Bacteria from fish and other aquatic animals: a practical identification manual

Color profile: Disabled Composite 150 lpi at 45 degrees Bacteria from Fish and Other Aquatic Animals A Practical Identification Manual 1 Z:\Customer\CABI\A4636 - Buller\A4657 - Buller - Vouchers #VP10 #L.vp Monday, January 12, 2004 2:35:14 PM Color profile: Disabled Composite 150 lpi at 45 degrees 2 Z:\Customer\CABI\A4636 - Buller\A4657 - Buller - Vouchers #VP10 #L.vp Monday, January 12, 2004 2:35:14 PM Color profile: Disabled Composite 150 lpi at 45 degrees Bacteria from Fish and Other Aquatic Animals A Practical Identification Manual Nicky B. Buller Senior Microbiologist Department of Agriculture South Perth Western Australia CABI Publishing 3 Z:\Customer\CABI\A4636 - Buller\A4657 - Buller - Vouchers #VP10 #L.vp Monday, January 12, 2004 2:35:14 PM Color profile: Disabled Composite 150 lpi at 45 degrees CABIPublishing is a division of CAB International CABIPublishing CABIPublishing CAB International 875 Massachusetts Avenue Wallingford 7th Floor Oxfordshire OX10 8DE Cambridge, MA 02139 UK USA Tel: +44 (0)1491 832111 Tel: +1 617 395 4056 Fax: +44 (0)1491 833508 Fax: +1 617 354 6875 E-mail:cabi@cabi.org E-mail:cabi-nao@cabi.org Web site:www.cabi-publishing.org ©N.B. Buller 2004. All rights reserved. No part of this publication may be reproduced in any form or by any means, electronically, mechanically, by photocopying, recording or otherwise, without the prior permission of the copyright owners. A catalogue record for this book is available from the British Library, London, UK. Library of Congress Cataloging-in-Publication Data Buller, Nicky B. Bacteria from fish and other aquatic animals : a practical identification manual / Nicky B. Buller. p. cm. Includes bibliographical references and index. ISBN 0-85199-738-4 1. Aquatic animals--Microbiology. I. Title. QR106.B85 2004 579.3?176--dc21 2003009624 ISBN 0 85199 738 4 Typeset by AMADataSet, UK. Printed and bound in the UK byBiddles Ltd, King’s Lynn. 4 Z:\Customer\CABI\A4636 - Buller\A4657 - Buller - Vouchers #VP10 #L.vp Monday, January 12, 2004 2:35:14 PM Color profile: Disabled Composite 150 lpi at 45 degrees Contents List of Tables and Figures vii Foreword: J.A. Plumb ix Acknowledgements x Introduction xii 1 Aquatic Animal Species and Organism Relationship 1 1.1 Host Species, Bacteria and Disease 1 1.2 Bacterial Diseases 1 1.3 Bacteria and Relationship to Host 37 1.4 Taxonomy and Disease Status of Bacteria 75 2 Bacteriological Culture Techniques: Microscopy, Culture and Identification 83 2.1 Specimen Collection and Submission 84 2.2 Culture and Incubation 85 2.3 Examination of Culture Plates 85 2.4 Biochemical Identification Tests 114 2.5 Inoculation of Biochemical Identification Sets 115 2.6 API Identification Systems 116 3 Interpretation of Biochemical Identification Tests and Sets 117 3.1 Conventional Media: ‘Biochem Set’ 117 3.2 Identification Tests and their Interpretation 117 3.3 Using the Biochemical Identification Tables 123 3.4 Interpretation and Identification of Genera and Species 123 3.5 Antisera Available 136 4 Biochemical Identification Tables 137 4.1 Results for Conventional Biochemical Tests – ‘Biochem Set’ 137 4.2 Results for API Kits 138 5 Technical Methods 222 5.1 Total Bacterial