Medical College,
Institute for Infection Biology, Berlin, Germany Durham, NC 27710
Carmen Buchrieser Philippe Glaser
Department of Genomes and Genetics, Institut Department of Genomes and Genetics, Institut
Pasteur, 75724 Paris, France Pasteur, 75724 Paris, France
vii
viii CONTRIBUTORS
Karl A. Hassan Stanley Maloy
Department of Chemistry and Biomolecular San Diego State University, Center for Microbial
Sciences, Macquarie University, Sydney, Sciences, San Diego, CA 92182-1010
New South Wales, Australia
Jinzhe Mao
Lien-I Hor
U.S. Department of Agriculture, Agricultural Research
Department of Microbiology and I mmunology,
Service, Beltsville Agricultural Research Center,
College of Medicine, National Cheng-Kung
Beltsville, MD 20705
University, Tainan 701, Taiwan
T. David Matthews
Tetsuya Iida
San Diego State University, Center for Microbial
Laboratory of Genomic Research on Pathogenic
Sciences, San Diego, CA 92182-1010
Bacteria, International Research Center for Infectious
Diseases, Research Institute for Microbial Diseases,
Osaka University, Suita, Osaka 565-0871, Japan Christelle Mazuet
Unité des Bactéries Anaérobies et Toxines, Institut
Kaori Izutsu Pasteur, Paris, France
Laboratory of Genomic Research on Pathogenic
Bacteria, International Research Center for I nfectious
Alan McNally
Diseases, Research Institute for M icrobial Diseases,
School of Science and Technology,
Osaka University, Suita, Osaka 565-0871, Japan
Nottingham Trent University, Clifton Lane,
Nottingham NG11 8NS, England
Mark C. Jenkins
Animal Parasitic Diseases Laboratory, Beltsville
William G. Miller
Agricultural Research Center, Agricultural Research
Produce Safety and Microbiology Research Unit,
Service, U.S. Department of Agriculture, Beltsville,
Agricultural Research Service, U.S. Department of
MD 20705
Agriculture, Albany, CA 94710
Qi Jin
State Key Laboratory for Molecular Virology and Katarzyna Miska
Genetic Engineering, Institute of Pathogen Biology, Animal Parasitic Diseases Laboratory, Beltsville
Chinese Academy of Medical Sciences, Beijing, China Agricultural Research Center, Agricultural Research
Service, U.S. Department of Agriculture,
Vivek Kapur
Beltsville, MD 20705
Pennsylvania State University, Department of Veterinary
and Biomedical Sciences, University Park, PA 16802
A. Christine Munk
Bioscience Division and DOE Joint Genome
Paul Keim
Institute, Los Alamos National Laboratory,
Bioscience Division, Los Alamos National Laboratory,
Los Alamos, NM 87545
Los Alamos, NM 87545, and The Microbial Genetics
and Genomics Center and The Translational Genomics
Research Institute, Northern Arizona University, Ronan A. Murphy
Flagstaff, AZ 86011 Department of Biological Sciences, University of
Delaware, Newark, DE 19716
David H. Kingsley
U.S. Department of Agriculture, Agricultural
Kumiko Nakada-Tsukui
Research Service, Microbial Food Safety Research Department of Parasitology, National Institute of
Unit, W. W. Baker Center, Delaware State University, Infectious Diseases, Tokyo 162-8640, Japan
Dover, DE 19901
Tomoyoshi Nozaki
Rickard Knutsson
Department of Parasitology, National Institute of
National Veterinary Institute (SVA), Uppsala,
Infectious Diseases, Tokyo 162-8640, Japan
Sweden
Chad R. Laing Greg OBrian
Laboratory for Foodborne Zoonoses, Public Health Department of Plant Pathology, North Carolina
Agency of Canada, Lethbridge, Alberta, Canada State University, Raleigh, NC 27695
CONTRIBUTORS ix
Richard T. Okinaka Nicholas R. Thomson
Bioscience Division, Los Alamos National The Pathogen Sequencing Unit, The Wellcome Trust
Laboratory, Los Alamos, NM 87545, and Sanger Institute, Wellcome Trust Genome Campus,
The Microbial Genetics and Genomics Center, Hinxton, Cambridge CB10 1SA, England
Northern Arizona University, Flagstaff, AZ 86011
Shih-Feng Tsai
Division of Molecular and Genomic Medicine, National
Craig T. Parker
Health Research Institutes, Miaoli 350, Taiwan
Produce Safety and Microbiology Research Unit,
Agricultural Research Service, U.S. Department of
Scott Weese
Agriculture, Albany, CA 94710
Department of Pathobiology, University of Guelph,
Guelph, Ontario, N1G 2W1 Canada
Ian T. Paulsen
Department of Chemistry and Biomolecular Antje Wollherr
Sciences, Macquarie University, Sydney, Göttingen Genomics Laboratory, Institute of
New South Wales, Australia Microbiology and Genetics, Göttingen, Germany
Gary A. Payne Brendan W. Wren
Department of Plant Pathology, North Carolina Department of Infectious and Tropical Diseases,
State University, Raleigh, NC 27695 London School of Hygiene and Tropical Medicine,
Keppel Street, London WC1E 7HT, England
Rosa M. Pintó
Keh-Ming Wu
Enteric Virus Laboratory, Department of
Division of Molecular and Genomic Medicine,
Microbiology, School of Biology and Institute of
National Health Research Institutes,
Nutrition and Food Safety, University of Barcelona,
Miaoli 350, Taiwan
Barcelona, Spain
Lihua Xiao
Michel R. Popoff Division of Foodborne, Waterborne and
Unité des Bactéries Anaérobies et Toxines, Institut Environmental Diseases, National Center for
Pasteur, Paris, France Emerging and Zoonotic Infectious Vector-Borne
and Enteric Diseases, Centers for Disease Control
Benjamin M. Rosenthal and Prevention, Atlanta, GA 30341
Animal Parasite Disease Laboratory, Agricultural
Research Service, U.S. Department of Agriculture, Jian Yang
Beltsville, MD 20705 State Key Laboratory for Molecular Virology and
Genetic Engineering, Institute of Pathogen Biology,
Chinese Academy of Medical Sciences, Beijing, China
Vartul Sangal
Strathclyde Institute of Pharmacy and Biomedical
Jiujiang Yu
Sciences, University of Strathclyde, Royal College,
United States Department of Agriculture, Agricultural
Glasgow, Scotland
Research Service, Southern Regional Research Center,
New Orleans, LA 70124
Siegfried Scherer
Lehrstuhl für Mikrobielle Ökologie, Department
Jun Yu
of Biosciences, Technische Universität München,
Strathclyde Institute of Pharmacy and Biomedical
Freising, Germany
Sciences, University of Strathclyde, Royal College,
Glasgow, Scotland
Joan M. Shields
U.S. Food & Drug Administration, Division of Yongxiang Zhang
Virulence Assessment/Virulence Mechanisms Branch, Laboratory for Foodborne Zoonoses, Public Health
Laurel, MD 20708 Agency of Canada, Lethbridge, Alberta, Canada
Hung-Yu Shu Guan Zhu
Department of Bioscience Technology, College of Department of Veterinary Pathobiology and Faculty
Health Science, Chang Jung Christian University, of Genetics Program, Texas A&M University,
Tainan County 711, Taiwan College Station, TX 77843