Veterinary Microbiology and Microbial Disease E-Book

P. J. Quinn

• Herausgeber: John Wiley & Sons
• Kategorie: Fachliteratur
• Sprache: Englisch

Seitenzahl: 2275

Veröffentlichungsjahr: 2011

Beschreibung

Microbiology is one of the core subjects for veterinary students, and since its first publication in 2002, Veterinary Microbiology and Microbial Disease has become an essential text for students of veterinary medicine. Fully revised and expanded, this new edition updates the subject for pre-clinical and clinical veterinary students in a comprehensive manner. Individual sections deal with bacteriology, mycology and virology. Written by an academic team with many years of teaching experience, the book provides concise descriptions of groups of microorganisms and the diseases which they cause. Microbial pathogens are discussed in separate chapters which provide information on the more important features of each microorganism and its role in the pathogenesis of diseases of animals. The international and public health significance of these pathogens are reviewed comprehensively. The final section is concerned with the host and is organized according to the body system affected.

Tables, boxes and flow diagrams provide information in an easily assimilated format. This edition contains new chapters on molecular diagnostics and on infectious conditions of the skin, cardiovascular system, urinary tract and musculoskeletal system. Many new colour diagrams are incorporated into this edition and each chapter has been updated.

Key features of this edition:

• Twelve new chapters included
• Numerous new illustrations
• Each chapter has been updated
• Completely re-designed in full colour
• Fulfils the needs of veterinary students and academics in veterinary microbiology
• Companion website with figures from the book as Powerpoints for viewing or downloading by chapter: www.wiley.com/go/quinn/veterinarymicrobiology

Veterinary Microbiology and Microbial Disease remains indispensable for all those studying and teaching this essential component of the veterinary curriculum.

Leseprobe

Contents

Preface

Acknowledgements

Author biographies

Section I Introduction to Microbiology Infection Immunity and Molecular Diagnostic Methods

1 Microbiology microbial pathogens and infectious disease

Further reading

2 Subdivisions classification and morphological characterization of infectious agents

Microscopical techniques

Pathogenic microorganisms

Biological classification and nomenclature

References

Further reading

3 Infection and immunity

Normal flora

Comparative aspects of innate and adaptive immunity

Recognition of pathogens

Cells involved in innate immune responses

Complement

Adaptive immunity

Immunity to bacteria

Immunity to fungi

Immunity to viruses

Concluding comments

References

Further reading

4 Immunodeficiency diseases

Severe combined immunodeficiency diseases

Thymic aplasia or hypoplasia

Wiskott-Aldrich syndrome

Primary immunodeficiency diseases involving B lymphocytes

Secondary immunodeficiency

Further reading

5 Vaccines and vaccination

Vaccination

Inactivated vaccines

Live attenuated vaccines

Vaccines produced by recombinant nucleic acid technology

Synthetic peptide vaccines

DNA vaccines

Reverse vaccinology

Adjuvants

Administration of vaccines

Adverse reactions following vaccination

Vaccination failure

References

Further reading

6 Molecular diagnostic methods

Analytical properties of nucleic acid

Molecular hybridization

DNA sequencing

Polymerase chain reaction (PCR)

Real-time PCR

Diagnostic approaches to surveillance and subtyping of bacteria a comparison of phenotyping and genotyping methods

Molecular subtyping for definitive identification of bacteria

Plasmid profiling

Restriction endonuclease analysis (REA)

Ribotyping

Pulsed-field gel electrophoresis (PFGE)

PCR-based subtyping methods

Multilocus sequence typing (MLST)