Count (TBC) 222 v 5 Z:\Customer\CABI\A4636 - Buller\A4657 - Buller - Vouchers #VP10 #L.vp Monday, January 12, 2004 2:35:14 PM Color profile: Disabled Composite 150 lpi at 45 degrees vi Contents 5.2 Microscopy 224 5.3 Storage of Isolates 224 6 Techniques for the Molecular Identification of Bacteria 225 6.1 Molecular Identification by PCR Using Specific Primers 225 6.2 PCR Protocols 234 6.3 Molecular Identification by 16S rDNA Sequencing 236 6.4 Fluorescencein SituHybridization (FISH) 242 7 Preparation of Media for Culture and Identification 244 7.1 General Isolation and Selective Media 244 7.2 Biochemical Test Media 261 Further Reading and Other Information Sources 278 Appendix: Common Name and Scientific Name of Aquatic Animals 281 Glossary of Terms 287 References 292 Index 329 6 Z:\Customer\CABI\A4636 - Buller\A4657 - Buller - Vouchers #VP10 #L.vp Monday, January 12, 2004 2:35:14 PM Color profile: Disabled Composite 150 lpi at 45 degrees List of Tables and Figures Tables Table 1.1. Hostspeciesandorganismrelationship. Table 1.2. Bacterialpathogensandsaprophytesoffishandotheraquaticanimals. Table 2.1. Outlineofstepsforcultureandidentification. Table 2.2. Generalculture. Table 2.3. Specificculturerequirementsoforganisms. Table 2.4. Microscopicandculturalcharacteristics. Table 3.1. Interpretationoftestsfor‘biochemset’. Table 3.2. Carnobacterium,Lactobacillus,VagococcusandRenibacteriumdifferentiation. Table 3.3. Differentialtestsforsomenon-fastidiousfishpathogenicGram-positivecocciandrods. Table 3.4. DifferentialcharacteristicsofthegenerawithinthefamilyFlavobacteriaceae. Table 3.5. FurtherdifferentialcharacteristicsforthegenerainthefamilyFlavobacteriaceae. Table 3.6. AdditionaltestsfordifferentiationofbiotypesofP.damselae. Table 3.7. DifferentiationofV.alginolyticusandV.harveyi. Table 4.1. Aeromonassalmonicida(non-motileAeromonasspecies). Table 4.2. Aeromonasspp.PhenotypictestsaccordingtoDNAhydridizationgroups. Table 4.3. Aeromonasspp.–motile. Table 4.4. Anaerobes. Table 4.5. Brucellaspp. Table 4.6. Cryptococcus. Table 4.7. Cytophaga–Flavobacteriaceae–Bacteroidesgroup–pathogenic. Table 4.8. Cytophaga–Flavobacteriaceae–Bacteroidesgroup–environmental. Table 4.9. Gram-negativecoccobacilliandcocci. Table 4.10. Gram-negative,oxidase-negativerods. Table 4.11. Gram-negative,oxidase-positiverods. Table 4.12. Helicobacterspp. Table 4.13. Gram-positivecocci. Table 4.14. Gram-positiverods. Table 4.15. MycobacteriumandNocardiaspp. Table 4.16. Mycobacteriumspp. – additional tests. Table 4.17. Mycoplasmaspp. Table 4.18. Listonellaspp. vii 7 Z:\Customer\CABI\A4636 - Buller\A4657 - Buller - Vouchers #VP10 #L.vp Monday, January 12, 2004 2:35:14 PM Color profile: Disabled Composite 150 lpi at 45 degrees viii List of Tables and Figures Table 4.19. Moritellaspp. Table 4.20. Photobacteriumspp. Table 4.21. Vibrio–pathogenicspecies. Table 4.22. Vibrio–environmentalspecies. Table 4.23. API20Edatabasebiochemicalresults. Table 4.24. API20Edatabasenumbers(organismslistedalphabetically). Table 4.25. API20Edatabasenumbers(numbersinascendingorder). Table 4.26. API20NEdatabasebiochemicalresults. Table 4.27. API50CHdatabasebiochemicalresults. Table 4.28. APICorynedatabasebiochemicalresults. Table 4.29. API20Strepdatabasebiochemicalresults. Table 