Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 5-31-2019 The seU of Geospatial Modeling and Novel Diagnostics to Detect and Map Risk Factors of Soil-Transmitted Helminths in Feira de Santana, Brazil Ryan Harry Avery Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Epidemiology Commons, Geographic Information Sciences Commons, Parasitic Diseases Commons, Parasitology Commons, Remote Sensing Commons, and the Veterinary Infectious Diseases Commons Recommended Citation Avery, Ryan Harry, "The sU e of Geospatial Modeling and Novel Diagnostics to Detect and Map Risk Factors of Soil-Transmitted Helminths in Feira de Santana, Brazil" (2019). LSU Doctoral Dissertations. 4953. https://digitalcommons.lsu.edu/gradschool_dissertations/4953 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. THE USE OF GEOSPATIAL MODELING AND NOVEL DIAGNSOTICS TO DETECT AND MAP RISK FACTORS OF SOIL-TRANSMITTED HELMINTHS IN FEIRA DE SANTANA, BRAZIL A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Pathobiological Sciences by Ryan Harry Avery B.S., State University of New York at Geneseo, May 2012 August 2019 This dissertation is dedicated to my family, especially my mother and father, without whom I would have never gotten to this point. I also dedicate this work to Maria Lauer, whose love, patience, and guidance have kept me together and allowed me to finish this. ii “Tactically it may be required that we concentrate attack for amelioration and control on persons and communities most severely affected. Strategically, at the world level, we need to know of the enemy wherever he rears his head, in order that over-all planning omit no favorable opportunity for neutralizing him.” -Norman R. Stoll “This Wormy World” iii Acknowledgments First and foremost, I would like to thank God, my savior and my rock, for he has shepherded me through this whole process and given me the strength and courage to see this research through to the end. To Maria Lauer, for the unending love, support, and understanding she has provided me with during this long dissertation process. To my mother, father, Tyler, and Kylie, who encourage me to follow my passion and inspired me to persevere through adversity. To my mentor Dr. John B. Malone, who has helped mold me into an inquisitive scientist and has ensured I never lost sight of the larger scientific picture. To my Geospatial Health laboratory friends: Dr. Moara Martins, Dr. Cassan Pulaski, Dr. Elivelton Fonseca, Brooke Delcambre, and Trevor Atkins, thank you for all your guidance and contributions throughout the years. You have all made this work possible. To my Graduate committee of Dr. Rebecca Christofferson, Dr. Thomas Klei, and Dr. James Miller, thank you for your advice and direction ensuring that I was able put forth my best effort and most complete work. iv Table of Contents Acknowledgments…………………………………………………………………………………………………………………….iv Abbreviations and Acronyms…….………………………………………………………………………………….………....vii Abstract…………………………………………………………………………………………………………………………..………..ix Chapter 1. Introduction: A Paradigm Shift Toward an Elimination Strategy for Soil- Transmitted Helminths…..……………………………………………………………………………………..…………………..1 1.1. Background………………………………………………………………………………………………………………..….1 1.2. Shifting From Morbidity Control Towards Elimination……………………………………………………2 1.3. Research Outline…………………………………………………………………………………………………………...5 1.4. References……………………..……………………………………………………………………………………………..6 Chapter 2. Literature Review………………………………………………………………………………………………………9 2.1 Soil-Transmitted Helminths………………………………………………………………………………………….…9 2.2. Diagnostic Techniques, Treatment, and Control………………………………………………………..…20 2.3. Geospatial Technologies…………………………………..………………………………………………………….22 2.4. Surveillance and Response Systems……………………………………………………………………………..23 2.5. References………………………………………………………………………………………………………………..…24 Chapter 3. Comparison of Kato-Katz, Mini-FLOTAC, and Multi-Parallel Real-time Polymerase Chain Reaction Techniques for Quantifying Intensity of Soil-Transmitted Helminth Infections in Feira de Santana, Brazil………………………………………………...………………………31 3.1. Introduction…………………………………………………………………………………………………………………31 3.2. Materials and Methods…………………………………………………………………………………….………….33 3.3. Results…………………………………………………………………………………………………………………………46 3.4. Discussion……………………………………………………………….…………………………………………………..53 3.5. Conclusion…………………………………………………………………………………………………………………..58 3.6. References…………………………………………………………………………………………..………………..