DNA microarray technology

Whole bacterial genome sequencing

References

Further reading

Section II Introductory Bacteriology

7 The structure of bacterial cells

Capsule

Cell wall

Cytoplasmic membrane

Cytoplasm

Ribosomes

Nuclear material

Flagella

Pili

Biofilms

Protein secretion systems

Endospores

Reference

Further reading

8 Cultivation preservation and inactivation of bacteria

Bacterial growth

Bacterial nutrition

Physical and chemical factors which influence growth

Preservation of microorganisms

Physical methods for inactivating microorganisms

Biosafety cabinets

Reference

Further reading

9 Bacterial genetics mechanisms of genetic variation and gene databases

Replication of bacterial DNA

Transcription and translation the expression of genetic information

Mechanisms contributing to genetic variation

Examples of mobile genetic elements

Genetic engineering of bacteria in the laboratory

Genetic databases and bioinformatics

Further reading

10 Laboratory diagnosis of bacterial disease

Selection collection and transportation of specimens

Identification of pathogenic bacteria

Serology

Further reading

11 Antibacterial agents

Development of chemotherapy for bacterial infections

Mode and site of action

Combined antibacterial therapy

Factors influencing a ntibacterial activity

Further reading

12 Antibacterial resistance

Resistance mechanisms

Multiple drug resistance

Strategies for limiting a ntibacterial resistance

Antibacterial susceptibility testing

References

Further reading

13 Bacterial colonization tissue invasion and clinical disease

Commensals

Pathogens

Colonization and growth

Pathogen-host interactions

Virulence factors

Responses of the host to bacterial pathogens

The clinical spectrum of bacterial disease

References

Section III Pathogenic Bacteria

14 Staphylococcus species

Usual habitat

Differentiation of Staphylococcus species

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

15 Streptococci

Usual habitat

Differentiation of the streptococci

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

16 Actinobacteria

Actinomyces Arcanobacterium and Actinobaculum species

Nocardia species

Dermatophilus congolensis

Crossiella equi

References

Further reading

17 Corynebacterium species

Usual habitat

Differentiation of the corynebacteria

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

18 Rhodococcus equi

Usual habitat

Clinical infections

References

Further reading

19 Listeria species

Usual habitat

Differentiation of Listeria species

Pathogenesis and pathogenicity

Clinical infections

References

Further reading

20 Erysipelothrix rhusiopathiae

Usual habitat

Definitive identification of Erysipelothrix rhusiopathiae

Pathogenesis and pathogenicity

Clinical infections

References

Further reading

21 Bacillus species

Usual habitat

Differentiation of Bacillus species

Clinical infections

Infections with Bacillus licheniformis

References

Further reading

22 Clostridium species

Usual habitat

Specimen collection and cultural requirements

Detection and differentiation of clostridia

Clinical conditions caused by neurotoxic clostridia

Clinical conditions caused by histotoxic clostridia

Enteropathogenic and enterotoxaemia-producing clostridia

References

Further reading

23 Mycobacterium species

Usual habitat

Differentiation of pathogenic mycobacteria

Clinical infections

References

Further reading

24 Enterobacteriaceae

Usual habitat

Differentiation of the Enterobacteriaceae

Escherichia coli

Salmonella serotypes

Yersinia species

Opportunistic pathogens

References

Further reading

25 Pseudomonas aeruginosa and Burkholderia species

Usual habitat

Differentiation of Pseudomonas and Burkholderia species

Clinical infections

References

Further reading

26 Actinobacillus species

Usual habitat

Differentiation of Actinobacillus species

Pathogenesis and pathogenicity

Clinical infections

References

Further reading

27 Pasteurella species Mannheimia haemolytica and Bibersteinia trehalosi

Usual habitat

Differentiation of Pasteurella Bibersteinia and Mannheimia species

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

28 Francisella tularensis

Usual habitat

Epidemiology

Clinical infections

References

29 Histophilus somni Haemophilus parasuis and Avibacterium paragallinarum

Usual habitat

Differentiation of Histophilus somni Haemophilus parasuis and Avibacterium paragallinarum

