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Investigating Foodborne Cryptosporidium and Giardia in Clams Harvested Near Iqaluit, Nunavut

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Investigating Foodborne Cryptosporidium and Giardia in Clams Harvested Near Iqaluit, Nunavut INVESTIGATING FOODBORNE CRYPTOSPORIDIUM AND GIARDIA IN CLAMS HARVESTED NEAR IQALUIT, NUNAVUT by Anna Jane Wilson Manore A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Population Medicine Guelph, Ontario, Canada © Anna J. W. Manore, August, 2018 ABSTRACT INVESTIGATING FOODBORNE CRYPTOSPORIDIUM AND GIARDIA IN CLAMS HARVESTED NEAR IQALUIT, NUNAVUT Anna Jane Wilson Manore Advisors: University of Guelph, 2018 Dr. Sherilee L. Harper Dr. Karen Shapiro High prevalences of Cryptosporidium and Giardia were reported in enteric illness patients in Nunavut, Canada, with a foodborne, waterborne, or animal source of parasites suspected. Clams (Mya truncata) are a commonly consumed, culturally important, and nutritious country food in Iqaluit, Nunavut; however, shellfish may concentrate pathogens from surrounding waters. EcoHealth approaches were used to investigate locally-harvested clams as a potential source of Cryptosporidium and Giardia for Iqaluit residents. Following molecular method validation, clam hemolymph (n=328) and digestive gland (n=390) samples were screened for Cryptosporidium and Giardia via PCR followed by sequence analyses. Giardia was confirmed in hemolymph from 2 clams, while Cryptosporidium was not detected. The Giardia sequences were identified as zoonotic Giardia enterica assemblage B, and may have originated from human or animal sources. Study results are intended to inform public health practice and planning. iii ACKNOWLEDGEMENTS This thesis would not be what it is without my fantastic co-advisors and advisory committee. Thanks first and foremost to my amazing co-advisors – Drs. Sherilee Harper and Karen Shapiro. Sheri, thank you so much for fostering such a welcoming, open, and encouraging space for me (and the whole lab) to work, and for always pushing me to do my best, and then do more. I have learned so much about how to do research, and be a researcher, and how to be aware of my role in the work that I do. Karen, thank you for your support while I travelled to a new place, your advice while I was attempting to set up a lab, and for your patience while I was learning and re-learning my way around the lab. I’ve learned so much from both of you. Thank you to all my committee members, Drs. Jan Sargeant, Scott Weese, and Ashlee Cunsolo, for your hard work in the planning of the PAWS project, and for offering your advice on my work and on my writing. Each of you brought a unique perspective to this research, and I’m so grateful for each of your contributions. Thanks as well to the Harper Lab (members past and present), for being such an excellent group of researchers, colleagues, friends, and people in general. I can’t imagine having done all this work without you! Thanks Carl, Viv, Jacquie, Steph, Danielle, Kate BW, Kate L, Alex, LJ, Amy, Paola, David, Manpreet, Lindsay, Isaac, Jess, Julia, Steven and Nia - this work was infinitely improved by having you all around, and it has been wonderful being able to work alongside, learn from, travel and grow with all of you. iv Thank you to everyone I worked with in Iqaluit for your time and energy supporting this work. At the Nunavut Research Institute: thank you Jamal Shirley, Mosha Cote, Rick Armstrong, and Mary Ellen Thomas for your interest, advice, and support during the clam collection phase of the PAWS project, and for the use of Nunavut Research Institute facilities and lab space. Thank you Enoo – for your generosity with your time, your music, and your knowledge. Your involvement truly made this project possible. Joanna Petrasek-MacDonald, Victoria Watson, and Anika Bychok – thank you for your friendly faces and company while in Iqaluit. Thank you to all the harvesters who gave their clams to the PAWS project. And, of course, thank you Stephanie Masina, Danielle Julien, and Anna Bunce for your help and support on PAWS in Iqaluit. In Davis, thank you so much to everyone who made me feel welcome while far from home: Beatriz Aguilar, Brittany Dalley, Andrea Packham, Pat Conrad, Minji Kim, Leslie Rueda, and Tiffany D’Arcy. Thanks in particular to Beatriz and Brittany for teaching (and re-teaching) me how to process the clam samples, and for being patient while I learned the ropes. Thanks also to Alica Buck, Nene Chantavarin, and Nora Beier for showing me around the best bits of Davis. In Guelph, thank you to Joyce Rousseau, for being so kind and helpful while I was learning my way around the CPHAZ lab. Thank you, Rebecca Fung, for being such a great student, for always being eager to learn, and of course for your help in processing clam samples. Thank you to the funding agencies that supported my research through: ArcticNet, the Ontario Graduate Scholarship, the Ontario Veterinary College Student Stipend; the Canadian Institutes of Health Research Canada Graduate Scholarship, the Arthur D. Latornell Travel Grant, the Northern Scientific Training Program, and the Michael Smith Foreign Study Supplement. v Thank you to all