NOVEL MOLECULAR STRATEGIES for the DETECTION and CHARACTERIZATION of TICK-BORNE PATHOGENS in DOMESTIC DOGS a Dissertation By
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NOVEL MOLECULAR STRATEGIES FOR THE DETECTION AND CHARACTERIZATION OF TICK-BORNE PATHOGENS IN DOMESTIC DOGS A Dissertation by JOSEPH JAMES MODARELLI II Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Maria D. Esteve-Gasent Co-Chair of Committee, James N. Derr Committee Members, Pamela J. Ferro John M. Tomeček Head of Department, David Threadgill December 2018 Major Subject: Genetics Copyright 2018 Joseph James Modarelli II ABSTRACT Tick-borne diseases (TBD) are common across the United States and can result in critical and chronic disease states in a variety of veterinary patients, specifically domesticated dogs. Borreliosis, anaplasmosis, rickettsiosis, ehrlichiosis, and babesiosis have been cited as the most common TBDs. Despite recent reports revealing past exposure of TBD, there are no molecular epidemiological reports for dogs in Texas. Therefore, data to support the level of actively infected dogs in the population is inadequate. Limited molecular data for TBDs is due, in part, to the lack of consolidated molecular tools available to researchers. Real-time PCR (qPCR) assays are a commonly utilized tool for molecular detection of TBDs, and achieve species specificity by assigning each pathogen a unique fluorogenic label. However, current limitations of qPCR instruments include restricting the number of fluorogenic labels that can be differentiated by the instrument per a given reaction. As such, this dissertation explored the development of a qPCR methodology, termed layerplexing, that would allow for the simultaneous detection and characterization of 11 pathogens responsible for causing common TBDs in domestic dogs. Additionally, an endogenous internal positive control was designed and integrated into the assay for quality assurance of attained molecular results. Analysis revealed that the layerplex assay format was comparable in terms of target sensitivity and specificity to other qPCR assays utilized in the field. The layerplex assay was then applied to conducting a molecular prevalence investigation of TBDs affecting dogs across Texas ecoregions. By conducting molecular prevalence studies for TBDs, updated rates of active exposure and specific regions that may contain sentinels of disease could be identified. Results obtained ii indicated molecular prevalence of borrelial, rickettsial, and babesial pathogens varied across the Texas study area and indicated specific regions where susceptible hosts may be at higher risk for infection with TBD. Furthermore, the layerplex assay lead to the first reported molecular detection of Anaplasma platys in Texas and coinfection with Ehrlichia canis and A. platys in Texas dogs. Overall, findings from this dissertation provided substantial evidence that the layerplex technique can be utilized for grouping multiple targets under a single fluorogenic label without impeding diagnostic efficacy. The layerplex technique also demonstrated utility in facilitating large scale molecular analyses of animals in Texas. Surveillance data obtained from this study may aid public health agencies in updating maps depicting high-risk areas of disease and provide baseline data for future research aiming to characterize TBDs in additional animal models. iii DEDICATION To my family, for always supporting my endeavors. To my friends, for humoring my passions. To the Interdisciplinary Graduate Program in Genetics, College of Veterinary Medicine, and the TVMDL, for providing me the opportunity to apply my research to the field of diagnostics. Most of all, to my wife, Rachel, who has never stopped encouraging or inspiring me. iv ACKNOWLEDGEMENTS I would like to thank my committee chair Dr. Esteve-Gasent for all her patience, guidance, and support; my co-chair Dr. Derr for introducing me to the field of genetics; and my committee members, Dr. Ferro for teaching me how to apply a pursuit in genetics to the field of veterinary diagnostics, Dr. Tomeček for introducing me to the importance of wildlife surveillance, and Dr. Walt Cook for his willingness to assist in my defense. Special thanks to the TVMDL for providing me the opportunity to pursue a graduate degree and equipping me with a wealth of knowledge from on-site subject matter experts. I want to extend additional thanks to Dr. Ferro for not only supporting my desire to pursue a career in research, but also for pushing me out of my comfort zone so that I can attain the full graduate student experience. Special thanks to Interdisciplinary Graduate Program in Genetics Chair Dr. Threadgill, Veterinary Pathobiology Department Head Dr. Vemulapalli, as well as the faculty and staff of the departments for their support. Thanks