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

30 Taylorella species

Usual habitat

Clinical infections

References

Further reading

31 Bordetella species

Usual habitat

Differentiation of Bordetella bronchiseptica and B. avium

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

32 Moraxella species

Moraxella bovis

References

33 Brucella species

Usual habitat

Differentiation of Brucella species

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

34 Campylobacter and Helicobacter species

Campylobacter species

Helicobacter species

References

Further reading

35 Lawsonia intracellularis

Usual habitat

Pathogenesis and pathogenicity

Clinical signs

Diagnosis

Treatment and control

References

Further reading

36 Spirochaetes

Leptospira species

Borrelia species

Brachyspira and Treponema species

References

Further reading

37 Pathogenic anaerobic non-spore-forming Gram-negative bacteria

Usual habitat

Diagnostic procedures

Differentiation of the non-spore-forming Gram-negative anaerobes

Pathogenesis and pathogenicity

Clinical infections

References

Further reading

38 Mycoplasmas

Usual habitat

Differentiation of the mycoplasmas

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

39 Chlamydia and Chlamydophila species

Usual habitat

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

40 Rickettsiales and Coxiella burnetii

Epidemiology

Pathogenesis and pathogenicity

Recognition and differentiation of members of the Rickettsiales

Clinical infections

References

Further reading

41 Bacterial species of limited pathogenic significance

Acinetobacter species

Bartonella species

Aeromonas species Plesiomonas shigelloides and Vibrio species

Chromobacterium violaceum

Ornithobacterium rhinotracheale

Riemerella anatipestifer

Streptobacillus moniliformis

References

Section IV Mycology

42 General features of fungi associated with disease in animals

Structure

Growth reproduction and colonial formation

General features of fungal disease

Diagnosis of fungal diseases

Differentiation of fungal species

Antifungal chemotherapy

References

Further reading

43 Dermatophytes

Usual habitat

Laboratory recognition and differentiation

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

44 Aspergillus species

Usual habitat

Recognition of Aspergillus species

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

45 Yeasts and disease production

Candida species

Cryptococcus species

Malassezia pachydermatis

‘Megabacteria’ (Macrorhabdus ornithogaster)

