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Evaluating the Importance of Zoonotic Bacteria

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Evaluating the Importance of Zoonotic Bacteria EVALUATING THE IMPORTANCE OF ZOONOTIC BACTERIA, ANTIMICROBIAL USE AND RESISTANCE IN AQUACULTURE AND SEAFOOD A Thesis Presented to The Faculty of Graduate Studies of The University of Guelph by NATASA TUSEVLJAK In partial fulfillment of requirements for the degree of Master of Science April, 2011 © Natasa Tusevljak, 2011 Library and Archives Biblioth6que et Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'^dition 395 Wellington Street 395, rue Wellington Ottawa ON K1A 0N4 Ottawa ON K1A 0N4 Canada Canada Your file Votre r6f6rence ISBN: 978-0-494-80085-0 Our file Notre r^f6rence ISBN: 978-0-494-80085-0 NOTICE; AVIS; The author has granted a non­ L'auteur a accorde une licence non exclusive exclusive license allowing Library and permettant a la Bibliotheque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par I'lnternet, preter, telecommunication or on the Internet, distribuer et vendre des theses partout dans le loan, distribute and sell theses monde, a des fins commerciales ou autres, sur worldwide, for commercial or non­ support microforme, papier, electronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in this et des droits moraux qui protege cette these. Ni thesis. Neither the thesis nor la these ni des extraits substantiels de celle-ci substantial extracts from it may be ne doivent etre imprimes ou autrement printed or otherwise reproduced reproduits sans son autorisation. without the author's permission. In compliance with the Canadian Conformement a la loi canadienne sur la Privacy Act some supporting forms protection de la vie privee, quelques may have been removed from this formulaires secondares ont ete enleves de thesis. cette these. While these forms may be included Bien que ces formulaires aient inclus dans in the document page count, their la pagination, il n'y aura aucun contenu removal does not represent any loss manquant. of content from the thesis. I*: Canada ABSTRACT EVALUATING THE IMPORTANCE OF ZOONOTIC BACTERIA, ANTIMICROBIAL USE AND RESISTANCE IN AQUACULTURE AND SEAFOOD Natasa Tusevljak Co-Advisors: University of Guelph, 2011 Dr. Andrijana Rajic Dr. Scott McEwen This thesis employs research synthesis methods (scoping study (ScS) and systematic review-meta-analysis (SR-MA)) to characterize and evaluate the existing primary research on antimicrobial use (AMU), antimicrobial resistance (AMR), selected zoonotic bacteria in aquaculture. It also describes an elicitation of global expert opinion on these topics. Evidence maps from the ScS identified knowledge gaps (AMU and the association between AMU-AMR), and strengths (prevalence/interventions for Vibrio and Aeromonas at the farm level). SR revealed consistent flaws in methodology/reporting of research on prevalence/concentration of Aeromonas, E. coli. Salmonella and Vibrio in clams, mussels, oysters, salmon, shrimp (including prawn), and tilapia from processing to retail. Retail level MA revealed significant heterogeneity across the studies. The questionnaire achieved a response rate of 32.9% (n=199) and was most representative of North Americans (n=152) involved in clinical work (n=91). Respondents reported quinolone use in North America, Europe and Asia; frequent tetracycline use and resistance across aquatic species. ACKNOWLEDGEMENTS I would like to extend my sincerest gratitude to my advisory committee, particularly Drs. Andrijana Rajic, Lucie Dutil and Scott McEwen who have provided constant guidance and support throughout my journey over the past two years. Your dedication to the field of Epidemiology and your students is truly inspiring. I would also like to thank my coworkers at PHAC who dedicated time in support of this project as well as PHAC for funding. To the many reviewers, pre-testers and procurers that were involved throughout the development and progression, this project was truly a team effort and my deepest thanks for your unwavering dedication. To my fellow graduate students who maintained their free spirits and lightheartedness, thank you for knowing just how to break up a busy day. To my parents, Dragomir and Vesna, and my sister, Dejana, I stand in awe of your strength and unyielding support in my attempts to create new paths. Thank you for the freedom in allowing me to do so. LIST OF TABLES Table 1.1. Comparisons between traditional literature reviews, scoping studies and systematic reviews 28 Table 2.1. Demographic characteristics of respondents to a questionnaire soliciting information on AMU and AMR administered globally to aquaculture professionals 49 Table 