A case-control study to investigate the serotypes and untypable Streptococcus suis strains recovered from nursery pigs on 12 farms in Ontario, Canada between 2017 and 2018 by Leann Cynthia Denich 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 © Leann Cynthia Denich, January, 2020 ABSTRACT A CASE-CONTROL STUDY TO INVESTIGATE THE SEROTYPES AND UNTYPABLE STREPTOCOCCUS SUIS STRAINS RECOVERED FROM NURSERY PIGS ON 12 FARMS IN ONTARIO, CANADA BETWEEN 2017 AND 2018 Leann Cynthia Denich Advisors: University of Guelph, 2020 Dr. Zvonimir Poljak, Dr. Vahab Farzan Streptococcus suis is an important bacterial pathogen in swine that naturally colonizes the nasal cavity and tonsil of many pigs. Outbreaks tend to be sporadic and are typically seen in piglets 4- 8-weeks of age. It is still unclear why some pigs remain healthy, while others become systemically ill with infection. A case-control study was conducted to better understand the serotypes and untypable strains that are recovered from clinically ill and healthy pigs from Ontario nursery pigs. Firstly, we identified that the S. suis serotypes most commonly found in clinically ill pigs, from systemic sites included serotype (2,1/2), 9 and untypable isolates. There was also no association between serotypes found in upper respiratory sites of clinically ill and healthy pigs. Secondly, based on whole genome sequencing we determined that untypable isolates could be classified into 3 groups with respect to their similarity to existing serotypes which included ≥99% similar, between 50-98% similar or <50% similar to existing serotypes. iii ACKNOWLEDGEMENTS Many people were influential to the completion of this thesis and I would like to take this opportunity to thank each of them for all their contributions. First, I would like to express my sincerest gratitude to my advisory committee, Dr. Zvonimir Poljak, Dr. Vahab Farzan, Dr. Robert Friendship, Dr. Nicole Ricker and Dr. Marcelo Gottschalk as without their continuous guidance and support, this thesis would not have been possible. A big thank you to Food from Thoughts First Excellence Fund for providing funding for this research and all additional members of the S. suis project team, as their input greatly assisted with the quality of this work. I would also like to thank the swine practitioners at South West Ontario Veterinary Services and Demeter’s Veterinary Services for helping organize farm visits and of course the swine producers for agreeing to take part in the study. I am grateful for the guidance and mentorship received from Emily Arndt, Maria Amezcua and Eric Perrin. I would also like to thank my fellow graduate students and lab mates Sarah Hill, Jeremy Wong, Kash Kuruppu, Chris Mclaren-Almond, Karen DeBruyn, Kayla Silva, Matthew McBride, Emily Hanna and Jordan Pelkmans, not only for their technical assistance during experimentation, statistical analysis and writing, but for their friendship, entertainment and support through many challenges. Thank you to my friends for making my academic career one to remember and last but by no means least, I would like to thank my family for providing me with unfailing support and continuous encouragement throughout my years of study and through the process of researching and writing this thesis. A very special thanks goes out to my biggest supporter, my brother, Eric iv Denich, who has provided me with moral and emotional support throughout this entire journey, I cannot thank you enough for putting up with me and listening to and editing every part of this project, this is just as much yours, as it is mine! v CONTRIBUTIONS Leann Denich contributed to the project planning, participated in field work, collection of samples, processing of samples, data management and analyses, interpretation of results, dissemination of results and was principal author of all the chapters in this manuscript. Maria Amezcua, Eric Perrin, Sarah Hill, Kash Kuruppu and Jeremy Wong participated in field work. Emily Arndt helped with the processing of samples. Dr. Zvonimir Poljak, Dr. Vahab Farzan and Dr. Robert Friendship assisted with project planning, data management and analyses, interpretation and dissemination of results and provided critical feedback on all chapters. Dr. Nicole Ricker provided insight to bioinformatic techniques, interpretation and dissemination of results and critical feedback on all chapters. Dr. Marcelo Gottschalk provided critical feedback on all chapters. Funding for this research was provided by Food from Thought First Excellence Fund vi TABLE OF CONTENTS Abstract .............................................................................................................................ii Acknowledgements ............................................................................................................ iii Contributions .................................................................................................................... v Table of Contents ..............................................................................................................vi List of Tables .................................................................................................................... x List of Figures ...................................................................................................................xi List of Abbreviations ......................................................................................................... xii Chapter 1: Literature review ........................................................................................ 1 Introduction ......................................................................................................... 1 Diagnosis ............................................................................................................ 1 Clinical ......................................................................................................... 1 Pathological ................................................................................................... 2 Epidemiological ............................................................................................. 2 Humans ......................................................................................................... 4 Pathogenesis .................................................................................................. 6 Cytokines ...................................................................................................... 8 Other Streptococcus species ............................................................................ 9 Microbiological .................................................................................................. 10 Identification ............................................................................................... 10 Phylogeny ................................................................................................... 11 Serotyping ................................................................................................... 13 Matrix-assisted laser desorption/ionization time of flight mass spectroscopy (MALDI-TOF MS) ................................................................................................... 15 vii Polymerase chain reaction (PCR) test ............................................................. 15 Multi-locus sequence typing (MLST) ............................................................. 17 Whole genome sequencing (WGS) ................................................................. 18 Virulence ........................................................................................................... 20 Capsular polysaccharide ............................................................................... 21 Muramidase-release protein and extracellular protein factor ............................. 24 Suilysin ....................................................................................................... 24 Other proteins .............................................................................................. 25 Phenotypes/genotypes................................................................................... 26 Pathogenicity islands .................................................................................... 27 Control .............................................................................................................. 29 Vaccination ................................................................................................. 29 Treatment .................................................................................................... 29 Antimicrobial resistance ............................................................................... 30 Management ...................................................................................................... 31 Environmental/farm factors ........................................................................... 31 Presence of other diseases ............................................................................. 32 Eradication .................................................................................................. 33 Purpose and research objectives ........................................................................... 33 References ........................................................................................................