Trichosporon beigelii

Geotrichum candidum

References

Further reading

46 Dimorphic fungi

Blastomyces dermatitidis

Histoplasma capsulatum

Coccidioides species

Sporothrix schenckii

References

Further reading

47 Zygomycetes of veterinary importance

Mucorales and Mortierellales

Entomophthorales

References

Further reading

48 Fungus-like organisms of veterinary importance

Pythium insidiosum

Rhinosporidium seeberi

Lacazia loboi

References

Further reading

49 Pneumocystis carinii

Usual habitat

Pathogenesis and pathogenicity

Diagnostic procedures

Clinical infections

References

Further reading

50 Opportunistic infections caused predominantly by phaeoid fungi

Usual habitat

Clinical infections

Diagnosis

Treatment

References

Further reading

51 Mycotoxins and mycotoxicoses

Aflatoxicosis

Citrinin toxicosis

Cyclopiazonic acid toxicosis

Diplodiosis

Ergotism

Facial eczema

Fescue toxicosis

Fumonisin toxicoses

Mouldy sweet potato toxicity

Mycotoxic lupinosis

Ochratoxicosis

Mycotoxic oestrogenism

Patulin toxicosis

Slaframine toxicosis

Sterigmatocystin toxicosis

Tremorgen intoxications

Trichothecene toxicoses

References

Further reading

52 Pathogenic algae and cyanobacteria

Prototheca species

Chlorella species

The cyanobacteria

References

Further reading

53 Antifungal chemotherapy

Antifungal drugs

Resistance to antifungal drugs

References

Further reading

Section V Introductory Virology

54 Nature structure and taxonomy of viruses

The origin of viruses

Structure of viruses

Taxonomy of viruses

References

Further reading

55 Replication of viruses

Replication of DNA viruses

Replication of RNA viruses

Protein synthesis

Assembly and release of virions

References

Further reading

56 Genetics and evolution of viruses

Mutation

Viral recombination

Viral genomic sequence analysis

Evolution of viruses

References

Further reading

57 Propagation of viruses and virus-cell interactions

Propagation of viruses

Determination of virus concentration

Virus-host cell interactions

Further reading

58 Pathogenesis of viral diseases

Routes of infection

Dissemination in the host

Clinical signs

Virus shedding and patterns of infection

Further reading

59 Laboratory diagnosis of viral infections

Collection preservation and transportation of samples

Detection of virus viral antigens or nucleic acid

Diagnostic serology

Interpretation of test results

Further reading

60 Antiviral chemotherapy

Introduction

Development of antiviral drugs

Viral infections and strategies for interrupting virus replication

Immunomodulators

Ion channel blocking compounds

Neuraminidase inhibitors

Antiviral drugs which inhibit viral genome replication

Antiretroviral drugs

Resistance to antiviral drugs

Future developments

References

Further reading

Section VI Viruses and Prions

61 Herpesviridae

Clinical infections

References

Further reading

62 Papillomaviridae

Clinical infections

References

Further reading

63 Adenoviridae

Clinical infections

References

Further reading

64 Poxviridae

Clinical infections

References

Further reading

65 Asfarviridae

Africans wine fever

References

Further reading

66 Parvoviridae

Clinical infections

References

Further reading

67 Circoviridae

Clinical infections

References

Further reading

68 Retroviridae

Clinical infections

References

Further reading

69 Reoviridae

Clinical infections

References

Further reading

70 Birnaviridae

Clinical infections

Further reading

71 Orthomyxoviridae

Clinical infections

References

Further reading

72 Paramyxoviridae

Clinical infections

References

Further reading

73 Rhabdoviridae

Clinical infections

References

Further reading

74 Bornaviridae

Clinical infections

References

Further reading

75 Bunyaviridae

Clinical infections

References

Further reading

76 Picornaviridae

Clinical infections

References

77 Caliciviridae

Clinical infections

References

Further reading

78 Astroviridae

Clinical infections

References

79 Coronaviridae

Clinical infections

References

Further reading

80 Arteriviridae

Clinical infections

References

Further reading

81 Flaviviridae

Clinical infections

References

Further reading

82 Togaviridae

Clinical infections

References

Further reading

83 Prions: unconventional infectious agents

Clinical infections

References

Further reading

Section VII Microbial Agents and Disease Production

84 Tissue and system preferences of bacterial fungal and viral pathogens and the nature of the diseases caused by these infectious agents

References

Further reading

85 Interactions of microbial pathogens with the nervous system

Haematogenous bacterial infections

Haematogenous viral infections

Infection via peripheral nerves

Infections with lentiviruses

Viral infections which cause developmental anomalies

Transmissible spongiform encephalopathies (TSEs)

