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Infectious Disease Epidemiology in Global Settings – Surveillance, Prevention, and ControlGLHLTH777Spring 2019Course SyllabusInstructorsWendy P O’Meara PhD Associate Professor in MedicineAssociate Research Professor of Global HealthDr. O’Meara is a faculty member in the Division of Infectious Diseases and the Duke Global Health Institute. She is based full-time in Eldoret, Kenya, where her research focuses on improving access to malaria diagnostics and controlling the spread of drug resistance by improving adherence to diagnostic testing in the formal and informal, for-profit health sector. Email: wpo@duke.eduWebsite: projects in: Kenya, TanzaniaL. Gayani Tillekeratne MD MSc Assistant Professor of MedicineAssistant Research Professor of Global HealthDr. Tillekeratne is a faculty member in the Division of Infectious Diseases and the Duke Global Health Institute. She is based half the year in Galle, Sri Lanka, where her research activities focus on exploring the etiologies of febrile and acute respiratory illnesses and using advanced diagnostics to improve antibiotic stewardship and decrease antimicrobial resistance. She provides medical care at the Durham VA Medical Center in Infectious Diseases and Medicine.Email: gayani.tillekeratne@dm.duke.edu Website: projects in: Sri LankaSteve M Taylor MD MPH (Course leader)Associate Professor of MedicineAssistant Research Professor of Global HealthDr Taylor is also a faculty member in the Division of Infectious Diseases. His research effort is focused on malaria parasites in sub-Saharan Africa: detecting them, understanding their biology, and preventing infection by them. He is also an infectious diseases clinician and internist and provides medical care at the Durham VA Medical Center.Email: steve.taylor@duke.eduWebsite: projects in: Mali, Kenya, Mozambique, MalawiOffice hours: By appointment Fridays 8:30-9:30AM Eastern Time via:Zoom (O’Meara or Tillekeratne) or Sands bldg. room 301 (Taylor)Importantly, please contact the appropriate instructor by email prior to office hours to make an appointment for this time. Each week, we will send an email with a URL link for a Zoom meeting room, and students can avail themselves of office hours by following this link.Course InformationLectures: Web-based videos will be reviewed by students on their own time. Lecture material and reading material for the upcoming week will be released mid-day each Thursday.Discussion Sessions: Thursdays 8:30AM-9:30AM, via Zoom teleconferenceCourse website: sakai.duke.eduThe course website has a lot of this and that, but the most important tabs (on the left gutter of the screen) are the Module tabs. These tabs have in running fashion the lectures (videos), required readings, suggested readings, and links to quizzes for each Lesson. This page will be populated each Thursday mid-day with the content for the coming week (ie 2 Lessons and their associated content).Readings: Required and suggested online readings will be linked to on the course website within the relevant Lesson.Other suggested general references. These are NOT required, and they are each available through the Duke Medical Center Library for deeper dives into specific topics.Nelson K.E. and Williams C. eds. Infectious Disease Epidemiology: Theory and Practice, 3rd ed. – As the title suggests, pretty relevant for this courseThomas J.C. and Weber D.J. eds. Epidemiologic Methods for the Study of Infectious Diseases, 1st ed. – For a deeper dive into methodsFarrar J et al. eds. Manson’s Tropical Diseases, 23rd ed. – The canonical tropical medicine textbookUpToDate () – Good medical reference, available on-campusCourse DescriptionThis on-line elective course provides an in-depth focus on the epidemiology of communicable diseases in global settings. The course content encompasses the individual-level of diagnosis and treatment of an infectious case as well as the population-level of disease surveillance, prevention and control. The course will also examine the relationships between infectious diseases and environmental health, including veterinary health, and end with an introduction to relatively understudied global communicable diseases and new approaches to epidemiologic studies. The course expands upon disease topics introduced in GH701 (Global Health Challenges), and aims to incorporate concepts from GH705/707 (Biostatistics and Epidemiology for Global Health), GH702 (Global Health Research: Design and Practice), and GH709 (Intermediate Epidemiology) in order to build towards an integrated understanding of applied infectious disease epidemiology and the methodologies for conducting global epidemiologic research and evaluating intervention programs. Owing to the level of instruction and content, some basic familiarity is necessary with biomedical human subjects research and/or clinical research in order to get the most out of the class. This course is organized into three complementary modules, each led by a different instructor: Foundations in Infectious Disease Epidemiology, (Wendy O’Meara)Disease Surveillance & Prevention, (Gayani Tillekeratne) and Frontiers in Infectious Disease Epidemiology. (Steve Taylor)Case studies will be utilized throughout in order to empower students to become global health scientists and practitioners with practical knowledge of how health programs – small and large – can confront communicable diseases in resource-limited settings. The course instructors bring a wealth of experience in the study and control of infectious diseases in sub-Saharan Africa and South Asia, as well as active