…….58 Chapter 4. A Comparison of Household-Habitat Scale Ecological Niche Models Using WorldView-2, GeoEye-1, and Landsat 8 Satellite Products to Determine Ecological Distribution of Soil-Transmitted Helminth Infections in Three Representative Communities of Feira de Santana, Brazil………………………………..……………………………………………….64 4.1. Introduction…………………………………………………….………………………………………………………….64 4.2. Materials and Methods……………………………………………….………………………………………………69 4.3. Results…………………………………………………………………………….…………………………………………..85 4.4. Discussion………………………………………………………………………..………………..………………………103 4.5. Conclusion………………………………………………………………………..…………………………………….…106 4.6. References…………………………………………………………………………..…………….………………………107 Chapter 5. Molecular Confirmation of Ascaris suum: Further Investigation into the Zoonotic Origin of Infection in an 8-Year-Old Boy with Loeffler Syndrome……………..………………113 v 5.1. Introduction………….……………………………………………………………………………..…………..……..113 5.2. Case Study…………………………………………………………………………………………….………………….113 5.3. Conclusion……………………………………………………………………………………………………………….116 5.4. References……………………………………………………………………………………………….………………118 Chapter 6. Conclusions, Policy Recommendations, and Future Directions………….……………….….120 6.1. References…………………………………………………………………………………………………………………123 Appendix A. Louisiana State University IRB Approval……………………………………..……………………….125 Appendix B. First Page of Approval From Brazilian National Commission of Research Ethics…..126 Appendix C. Family Questionnaire in English……………………………………………………………..…………..127 Appendix D. Family Questionnaire in Portuguese…………………………………………………….……………..128 Appendix E. Individual Questionnaire in English……………………………………………………………………..129 Appendix F. Individual Questionnaire in Portuguese………………………..……………………………………..130 Appendix G. Informed Consent in English………………………………………………………….……………………131 Appendix H. Informed Consent in Portuguese…………………………………………………………………………132 Appendix I. Parental Consent Form in English…………………………………………………..…………………….133 Appendix J. Parental Consent Form in Portuguese …………………………………………………………………134 Appendix K. Minor Assent Form in English………………………………………………………………………………136 Appendix L. Minor Assent Form in Portuguese…………………………………………………………………….…137 Appendix M. Copyright Agreement…………………………………………………………………………………………138 Vita…………………………………………………………………………………………………..……………………………………141 vi Abbreviations and Acronyms DALY: Disability-Adjusted Life Years AUC: Area under the curve ROC: Receiver operating characteristic STH: soil-transmitted helminths A. lumbricoides: Ascaris lumbricoides T. trichiura: Trichuris trichiura N. americanus: Necator americanus A. duodenale: Ancylostoma duodenale WHO: World Health Organization NTD: Neglected Tropical Diseases CDC: Center for Disease Control and Prevention PCR: polymerase chain reaction qPCR: quantitative polymerase chain reaction WV2: WorldView-2 GE1: GeoEye-1 CDGN: Campo do Gado Novo MOH: Ministry of Health RS: Remote Sensing GIS: Geographic Information Systems Maxent: maximum entropy species distribution Pre-SAC: pre-school aged children SAC: school-aged children VHR: very high-resolution ENM: ecological niche model UEFS: Universidade Estadual do Feira de Santana vii UFBA: Universidade Federal da Bahia viii Abstract Soil-transmitted helminth (STH) infections impact billions of people worldwide. The traditional STH control approach is a morbidity control strategy implementing mass drug administration (MDA) programs targeting school-aged children (SAC). In Brazil, this control strategy has decreased STH prevalence to less than 20% in most of the country and providing an opportunity to transition from the morbidity control program and towards a surveillance and response system geared towards STH elimination. Surveillance and response systems geared towards elimination require the implementation higher accuracy diagnostics to detect infection in low-transmission communities, surveillance of entire households, high-resolution modeling at the household-habitat scale, and targeted treatment approaches tailored to specific communities. This study proposed to create a STH elimination surveillance and response system for the city of Feira de Santana, Brazil. Three communities were evaluated using three diagnostic techniques, entire households were sampled, and high resolution (30 m2) and very high- resolution (VHR) (<5 m2) satellite products were utilized to produce STH ecological niche models (ENMs). In a separate study, a zoonotic Ascaris case in the southern United States