Algal bacterial and fungal neurotoxicity

Algal and fungal infections

Further reading

86 Interactions of microbial pathogens with the male and female reproductive systems

Infections of the male reproductive system

Infections of the non pregnant uterus

Infections of the pregnant uterus

Further reading

87 The role of microbial pathogens in intestinal disease

Intestinal structure and function

Normal flora

Pathogenetic mechanisms in enteritis

Further reading

88 The role of microbial pathogens in respiratory disease

Defence mechanisms in the conducting airways

Defence mechanisms in the lungs

Microbial diseases of the conducting airways

Microbial diseases of the lungs

References

Further reading

89 Interactions of microbial pathogens with the renal system

Ascending infection of the excretory pathway

Structure and function of the excretory passages

Virulence factors of uropathogens

Responses of the host to ascending bacterial infection of the excretory pathway

Infectious diseases of the kidneys

References

90 Microbial diseases of the cardiovascular system

The heart: structural and functional relationships

Infections of the heart

Infections of the vascular channels

References

91 Interactions of microbial pathogens with the musculoskeletal system

Responses of muscle to microbial pathogens

Distinctive structural features of skeletal muscle

Responses of muscle to injury

Responses of muscle to bacterial infection

Responses of bone to microbial pathogens

Responses of joints to microbial pathogens

Foot infections of cattle sheep and pigs associated with microbial agents

References

92 The role of microbial pathogens in diseases of the integumentary system

Structural and functional perspectives

Responses of the skin to microorganisms

Bacterial diseases of skin

Viral diseases of skin

Fungal diseases of skin

References

93 Bacterial causes of bovine mastitis

Mammary gland defence mechanisms

Contagious mastitis

Environmental mastitis

Diagnosis

Treatment

Prevention and control

References

94 Disinfection biosecurity and other aspects of disease control

Survival of infectious agents in the environment

Transmission of infectious agents

Biosecurity

Animals

Feed

Water

Environment of domestic animals

Vehicular and pedestrian traffic

Equipment

Animal waste

Wild mammals and birds

Cleaning and disinfection of farm buildings

Thermal inactivation of microbial pathogens

Disinfection antisepsis and sterilization

Characteristics modes of action and selection of chemical disinfectants

Chemical inactivation of microbial pathogens

Bacteria

Fungal pathogens

Viruses

Prions

Chemicals used as disinfectants in veterinary medicine

Microbial resistance to disinfection

Disinfection procedures

References

Further reading

Appendix: Relevant websites

General topics

Genomic analysis

Bacteriology

Mycology

Virology

Infectious diseases

Index

This edition first published 2011

© 2002 by Blackwell Science Ltd

© 2011 by P.J. Quinn, B.K. Markey, F.C. Leonard, E.S. FitzPatrick, S. Fanning and P.J. Hartigan

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Library of Congress Cataloging-in-Publication Data

Veterinary microbiology and microbial disease / P.J. Quinn, MVB, PhD, MRCVS, Professor Emeritus, Former Professor of Veterinary Microbiology and Parasitology, School of Veterinary Medicine, University College, Dublin, B.K. Markey, MVB, PhD, Dip Stat, MRCVS, Senior Lecturer in Veterinary Microbiology, School of Veterinary Medicine, University College, Dublin, F.C. Leonard, MVB, PhD, MRCVS, Senior Lecturer in Veterinary Microbiology, School of Veterinary Medicine, University College, Dublin, E.S. FitzPatrick, FIBMS, Chief Technical Officer, School of Veterinary Medicine, University College, Dublin, S. Fanning, BSc, PhD, Professor of Food Safety and Zoonoses, Director of Academic Centre for Food Safety, University College Dublin, P.J. Hartigan, BSc, MVM, MA, PhD, MRCVS, Former Senior Lecturer in Veterinary Pathology, Trinity College, Dublin. - Second Edition.

p. ; cm.

Includes bibliographical references and index.

ISBN 978-1-4051-5823-7 (pbk. : alk. paper) 1. Veterinary microbiology. I. Quinn, P. J. (Patrick J.), author. II. Markey, B. K. (Bryan K.), author. III. Leonard, F. C., author. IV. FitzPatrick, E. S., author.

V. Fanning, S., author. VI. Hartigan, P. J., author.

[DNLM: 1. Microbiology. 2. Veterinary Medicine. 3. Communicable Diseases—microbiology.

4. Communicable Diseases—veterinary. QW 70]

SF780.2.V485 2011

636.089′69041–dc22

2010049404

This book is dedicated to the memory of Margery E. Carter and W.J.C. (Bill) Donnelly, co-authors of the first edition

Preface

The pace of change in microbiology has accelerated in recent years as molecular techniques, applied to microbial pathogens, elucidate the pathogenesis of many infectious diseases and improve the reliability of diagnostic test procedures. Today, microbiology occupies a central position in the veterinary curriculum and has developed into a subject of vast complexity. Since the publication of Veterinary Microbiology and Microbial Disease in 2002, many changes have occurred in veterinary microbiology, some on the recommendations of international committees and others as a consequence of relevant research.

The second edition of our book incorporates changes in individual chapters which have been updated and expanded. In addition, new chapters on immunodeficiency diseases, vaccines and vaccination, molecular diagnostic methods, antibacterial resistance, antifungal chemotherapy, antiviral chemotherapy and microbial diseases of the urinary tract, cardiovascular system, musculoskeletal system and the integumentary system have been added.

