Clinical Veterinary Microbiology 2nd Edition
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Clinical Veterinary
Microbiology
Second edition
BK Markey MVB PhD DipStat MRCVS A Cullinane MVB PhD MRCVS
Senior Lecturer in Veterinary Microbiology Head of Virology Unit
School of Veterinary Medicine Irish Equine Centre
University College Dublin Johnstown, County Kildare, Ireland
Dublin, Ireland
D Maguire AIMLS
FC Leonard MVB PhD MRCVS School of Veterinary Medicine
Senior Lecturer in Veterinary Microbiology University College Dublin
School of Veterinary Medicine Dublin, Ireland
University College Dublin
Dublin, Ireland
M Archambault DMV MSc PhD DiplACVM
Professeur agrégée/Associate Professor
Faculté de Médecine Vétérinaire
Université de Montréal
Saint-Hyacinthe, Canada
Edinburgh London New York Oxford Philadelphia St Louis Sydney Toronto 2013
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First edition 1994
Second edition 2013
ISBN 9780723432371
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Notices
Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding,
changes in research methods, professional practices, or medical treatment may become necessary.
Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information,
methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own
safety and the safety of others, including parties for whom they have a professional responsibility.
With respect to any drug or pharmaceutical products identified, readers are advised to check the most current information provided
(i) on procedures featured or (ii) by the manufacturer of each product to be administered, to verify the recommended dose or
formula, the method and duration of administration, and contraindications. It is the responsibility of practitioners, relying on their
own experience and knowledge of their patients, to make diagnoses, to determine dosages and the best treatment for each individual
patient, and to take all appropriate safety precautions.
To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury
and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any
methods, products, instructions, or ideas contained in the material herein.
The
publisher’s
policy is to use
paper manufactured
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Printed in China
Dedication
This book is dedicated to the memory of
Margery E Carter
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Contents
Preface................................................................. ix 15. Non-spore-forming anaerobes...............205
Acknowledgements............................................ xi 16. Clostridium species.................................. 215
17. Enterobacteriaceae.....................................239
18. Pseudomonas, Burkholderia and
SECTION 1: General procedures Stenotrophomonas species........................275
in microbiology 19. Aeromonas, Plesiomonas and
Vibrio species...........................................289
1. Collection and submission of
20. Actinobacillus species...............................297
diagnostic specimens.................................. 3
21. Pasteurella, Mannheimia, Bibersteinia
2. Bacterial pathogens: Microscopy,
and Avibacterium species.........................307
culture and identification........................... 9
22. Francisella tularensis................................. 317
3. Serological diagnosis................................49
23. Brucella species........................................325
4. Molecular techniques in diagnostic
24. Campylobacter, Arcobacter and
microbiology . ..........................................59
Helicobacter species.................................335
5. The isolation of viruses and
25. Lawsonia intracellularis............................345
the detection of virus and .