2.2. Reported respondent level of experience with various aquatic species 51 Table 2.3. Reported antimicrobial use and observation of resistance to antimicrobial drug classes for various aquatic species 52 Table 2.4. Reporting of antimicrobial usage per region for all aquatic species presented for all respondents and excluding those responding only for ornamental fish 55 Table 2.5. Reported observed bacterial resistance for selected bacteria and antimicrobial drug classes ...58 Table 3.1. Number of relevant quality-assessed studies submitted to data extraction by aquatic species, bacteria and point in food chain 88 Table 3.2. A summary of various subsets of data reporting the prevalence of four selected bacteria in four aquatic species-seafood categories at retail (including RTE) and sub-grouped by region of sampling to improve interpretation and decrease heterogeneity 90 Table 3.3. A summary of various subsets of data reporting the concentration of three selected bacteria in selected aquatic species-seafood categories at retail (including RTE) and sub-grouped by region of sampling to improve interpretation and decrease heterogeneity 93 ii LIST OF FIGURES Figure 1.1. A stepwise depiction of the study goals and components: scoping study- systematic review and expert questionnaire 29 Figure 3.1. Scoping study and systematic review process flow-chart 94 Figure 3.2. Evidence mapping. Distribution of primary research according to type of study, topic, pathogen, aquatic species and point in food chain 96 Figure 3.3. Random effects meta-analysis of the prevalence (expressed as proportion) of Aeromonas, E. coli and Salmonella on salmon 97 iii TABLE OF CONTENTS ACKNOWLEDGEMENTS I LIST OF TABLES II LIST OF FIGURES Ill TABLE OF CONTENTS IV CHAPTER ONE INTRODUCTION, LITERATURE REVIEW AND OBJECTIVES .1 INTRODUCTION 1 LITERARATURE REVIEW 2 Overview of the Global Aquaculture Industry 2 Overview of Aquaculture and Seafood Industries in Canada 4 Food Safety Risks Associated With Aquaculture and Seafood 5 Zoonotic Bacteria in Aquaculture and Seafood 6 Antimicrobial Use (AMU) in Aquaculture 8 Antimicrobial Resistance (AMR) in Aquaculture , 9 Monitoring of AMR and AMU and Control of AMR 10 Current Legislative Framework for Production of Safe Seafood in Canada 11 Research Synthesis Methods and Their Application in Zoonotic Public Health 11 Scoping Studies as Tools for Evidence Mapping 12 Systematic Review -Methodology and Comparison to Scoping Study 13 The Meta-Analysis Approach to Understanding Global Evidence 14 The Use of Questionnaires in Epidemiological Research 14 STUDY RATIONALE AND OBJECTIVES 16 REFERENCES 19 CHAPTER TWO ANTIMICROBIAL USE AND RESIT ANCE IN AQUACULTURE: FINDINGS OF A GLOBALLY ADMINSITERED SURVEY OF AQUACULTURE-ALLIED PROFESSIONALS 30 iv SUMMARY 30 INTRODUCTION 31 MATERIALS AND METHODS 32 Questionnaire design description 32 Database of aquaculture-allied professionals 33 Survey administration 34 Data analysis 34 RESULTS 35 Respondent demographic characteristics and non-response bias evaluation 35 Overview of respondent professional experience 35 Opinions on Frequency of AMU and AMR in various aquatic species ..36 AMR in selected bacteria 37 Knowledge of AMR monitoring and surveillance 38 DISCUSSION 38 ACKNOWLEDGEMENTS 42 REFERENCES 43 CHAPTER THREE PREVALENCE OF SELECTED ZOONOTIC BACTERIA IN SELECTED AQUATIC SPECIES AND SEAFOOD: A SCOPING STUDY, SYSTEMATIC REVIEW AND META-ANALYSIS OF PUBLISHEDRESEARCH .61 ABSTRACT 61 INTRODUCTION 62 MATERIALS AND METHODS 64 ScS Study: Defining its broad scope 64 Search Strategy and Execution 65 Relevance Screening and Exclusion Criteria 66 Development of Focused Question for SR 67 SR; Inclusion of Studies, Methodological Assessment and Data Extraction 67 Management of ScS and SR i 69 Meta-analysis 69 RESULTS 71 ScS: Research Themes, Study Characteristics and the Focused Question 71 SR Database and Meta-Analysis 72 V DISCUSSION 73 SR-MA highlights 73 Knowledge gaps 75 Recommendations for future seafood surveys 77 Limitations and strengths of the study 78 Relevance in the Canadian context 79 CONCLUSION 80 ACKNOWLEDGEMENTS 81 REFERENCES 82 CHAPTER FOUR SUMMARY DISCUSSION AND CONCLUCIONS 98 SUMMARY DISCUSSION 98 CONCLUSION 104 REFERENCES 106 APPENDIX 2. QUESTIONNAIRE: SURVEY ON ANTIMICROBIAL USE AND RESISTANCE IN ZOONOTIC BACTERIA IN AQUACULTURE, SEAFOOD AND ORNAMENTAL/PET FISH 109 APPENDIX 2.1. Questionnaire-English Version 109 APPENDIX 2.2. Questionnaire-Spanish Version 123 APPENDIX 2.3. Descriptive Statistics Report 141 APPENDIX 3. PREVALENCE OF SELECTED ZOONOTIC BACTERIA IN SELECTED AQUATIC SPCOES AND SEAFOOD: A SCOPING STUDY, SYSTEMATIC REVIEW AND META-ANALYSIS OF PUBLISHED RESEARCH
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