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Improving Traceability and Detection of Food Fraud

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Improving Traceability and Detection of Food Fraud Improving traceability and detection of food fraud: An exploration of current seafood authentication methods and validation of a novel qPCR and closed- tube barcoding method for commercial species of fish, FASTFISH-ID by Maleeka Singh A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Food Science Guelph, Ontario, Canada © Maleeka Singh, September, 2020 ABSTRACT IMPROVING TRACEABILITY AND DETECTION OF FOOD FRAUD: AN EXPLORATION OF CURRENT SEAFOOD AUTHENTICATION METHODS AND VALIDATION OF A NOVEL QPCR AND CLOSED-TUBE BARCODING METHOD FOR COMMERCIAL SPECIES OF FISH, FASTFISH-ID Maleeka Singh Advisor(s): University of Guelph, 2020 Advisor Name: Dr. Jeffrey Farber Advisor Name: Dr. Robert Hanner Food fraud is a global issue, which not only defrauds the consumer, but presents a food safety risk. Seafood is one of the most adulterated foods due to the vast and complex supply chains. Over the past 20 years, 236 original DNA-based assays have been published for the authentication of commercial species of fish. qPCR has been the most researched DNA-based authentication method, followed by DNA sequencing. The target genes cytb (cytochrome b) and COI (cytochrome c oxidase 1) are also the most researched in the literature. However, in silico testing on a select set of published assays showed a lack of assay reliability. A total of 77.78% of the tested assays were found to be non-specific. A novel DNA-based authentication method, using qPCR and closed-tube barcoding technology, called FASTFISH-ID, can provide a quick and reliable, first-screening step, in fish authentication. iii DEDICATION This thesis is dedicated to the women in my family, and the men who continue to support us in each and every way. To my mom, dad, brothers and grandparents, you are my inspiration. iv ACKNOWLEDGEMENTS I would like to acknowledge my advisors Dr. Jeffrey Farber and Dr. Robert Hanner for their continued support and guidance throughout my graduate school journey. Thank you both for being the most amazing mentors, pushing me to aim higher, and helping me achieve all of my goals. I would also like to acknowledge my Hanner Lab mates. You have been amazing resources and without you all, this journey would have seemed lonely and a lot less fun. To Tzitizki, Yoamel, Kevin, Danielle and Lauren, thank you for always being there when I required your technical expertise, or when I just needed to talk…which was a lot! Thank you to my grandparents. Without your sacrifices, I would not have had the privilege or motivations to pursue graduate school. From not being able to read or write, or teaching yourselves how to read, you have showed me the meaning of perseverance, determination and resilience. To Yuri, thank you for always being a phone call away and for your continued support and encouragement. I am grateful for everything that you do. To my brothers, Vedatma and Govinda, words cannot describe how grateful I am to have you both in my life. Thank you for being with me every step of the way, supporting me through all of my emotions, brother-sister times and being my truest confidants. To my mom and dad: Mom, thank you for being my #1 cheerleader and giving me the courage to pursue my dreams. Dad, thank you for being my best friend, workout partner, role model and everything in between. You are both my inspiration and without you, I would not be who I am today. Thank you v TABLE OF CONTENTS Abstract ........................................................................................................................................... ii Dedication ...................................................................................................................................... iii Acknowledgements ........................................................................................................................ iv Table of Contents ............................................................................................................................ v List of Tables ................................................................................................................................. ix List of Figures ................................................................................................................................ xi Prologue .......................................................................................................................................... 1 Research questions and hypotheses ............................................................................................ 2 References ................................................................................................................................... 3 1 Chapter 1: The impact of food fraud on food safety: A review .............................................. 4 1.1 Abstract ........................................................................................................................... 4 1.2 Introduction ..................................................................................................................... 5 1.2.1 What is food safety? ................................................................................................ 5 1.2.2 What is food fraud? ................................................................................................. 5 1.2.3 Food safety concerns regarding food fraud ............................................................ 6 1.3 Methods ........................................................................................................................... 6 1.4 Food Products/Ingredients Most Commonly Adulterated and Case Studies .................. 7 1.4.1 Alcohol .................................................................................................................... 7 1.4.2 Coffee ...................................................................................................................... 8 1.4.3 Fruit juices .............................................................................................................. 9 1.4.4 Honey .................................................................................................................... 10 1.4.5 Meat ...................................................................................................................... 11 vi 1.4.6 Milk ....................................................................................................................... 12 1.4.7 Olive Oil ................................................................................................................ 14 1.4.8 Seafood ................................................................................................................. 14 1.4.9 Herbs and spices ................................................................................................... 16 1.4.10 Rice (cereals and grains) ....................................................................................... 17 1.4.11 Consumer demand and disruption in the supply chain ......................................... 18 1.5 Prevention Strategies .................................................................................................... 19 1.5.1 Regulations ........................................................................................................... 19 1.5.2 Prevention Strategies Through Risk Management Systems ................................. 20 1.5.3 Vulnerability Assessment Tools ........................................................................... 23 1.6 Conclusions ................................................................................................................... 25 1.7 Funding ......................................................................................................................... 26 1.8 References ..................................................................................................................... 27 1.9 Tables ............................................................................................................................ 35 2 Chapter 2- Review of commercial fish assays from 2000-2020 ........................................... 41 2.1 Abstract ......................................................................................................................... 41 2.2 Introduction ................................................................................................................... 42 2.3 Methods and inclusion criteria ...................................................................................... 43 2.3.1 Data recorded ........................................................................................................ 43 2.3.2 Fish families/order groupings ............................................................................... 43 2.4 Detection method review and limitations ..................................................................... 43 2.4.1 Orders of fish in the literature ............................................................................... 43 2.4.2 Assay type ............................................................................................................. 51 2.4.3 DNA target/ assay region ...................................................................................... 62 vii 2.5 Discussion ..................................................................................................................... 69 2.5.1
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