26. Haemophilus and Histophilus
viral antigens.............................................67
species......................................................349
6. Antimicrobial agents................................79
27. Taylorella species......................................355
28. Bordetella species.....................................359
SECTION 2: Bacteriology 29. Moraxella species.....................................369
30. Glucose non-fermenting,
7. Staphylococcus species.............................. 105 Gram-negative bacteria...........................375
8. The streptococci and related cocci......... 121 31. The spirochaetes..................................... 381
9. Corynebacterium species and 32. Miscellaneous Gram-negative
Rhodococcus equi .....................................135 bacteria....................................................399
10. The Actinobacteria..................................147 33. Chlamydiales.............................................407
11. Mycobacterium species............................. 161 34. Rickettsiales and Coxiella burnetii............ 417
12. Listeria species.........................................177 35. The mycoplasmas
13. Erysipelothrix species................................187 (class: Mollicutes)...................................423
14. Bacillus species........................................195 36. Mastitis ...................................................433
vii
Contents
56. Birnaviridae.............................................. 613
SECTION 3: Mycology 57. Flaviviridae............................................... 617
37. Introduction to the pathogenic 58. Arteriviridae..............................................629
fungi.........................................................457 59. Togaviridae................................................635
38. The dermatophytes................................. 471 60. Orthomyxoviridae......................................639
39. Aspergillus species and 61. Paramyxoviridae........................................645
Pneumocystis carinii.................................. 481 62. Coronaviridae............................................655
40. The pathogenic yeasts.............................487 63. Rhabdoviridae...........................................665
41. The dimorphic fungi..............................497 64. Bunyaviridae.............................................673
42. The pathogenic Zygomycetes...................505 65. Retroviridae...............................................679
43. Fungi causing subcutaneous 66. Bornaviridae............................................. 691
mycoses................................................... 513 67. Prions (proteinaceous infectious
44. Mycotoxins and mycotoxicoses............. 521 agents).....................................................693
SECTION 5: Zoonoses
SECTION 4: Virology
(including prions) 68. Zoonoses.................................................703
45. Parvoviridae.............................................. 541
46. Circoviridae...............................................547 SECTION 6: A systems approach
47. Papillomaviridae....................................... 551 to infectious diseases on
48. Adenoviridae.............................................555 a species basis
49. Herpesviridae............................................559
50. Asfarviridae...............................................575 69. Infectious diseases..................................735
51. Poxviridae.................................................579
52. Picornaviridae...........................................587 Appendix 1 Reagents and stains...................845
53. Caliciviridae..............................................597 Appendix 2 Culture and transport media.... 851
54. Astroviridae...............................................603
55. Reoviridae.................................................605 Index................................................................857
viii
Preface
A lot of water has passed under the bridge since the popular first edition of this book. Needless to
say the writing of textbooks is not a full-time occupation for any of the authors but rather a com-
plementary activity to teaching, research and diagnostic service. This project was driven by a love
of books. On more than one occasion the writing faltered due to other more pressing commitments
and the vicissitudes of life in general. We have tried to retain the essential structure and character
of the first edition while updating and adding new material as necessary. In particular, the virology
section has been greatly expanded with the addition of a chapter for each of the families containing
viruses of veterinary importance. For taxonomy we have relied heavily on resources such as the List
of Prokaryotic Names with Standing in Nomenclature (www.bacterio.cict.fr/), the virus list of the
International Committee on Taxonomy of Viruses (ictvonline.org/index.asp) and Index Fungorum
(www.indexfungorum.org/). For information on the diagnosis of many of the more important
infectious diseases of farm animals we have frequently consulted the Manual of Diagnostic Tests
and Vaccines for Terrestrial Animals on the website (www.oie.int/en/international-standard-setting/
terrestrial-manual/access-online/) of the OIE (Office International des Epizooties – World Organisa-
tion for Animal Health). We hope we have succeeded in producing a book that is useful, informative
and appealing.
Dublin, 2013
ix
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Acknowledgements
Assembling material for a book requires forward planning, attention to detail and the means to put
in place the knowledge and ideas of the authors. We were fortunate to have the resources of the
first edition to draw upon in bringing this project to fruition. We are indebted to Professor Emeritus
Joe Quinn for being our mentor and greatest supporter in this endeavour.
Veterinary microbiology lends itself to illustration and we have tried to include suitable illustrative
material in the form of colour images and line drawings. A number of colleagues supplied images
which we would like to acknowledge: Professor KP Baker (38.7), Centres for Disease Control (31.13
and 34.2), Dr SJ Cook and Professor CJ Issel (3.3, 3.16 and 3.22), Dr DO Cordes (11.14, 42.7, 42.8,
42.9 and 44.7), Professor FWG Hill (29.1), Dr L Hoffmann (31.12), Dr G Joseph (18.7, 18.8 and
22.1), Professor JF Kazda (11.5, 11.6 and 11.7), Mr Aonghus Lane (36.21 and 36.22) and Dr N
Seiranganathan (35.8).