4.30. APIRapidID32Strepdatabasebiochemicalresults. Table 4.31. APIZymdatabaseresults. Table 4.32. Strainsquotedinreferences. Table 5.1. Total bacterial counts at sites in oyster hatcheries: indication of healthy and diseased states. Table 6.1. ListofspecificprimersavailableforPCRdetectionofaquaticorganisms. Table 6.2. StandardPCRprotocol. Table 6.3. Universaleubacterialprimersfor16SrDNAsequencing. Table 6.4. Suggestedprimerpairs. Table 6.5. Universalprimersforamplificationof16SrDNAfromVibriospp. Table 6.6. Sequencingprimersforthe16SrDNAfromVibriospp. Table 6.7. SequencingPCRmastermix. Figures Figure 4.1. Schematicforusingthebiochemicalidentificationtables. Photographic section after p. xiv 8 Z:\Customer\CABI\A4636 - Buller\A4657 - Buller - Vouchers #VP10 #L.vp Monday, January 12, 2004 2:35:15 PM Color profile: Disabled Composite 150 lpi at 45 degrees Foreword While aquatic animal diseases have been a concern for centuries, a profusion of marine and fresh- water aquaculture and environmental concerns across the globe in the last 75 years has prompted increasedinterestinthesediseases,particularlythosecausedbybacteria.Asaquaculturecontinuesto become more intensive and expands into new frontiers, fish health problems are likely to become moresignificant.Nogroupofmarineorfreshwateranimals,includingmammals,fish,birds,molluscs, shellfish,reptilesandamphibians,haveescapedtheeffectsofbacterialdiseases.Hundredsofbacterial speciescanbeeitherpathogenictowildandculturedaquaticanimalsorposeapotentialdiseasethreat under favourable conditions. Furthermore, the costs incurred by governments, private aquaculture andthepublic,duetobacterial-relateddiseasesandattemptstocontrolthem,totalsmillionsofdollars annuallyasaresultoflostaquaticresources.Inordertosuccessfullycopewiththesedisease-producing microbes in a cost-effective manner, prompt and accurate identification is essential. Untilnowtherehasbeennosinglesourceavailableforuseinidentifyingbacterialmicrobesfromso manydiversemarineandfreshwateranimals.However,BacteriafromFishandOtherAquaticAnimals: aPracticalIdentificationManualnowprovidesjustsuchasourcewithglobalapplication.Thispractical, user-friendlyidentificationmanualwillbeofgreatvaluetoinexperiencedandexperiencedbacteriolo- gists,microbiologyteachersand/orstudents,aquaticanimalhealthresearchersordiagnosticians,aswell astoworkersinpublichealthfacilitiesormedicallaboratorieswhoworkwithmarineandfreshwaterfish, birds, mammals, molluscs, shellfish, reptiles or amphibians. Aided by numerous tables and colour figures the author discussesconventional bacterial identificationprocedures, commerciallyavailable data-basedidentificationkits,molecularlybasedPCRand16SrDNAsequencing,thusprovidingutility toabroadscientificsector.Inthissinglevolumeonecanfindbiochemical,biophysicalandmolecular characteristicsofnearly400speciesofaquaticbacteria,mediaonwhichtheyareculturedandabrief discussionofmanydiseaseswithwhichtheyareassociated.Assemblingthismanualwasamonumental taskanditsauthor,NickyB.Buller,istobehighlycommendedforprovidingthisinvaluableadditionto aquatic microbiology. John A. Plumb Department of Fisheries and AlliedAquacultures Auburn University Alabama, USA ix 9 Z:\Customer\CABI\A4636 - Buller\A4657 - Buller - Vouchers #VP10 #L.vp Monday, January 12, 2004 2:35:15 PM