This edition is divided into seven sections. The first section provides an introduction to microbiology, infection, immunity and molecular diagnostic methods. Section II contains chapters on introductory bacteriology. Pathogenic bacteria are dealt with in Section III. The twelve chapters in Section IV are concerned with mycology. Introductory virology is presented in Section V. Viruses and prions are covered in Section VI. The final section, Section VII, includes chapters on the interactions of microbial pathogens with body systems. A separate chapter in this section deals with bovine mastitis and the final chapter provides a comprehensive review of disinfection, biosecurity and other aspects of disease control.

To facilitate readers requiring additional information on topics included in the book, a list of websites is provided at the end of Section VII.

The use of colour in this edition enhances the quality of the illustrations and facilitates the interpretation of complex diagrams.

The authors would be pleased to receive notification of errors or inaccuracies in this edition of our book.

Acknowledgements

We wish to acknowledge the constructive comments of the following colleagues who offered scientific, technical and editorial advice on individual chapters or who assisted in other ways: Hester McAllister, Marijka Beltman, Aidan Kelly, Paul Stanley, Carolyn Cummins, Eva Maischberger, Jane Irwin, Robert Shiel, Clodagh Kearney, Gráinne McCarthy, Hanne Jahns, Joe Cassidy, Yvonne Abbott, Dores Maguire, Frances LeMatti, Ruth Henry, Pauline Coyle, Sean Hogan, Jarlath Nally, Steve Gordon, Brian Sheahan, Mark Rogers, Shane Cooney, Orla Condell, Marta Martins, Matthew McCusker, Stephen O’Brien, Katie Solomon, Karen Power, Paul Whyte, Patrick Wall and Theo De Waal, School of Veterinary Medicine, University College Dublin; Cliona O’Farrelly, Tim Foster and Patrick Prendergast, Trinity College Dublin; Pat Lenihan, Maire McElroy, Kevin Kenny, Peter O’Neill and Pat Raleigh, Central Veterinary Research Laboratory, Backweston; Patrick Rogan, Department of Agriculture, Fisheries and Food; Hywel Ball, Agri - Food and Biosciences Institute, Stormont; Patrick McDonough, College of Veterinary Medicine, Cornell University; Helen O’Shea, Department of Biological Sciences, Cork Institute of Technology; Alan Reilly and Wayne Anderson, Food Safety Authority of Ireland; Brendan Crowley, Department of Medical Microbiology, St. James’s Hospital, Dublin; Donal Walsh, School of Veterinary Medicine, University of California, Davis; Ross Fitzgerald, Universitry of Edinburgh; Davida Smyth, NewYork University; Clive Lee, Royal College of Surgeons in Ireland; James Buckley, Veterinary Department, Cork County Council.

The facilities and support provided by the librarian, Mr. Diarmuid Stokes, and staff at the veterinary library, Paul Gogarty, Michelle Latimer, Vanessa Buckley, Kathryn Smith and Marie McGourn is acknowledged with gratitude.

Justinia Wood, Nick Morgan, Lucy Nash and their colleagues at Wiley-Blackwell provided advice and assistance throughout this long project. The careful editing of the manuscript by Mary Sayers, copy editor, improved the accuracy of the text, illustrations and references. As Project Manager, Ruth Swan coordinated corrections and advised the authors on technical aspects of changes to the manuscript.

Dublin, July 2011

Author biographies

P.J. Quinn, MVB, PhD, MRCVS, was Professor of Veterinary Microbiology and Parasitology and Head of the Department in the Faculty of Veterinary Medicine, University College Dublin, from 1985 to 2002. After graduating from University College Dublin in 1965, he spent some time in veterinary practice before enrolling as a postgraduate student in Ontario Veterinary College, University of Guelph, Canada. In 1970, he was awarded a PhD for research in veterinary immunology and he remained on the staff of Ontario Veterinary College until his return to the Faculty of Veterinary Medicine, University College Dublin, in 1973.