We also wish to acknowledge our predecessors in the Dublin Vet School, particularly Mr BT
Whitty, Mr MA Gallaher, Professor PJ Quinn and Dr Margery Carter who were prominent in our
formative training and who left for posterity a wealth of illustrative material and stained smears,
many of which we have used to illustrate individual chapters. We would also like to record our
appreciation to colleagues who furnished material for photography: Dr HF Bassett (10.17), Mr MJ
Casey (68.4), Mr RP Cooney (11.12), Mr P Costigan (5.4, 5.5, 51.1 and 51.2), Dr WJC Donnelly
(12.2, 12.3 and 67.2), Mr E Fitzpatrick (41.2), Dr HA Larkin (35.2), Dr GHK Lawson (33.4), Mr JB
Power (31.8 and 31.10), Dr GR Scott (34.1 and 35.1) and Professor Emeritus BJ Sheahan (39.2).
Finally, the authors would like to record their appreciation to the publishers for their patience
and encouragement while the book was in preparation, in particular Joyce Rodenhuis, Rita Deme-
triou-Swanwick, Louisa Welch, Robert Edwards, Veronika Watkins and Clive Hewat.
xi
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Section 1
General procedures in microbiology
1
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Chapter 1
Collection and submission of
diagnostic specimens
Choosing and Working with strains of viruses. This facilitates the updating of vaccines
with epidemiologically relevant viruses.
a Laboratory Some laboratories are involved in contract research and
In choosing a laboratory clinicians must consider the cost perform safety and efficacy studies for the regulatory
of the service and the ease of access. However, it is equally authorities. All diagnostic laboratories have a role to play
important to determine if a laboratory is accredited, has a in the monitoring of the efficacy of existing products. Cli-
specialization in the relevant species, offers a service at nicians have a responsibility to inform the microbiologist
weekends and holidays and has staff with the necessary of the vaccination and/or therapeutic history of the animal
expertise and training to assist with disease investigations. to facilitate independent assessment of different products
The quality of the dialogue between the veterinary practice and treatment regimens. Microbiologists in turn have a
and the laboratory has an enormous influence on the responsibility to advise clinicians with regard to their
effectiveness of the service. Good communication is essen- findings.
tial. The clinician and the microbiologist must establish
and maintain contact with each other. An accurate diag- General Principles for
nosis is based on the interpretation of both clinical and
laboratory data.
Sample Collection
If the clinician is not absolutely certain of the correct • Samples should be taken from the affected site(s) as
sample to collect they should seek advice from the labora- early as possible following the onset of clinical signs.
tory prior to collecting the samples. The samples must be This is particularly important in viral diseases as
appropriate for the purpose required which may be diag- shedding of virus is usually maximal early in the
nosis, certification, surveillance or the monitoring of infection. This is also true of enteric bacterial
vaccine efficacy or the response to antimicrobial therapy. pathogens.
A clinical diagnosis cannot be confirmed by the examina- • It is useful to collect samples from clinical cases and
tion of inappropriate samples. In disease control situa- in-contact animals, particularly if there has been
tions samples must be collected systematically for a an outbreak of disease. In-contact animals may
definite purpose, for example, the lifting of movement be at an earlier stage in the infection with a greater
restrictions or the commencement of breeding. Laboratory chance of them shedding substantial numbers of
tests can be both expensive and time-consuming. It is microorganisms.
important for all concerned that resources are not wasted • Samples should be obtained from the edge of lesions
in the generation of irrelevant information. and some macroscopically normal tissue included.
Both the veterinary practitioner and the laboratory have Microbial replication will be most active at the
an essential role in the isolation of new agents and the lesion’s edge.
detection of emerging disease patterns. In influenza out- • It is important to collect specimens as aseptically as
breaks, for example, the submission of samples to the possible, otherwise the relevant pathogen may be
laboratory for virus isolation is necessary to identify new overgrown by numerous contaminating bacteria
© 2013 Elsevier Ltd 3