my friends who have supported me during these last few years, and in particular Emily Hawkins and Shveta Kanetkar, for your messages, your support, for always being ready with the worst (best) puns, and a plan for an adventure. Thank you, of course, to my parents and my brother for all your love and support. And, last but not least, thanks to Ann and Sandy and all the Middletons for being my family in Guelph these last few (eight) years – it has meant the world to me! vi STATEMENT OF WORK This thesis research was designed and carried out by a collaborative and interdisciplinary team of researchers, community members, and members of Northern governmental and non- governmental organizations. The use of an EcoHealth framework, in particular the participatory and interdisciplinary nature of the PAWS project, was crucial to the success of this research. Introduction and Literature Review The review protocol, including research question and search terms, was developed in collaboration with my advisory committee (Drs. Sherilee Harper, Karen Shapiro, Jan Sargeant, Scott Weese, and Ashlee Cunsolo) and with a consultation with Ali Versluis, an Open Education Resources Librarian at the University of Guelph. I conducted the final search, de-duplicated references in Mendeley© reference management software, imported references and created screening forms in DistillerSR© (Evidence Partners, Ottawa, ON, Canada) systematic review software. I reviewed titles and abstracts in DistillerSR© with Stephanie Masina (MSc Student), Isaac Bell (BSc Student), and Jessica Purbrick (BSc Student). I downloaded PDF files for articles that proceeded to level 2 screening with Isaac Bell, Jessica Purbrick, and Rebecca Ma (BSc Student). I screened full-text articles in DistillerSR© and exported reference information for each article that passed level 2 screening to Microsoft® Excel. I wrote this chapter under the supervision of Drs. Sherilee Harper and Karen Shapiro and with edits from my advisory committee (Drs. Jan Sargeant, Scott Weese, and Ashlee Cunsolo). Optimization of Nucleic Acid Extraction and Detection Brittany Dalley (Laboratory Technician) and I extracted Cryptosporidium parvum DNA using different numbers of freeze-thaw (FT) cycles and performed PCR to detect DNA under the supervision of Beatriz Aguilar (Staff Research Associate). Dr. Heather Fritz produced and vii provided Toxoplasma gondii oocysts, and Beatriz Aguilar spiked mussel tissue and water samples, extracted oocyst DNA and performed the PCR to detect T. gondii DNA. Dr. Karen Shapiro conceptualized and designed this study; I conducted this research under the supervision of Dr. Karen Shapiro and wrote the manuscript for this study under the supervision of Drs. Karen Shapiro and Sherilee Harper, and with edits from Dr. Scott Weese and Beatriz Aguilar. Cryptosporidium and Giardia in Locally-Harvested Clams in Iqaluit, Nunavut This project is one component of the People, Animals, Water, and Sustenance (PAWS) project, which is a collaboration between researchers at the University of Guelph, the Labrador Institute at Memorial University, the Nunavut Research Institute, and governmental and non- governmental organizations in Iqaluit, Nunavut. The PAWS Project was designed by Drs. Sherilee Harper, Jan Sargeant, Karen Shapiro, Rebecca Guy, Scott Weese, Ashlee Cunsolo, and Anna Bunce, alongside community partners, and aims to develop a community-based monitoring system of environmental pathogens in Iqaluit, Nunavut. I assisted the PAWS team in the planning and management of the “Sustenance” component of this project, along with Jamal Shirley from the Nunavut Research Institute and Enooyaq Sudlovenick (BSc Student). I travelled to Iqaluit for two weeks in July 2016 to plan the logistics of the project and four weeks in September 2016 to conduct the clam collection from local harvesters, and process clam tissue samples. I worked with Stephanie Masina, Anna Bunce (PAWS Project Manager) and Dr. Sherilee Harper to write and submit appropriate research licenses and permits to the Nunavut Impact Review Board, the Nunavut Planning Commission, and Fisheries and Oceans Canada. I worked with Dr. Karen Shapiro to write the protocol for clam tissue processing in Iqaluit, and I sought out equipment options and ordered the needed equipment for clam sampling and clam collection. I worked with Stephanie Masina, Enooyaq viii Sudlovenick, Anna Bunce, Danielle Julien, Garry Akpik (Research Assistant), and Pudloo Davidee (Research Assistant) to collect clams from local harvesters. Enooyaq Sudlovenick, Garry Akpik, and Pudloo Davidee also worked as interpreters during clam collection. Enooyaq Sudlovenick, Stephanie Masina, Danielle Julien and I worked together to process clam tissue samples in Iqaluit at the Nunavut Research Institute. Enooyaq Sudlovenick transferred clam collection data from handwritten sheets into Microsoft® Excel. I later cleaned and analyzed these data in Microsoft® Excel, Stata® 13.1 (StataCorp, College Station, TX, USA), and ArcGIS 10.4.1 (Esri, Redlands, CA, USA). I investigated options and arranged shipping of clam samples to the University of California, Davis for DNA extraction and PCR.
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