His research interests have included allergic skin reactions in the horse to biting insects, the epidemiology of toxoplasmosis in sheep, immune mechanisms in the respiratory tract of calves, leptospirosis in dairy cattle, immunomodulation, mechanisms of immunity in the respiratory tract of specific pathogen-free and conventional cats, botulism in gulls around the Irish coastline, factors influencing the tuberculin test in cattle, airborne dispersal of bacteria during slurry spreading, and evaluation of the efficacy of chemical disinfectants against Brucella abortus and Mycobacterium bovis.

In addition to many refereed publications in journals and chapters in books, he edited Cell-mediated Immunity (1984), is senior co-author of Animal Diseases Exotic to Ireland (1992), Clinical Veterinary Microbiology (1994), Microbial and Parasitic Diseases of the Dog and Cat (1997), Veterinary Microbiology and Microbial Disease (2002) and Concise Review of Veterinary Microbiology (2003) and is co-author of Veterinary Embryology (2006).

He was awarded the title Professor Emeritus by University College Dublin in 2002. In 2006, he was recipient of the Association of Veterinary Teachers and Research Workers outstanding teaching award. For his contribution to teaching and faculty development in the Faculty of Veterinary Medicine in Tirana, he was awarded an honorary doctorate by the Agricultural University of Tirana, Albania, in May 2010.

Bryan K. Markey, MVB, PhD, MRCVS, Dip Stat, graduated from the Faculty of Veterinary Medicine, University College Dublin, in 1985. Following a short period in general practice he was appointed house surgeon in the Faculty of Veterinary Medicine, University College Dublin. In 1986, he joined the academic staff as an assistant lecturer in the Department of Veterinary Microbiology and Parasitology. He spent one year on study leave at the Veterinary Sciences Division, Belfast, and enrolled for a PhD degree at Queen’s University. He was awarded a PhD from Queen’s University, Belfast in 1991 and was promoted to senior lecturer in veterinary microbiology in 1997. From 2002 to 2004 he served as Head of Department. In 2005 he was visiting professor at the College of Life Sciences, Queensland University of Technology, Brisbane.

His research interests include chlamydial infections of domestic animals and methicillin-resistant Staphylococcus aureus infection in veterinary species. He has contributed chapters to books on veterinary disinfection and is co-author of Animal Diseases Exotic to Ireland (1992), Clinical Veterinary Microbiology (1994), Microbial and Parasitic Diseases of the Dog and Cat (1997), Veterinary Microbiology and Microbial Disease (2002) and Concise Review of Veterinary Microbiology (2003).

Finola C. Leonard, MVB, PhD, MRCVS, graduated from the Faculty of Veterinary Medicine, University College Dublin, in 1983. She was house surgeon in the Department of Large Animal Medicine, Royal (Dick) School of Veterinary Studies, Edinburgh, for one year and engaged in veterinary practice for three years. She commenced postgraduate studies in the Faculty of Veterinary Medicine, University College Dublin, on leptospirosis in dairy cattle while based at Teagasc, Moorepark, Co. Cork, and was awarded a PhD for research on this topic in 1991. She remained in Moorepark as a postdoctoral research worker until 1997. Her research was concerned with foot lameness in dairy cattle and the influence of housing on the behaviour and welfare of cattle and pigs.

She was appointed college lecturer in the Department of Veterinary Microbiology and Parasitology in the Faculty of Veterinary Medicine, University College Dublin in 1997 and was promoted to senior lecturer in veterinary microbiology in 2002. Her research interests include Salmonella infection in pigs, other zoonotic infections, and antimicrobial resistance, including methicillin-resistant Staphylococcus aureus infection in farm and companion animals.

Eamonn S. FitzPatrick, FIBMS, was awarded Fellowship of the Institute of Biomedical Science in 1978 and was appointed to the post of Principal Technician in the Department of Veterinary Anatomy, University College Dublin. He was appointed to the Histopathology Advisory Committee of the Irish Academy of Medical Laboratory Sciences in 1979. From 1987 to 1989 he was External Examiner for the Diploma in Medical Laboratory Science—Histopathology Option, at the Dublin Institute of Technology, where he also lectured for many years on electron microscopy in the Medical Laboratory Sciences Degree course. He was appointed Chief Technical Officer in the Veterinary Science Unit of the School of Veterinary Medicine, University College Dublin, in 2006. He has been teaching veterinary anatomy and histology for over 25 years.