also to our laboratory’s former students Dr. Christina Brock and Dr. Amer Fadhl Alhaboubi, and all of my current laboratory colleagues Dr. Wisam Hassan, Dr. Reem Elkalouby, Bonnie Gulas-Wroblewski, Rachel Cook, Wojciech Futoma, Roukaya Mabizari; as well colleagues and collaborators from numerous Departments for making my time at Texas A&M University a great experience. It also goes without saying how thankful and appreciative I am for my wife, Dr. Rachel Modarelli. She has been a shining example of excellence in academia, and a constant source of motivation as I pursued this degree. v CONTRIBUTORS AND FUNDING SOURCES Contributors This work was supervised by a dissertation committee consisting of Dr. Maria D. Esteve-Gasent (chair), Dr. James N. Derr (co-chair), and Dr. Pamela J. Ferro of the Department of Veterinary Pathobiology and Dr. John M. Tomeček of the Department of Wildlife and Fisheries Sciences (members). All work for this dissertation was completed independently under the supervision of Dr. Esteve-Gasent. Contributors include TVMDL, College Station, TX; Rocky Mountain Laboratories, Hamilton, Montana; UC Davis School of Veterinary Medicine, Davis, California; and USDA-ARS, Kerrville, TX. Funding Sources Graduate study was supported by Texas A&M AgriLife and Texas A&M Veterinary Medical Diagnostic Laboratory (TVMDL) seed grant Molecular Diagnosis of Zoonotic Tick-Borne Diseases. vi NOMENCLATURE CDC Centers for Disease Control and Prevention CGE Canine granulocytic ehrlichiosis CME Canine monocytic ehrlichiosis cnPCR Conventional polymerase chain reaction Cq Quantification cycle DIVA Differentiating infected and vaccinated animals DNA Deoxyribonucleic acid EIPC Endogenous internal positive control ELISA Enzyme-linked immunosorbent assay GCE Genome copy equivalents GG Genomic groups HME Human monocytic ehrlichiosis IFA Immunofluorescence assay LD Lyme Disease PCR Polymerase chain reaction qPCR Quantitative real-time polymerase chain reaction RMSF Rocky Mountain spotted Fever SFGR Spotted fever group rickettsioses SNP Single nucleotide polymorphism TBD Tick-borne disease TBRF Tick-borne relapsing Fever vii TVMDL Texas A&M Veterinary Medical Diagnostic Laboratory Tm Melting temperature µl Microliter U.S. United States viii TABLE OF CONTENTS Page ABSTRACT .......................................................................................................................... ii DEDICATION ..................................................................................................................... iv ACKNOWLEDGEMENTS ...................................................................................................v CONTRIBUTORS AND FUNDING SOURCES ................................................................ vi NOMENCLATURE ............................................................................................................ vii TABLE OF CONTENTS ..................................................................................................... ix LIST OF FIGURES ............................................................................................................. xii LIST OF TABLES ............................................................................................................. xiii CHAPTER I INTRODUCTION AND LITERATURE REVIEW ........................................1 Tick-borne diseases affecting dogs ...................................................................................1 Borrelial pathogens............................................................................................................1 Borreliosis ....................................................................................................................2 Rickettsial pathogens .........................................................................................................8 Anaplasmosis................................................................................................................9 Rickettsiosis............................................................................................................... 12 Ehrlichiosis ................................................................................................................ 14 Babesial pathogens ..........................................................................................................19 Prevalence of tick-borne pathogens within Texas dogs ..................................................22 Significance to public health ...........................................................................................27 Limitations in detecting tick-borne pathogens ................................................................28 A brief history of molecular diagnostic tools ..................................................................32