BACTERIOPHAGES Edited by Ipek Kurtböke Bacteriophages Edited by Ipek Kurtböke Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Maja Bozicevic Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published March, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Bacteriophages, Edited by Ipek Kurtböke p. cm. ISBN 978-953-51-0272-4 Contents Preface IX Part 1 Biology and Classification of Bacteriophages 1 Chapter 1 Bacteriophages and Their Structural Organisation 3 E.V. Orlova Chapter 2 Some Reflections on the Origin of Lambdoid Bacteriophages 31 Luis Kameyama, Eva Martínez-Peñafiel, Omar Sepúlveda-Robles, Zaira Y. Flores-López, Leonor Fernández, Francisco Martínez-Pérez and Rosa Ma. Bermúdez Chapter 3 Gels for the Propagation of Bacteriophages and the Characterization of Bacteriophage Assembly Intermediates 39 Philip Serwer Part 2 Bacteriophages as Contaminants and Indicator 55 Chapter 4 Bacteriophages as Surrogates for the Fate and Transport of Pathogens in Source Water and in Drinking Water Treatment Processes 57 Maria M.F. Mesquita and Monica B. Emelko Chapter 5 Bacteriophages in Dairy Industry: PCR Methods as Valuable Tools 81 Beatriz del Río, María Cruz Martín, Víctor Ladero, Noelia Martínez, Daniel M. Linares, María Fernández and Miguel A. Alvarez Chapter 6 Bacteriophages of Bacillus subtilis (natto) and Their Contamination in Natto Factories 95 Toshirou Nagai Part 3 Bacteriopgahes as Tools and Biological Control Agents 111 VI Contents Chapter 7 Bacteriophages of Ralstonia solanacearum: Their Diversity and Utilization as Biocontrol Agents in Agriculture 113 Takashi Yamada Chapter 8 Application of Therapeutic Phages in Medicine 139 Sanjay Chhibber and Seema Kumari Chapter 9 Successes and Failures of Bacteriophage Treatment of Enterobacteriaceae Infections in the Gastrointestinal Tract of Domestic Animals 159 L.R. Bielke, G. Tellez and B.M. Hargis Chapter 10 Phages as Therapeutic Tools to Control Major Foodborne Pathogens: Campylobacter and Salmonella 179 Carla M. Carvalho, Sílvio B. Santos, Andrew M. Kropinski, Eugénio C. Ferreira and Joana Azeredo Chapter 11 Bacteriophages of Clostridium perfringens 215 Bruce S. Seal, Nikolay V. Volozhantsev, Brian B. Oakley, Cesar A. Morales, Johnna K. Garrish, Mustafa Simmons, Edward A. Svetoch and Gregory R. Siragusa Chapter 12 A Phage-Guided Route to Discovery of Bioactive Rare Actinomycetes 237 D.I. Kurtböke Preface Therapeutic use of bacteriophages for the prevention and treatment of bacterial diseases has been pursued since the discovery of phages in 1917 by d'Herelle. Following the advancement of biomedical research, phages have gained further importance in biomedicine and examples include the use of polysaccharide-specific phages to treat encapsulated pathogenic bacteria forming biofilms on medical devices. Genetic engineering of bacteriophages to produce cell death without lysis, hence avoiding the release of unwanted endotoxins during control of pathogenic bacteria, has also been in progress. Due to increasing antibiotic resistance, phage-derived lytic enzymes are also being exploited to control infectious bacteria. In antibiotic resistant Gram-positive bacteria, even small quantities of purified recombinant lysin added externally have been reported to lead to immediate lysis of the pathogenic cell wall making them ideal anti-infectives due to lysin specificity against the pathogens. Improved understanding of bacteriophage injectory mechanisms also contributes to our knowledge of bacterial secretion mechanisms, particularly the ones in Type VI secretion systems (T6SS), which seem to use the same mechanism as bacteriophages to inject their DNA into bacterial cell. Moreover, advancements in prophage genomics improve the understanding of phage-bacterium interaction at the genetic level revealing prophage gene derived-virulence factors and their contribution to fitness increase of the pathogenic bacteria. Targeting host bacterial functional diversity, in which certain metabolic activities might be triggered in a defined ecosystem following phage-mediated gene transfer might also offer clues for host biosynthetic activities. As a result, an evaluation of the role of host-phage interactions in antibiotic production as well as in rendering antibiotics ineffective via lysogenation or prophage exertion will further complement therapeutic success. Bacteriophages are also utilized as successful biocontrol agents in agriculture as well as surrogates and tracers of the fate and transport of pathogens in source water and drinking water treatment processes. However, they can also result in significant economic losses as contaminants of dairy and natto factories, therefore their detection with the aid of effective methods and removal of extreme importance for the industry. Bacteriophages is therefore intended to serve as a reference book covering both X Preface background information as well as current advancements in the field including the use of molecular techniques for early detection of bacteriophage contamination in industrial operations. I thank all contributing Authors who have generously given their time and expertise to make Bacteriophages a key collection and their timely meeting of the deadlines has been greatly appreciated. I also thank Hans-Wolfgang Ackermann (Canada), Stephen Abedon (USA), Nina Chanishvili (Georgia) and Ian Macreadie (Australia) for their invaluable contribution to the peer review process. Technical assistance provided by Intech Editorial Office during the production of the book is also gratefully acknowledged. Ipek Kurtböke University of the Sunshine Coast, Australia Part 1 Biology and Classification of Bacteriophages 1 Bacteriophages and Their Structural Organisation E.V. Orlova Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, UK 1. Introduction Viruses are extremely small infectious particles that are not visible in a light microscope, and are able to pass through fine porcelain filters. They exist in a huge variety of forms and infect practically all living systems: animals, plants, insects and bacteria. All viruses have a genome, typically only one type of nucleic acid, but it could be one or several molecules of DNA or RNA, which is surrounded by a protective stable coat (capsid) and sometimes by additional layers which may be very complex and contain carbohydrates, lipids, and additional proteins. The viruses that have only a protein coat are named “naked”, or non- enveloped viruses. Many viruses have an envelope (enveloped viruses) that wraps around the protein capsid. This envelope is formed from a lipid membrane of the host cell during the release of a virus out of the cell. Viruses interacting with different types of cells in living organisms produce different types of disease. Each virus infects a certain type of cell which is usually called “host” cell. The major feature of any viral disease is cell lysis, when a cell breaks open and subsequently dies. In multicellular organisms, if enough cells die, the entire organism will endure problems. Some viruses can cause life-long or chronic infections, where the viruses continue to replicate in the body despite the host's defence mechanisms. The other viruses cause lifelong infection because the virus remains within its host cell in a dormant (latent) state such as the herpes viruses, but the virus can reactivate and produce further attacks of disease at any time, if the host’s defence system became weak for some reason (Shors, 2008). Viruses have two phases in their life cycle: outside cells and within the cells they infect. Viral particles outside cells could survive for a long time in harsh conditions where they are inert entities called virions. Outside living cells viruses are not able to reproduce since they lack the machinery to replicate their own genome and produce the necessary proteins. Viruses can infect host cells, recognising their specific receptors on the cell surface. The viral receptors are normal surface host cell molecules involved in routine