Recent published work includes papers on hormone receptors in the bovine reproductive tract and the effect of diet supplements on the alimentary tracts of weanling pigs. His current research interests are centred mainly on mucins, mucus gels and the interaction of microbial pathogens with epithelial surfaces, especially of the bovine and equine reproductive tracts. He is co-author of Veterinary Embryology (2006).

Séamus Fanning, BSc, PhD, graduated in Biochemistry and Microbiology from University College Cork. He was awarded a Fulbright Fellowship in 1995 and worked at Baylor College of Medicine, Houston. In 2002 he was appointed as the Professor of Food Safety and Zoonoses at University College Dublin and set up the UCD Centre for Food Safety. Currently, his research interests include the application of molecular methods to food safety to aid in the control of zoonotic bacteria. A significant part of his research is related to the characterization of the genetic mechanisms contributing to the emergence of multiple drug resistance in food - borne pathogens. In particular, this work is related to strain virulence and its influence on survival in the food chain. His research group is involved in characterizing the emerging pathogen, Cronobacter species (formerly known as Enterobacter sakazakii), linked to powdered infant milk formula. The UCD Centre for Food Safety was designated as the World Health Organization (WHO) Collaborating Centre for Research, Reference and Training on Cronobacter.

Patrick J. Hartigan, BSc, MVM, MA, PhD, MRCVS, graduated from the Veterinary College of Ireland in 1955. After a decade in large animal practice in Co. Kerry, he registered as a graduate student at the School of Veterinary Medicine, Trinity College, Dublin. His studies on uterine pathology in repeat breeder cows were rewarded with a PhD in 1970. After 10 years as a pathologist in the School of Veterinary Medicine, he moved to a post as Senior Lecturer in Reproductive Physiology at the Department of Physiology in the Faculty of Health Sciences at Trinity College, where he remained until retirement. At present, he is a Research Associate in the Department of Physiology.

Section IIntroduction to Microbiology, Infection, Immunity and Molecular Diagnostic Methods

Chapter 1

Microbiology, microbial pathogens and infectious disease

The earliest forms of life on this planet are presumed to have had characteristics resembling those of bacteria, most likely anaerobic bacteria. It is postulated that prokaryotes evolved from primitive forms of life and that the subsequent availability of oxygen resulting from photosynthesis contributed to microbial diversity. The chronological sequence of evolutionary events relating to the emergence of microbial life and, subsequently, eukaryotic cells is outlined in Fig. 1.1. This proposed scheme is based on limited factual information, some deriving from information gleaned from fossilized remains of prokaryotic cells approximately 3.5 billion years old and also from studies of ribosomal RNA among microorganisms.

Before the causes of infectious diseases could be discussed and evaluated in a rational manner, events associated with the emergence of life forms required explanation. Traditional views on the origin of life were strongly influenced by the writings of classical Greek and Roman scholars, many of whom espoused the view of spontaneous generation of small living entities. Disease was often attributed to evil forces associated with disturbances in the upper atmosphere, poisonous vapours called miasmas, supernatural events and other influences unrelated to biology. Awareness of the possible existence of forms of life not visible to the naked eye emerged slowly. As early as 1546, in his treatise , Girolamo Fracastoro suggested that animate agents were responsible for disease. Concepts of infectious diseases were closely related to the demonstration of organisms too small to be observed without magnification and to the isolation and characterization of these small organisms, termed microorganisms. Major developments in microbiology, the study of these microorganisms, began with theories relating to the causes of infectious diseases and continued with the development of microscopy, which confirmed the existence of microorganisms visible only by substantial magnification. Towards the middle of the nineteenth century, the pioneering work of Louis Pasteur and Robert Koch confirmed the microbial aetiology of infectious diseases. Progressive developments contributed to the rapid expansion of knowledge and the establishment of microbiology as a subject of major importance not only in human and animal health but also in food processing and preservation.