research programs in these settings. As a result, the instructors are semi-permanently or frequently overseas, and this course is taught exclusively on-line via lecture-based tutorials and weekly tele-conferenced discussion sessions.Learning ObjectivesBy the end of this course, students will have a comprehensive understanding of: The fundamental processes driving infectious disease transmission, persistence, epidemic patterns and pathogen evolutionThe opportunities for intervention depending on the pathogen dynamics and mode of transmissionHow to measure the burden of infectious disease in a populationPrinciples of infectious disease surveillance Novel technologies for conducting infectious disease surveillanceEffective methods for preventing infectious diseases, including vaccination and mass treatmentImportance of hospital-based epidemiology and infection control in low- and middle-income countries (LMICs)Global burden of emerging, neglected, and intractable communicable diseasesModern approaches to epidemiology that enhance traditional disease surveillance In addition, this course will train students as global health practitioners by focusing on the development of general and specific methods for epidemiologic studies. These skills will be developed by modeling skills in didactic video lectures, demonstrated in additional “Epi-torial” videos (see Section G, below), and performed by students during weekly discussion sessions. Specifically, students will learn to:Critically evaluate published epidemiologic literature on communicable diseases of global health importanceApply different metrics and methodologies for quantifying disease burden and spread in a populationPredict and measure intervention success based on mode of pathogen transmission, population characteristics, and contact networksConduct outbreak investigations in community- and facility-based settingsDesign surveillance programs tailored to disease transmission and epidemiologyIncorporate molecular approaches into epidemiologic studies in order to define transmission networks and pathogen phenotypesReadingsRequired readings will be posted on course Sakai website (‘Course’ tab). Readings are mainly scholarly scientific articles with some book chapters, and the course emphasizes cultivating critical & analytical engagement with the medical and public health literature on infectious diseases. Among the suggested readings, students may find that, for some weeks, there are ‘Resources for Lifelong Learning’ listed by the instructor. These are materials or resources that the instructor has deemed noteworthy for future global health practitioners. It is not intended that students read all of these very large documents. Rather, such documents or websites are included so that students develop knowledge of what resources exist and where they might go for answers when different situations arise in their careers.Assignments & AssessmentsQuizzes30%Scholarly Article Analysis (written assignments)45%Scholarly Article Analysis (oral presentation)10%Discussion Session Participation (discussion session/short reflections)15%Quizzes: Each week there will be a short quiz consisting of short-answer or multiple choice questions drawn from the week’s lectures and required readings. The quiz will be accessed through the course site on Sakai (‘Lessons’ tab), and will only become available once the student has completed his/her viewing of the lecture tutorials. Scholarly Article Analysis (Written Assignments):The learning objective of this activity is to analyze the scientific medical and public health literature on infectious diseases and demonstrate mastery of course concepts through a structured critical appraisal of the employed methods. Students will be given an analytical rubric which they will utilize in order to critically analyze selected published manuscripts. There will be 3 written assignments in which students rigorously assess a required reading from the course (note: each analysis assignment will have one article selected by the instructor such that all students are analyzing the same article). These written assessments will be no more than 2-pages single-spaced. Scholarly Article Analysis (Oral Presentation): The learning objective of this activity is to analyze a published study of the student’s choosing investigating infectious disease epidemiology and communicate summary findings to fellow learners in a succinct and compelling manner. Each student will be required to give one 15-minute presentation of an article he/she found via a targeted literature search. Students will sign up for the week they wish to present, and are expected to present an article relevant to the topics being covered in the course that week. After identifying a public health question relevant to the week’s topic, performing an appropriate literature search and selecting an article, the student will present the article as part of the weekly discussion sessions. These presentations are meant to be casual and collegial—no powerpoint, no handouts, just a structured assessment of a relevant article that the student found interesting or noteworthy.Student-selected articles should be peer-reviewed, published manuscripts reporting the conduct, results, and analysis of an original research study. They do not have to be directly relevant to the week’s lesson content, although they certainly can be. It is most important to pick a study within the listed parameters about which you can learn and engagingly communicate your analysis to your classmates. Class Participation:This component will be based upon attendance and participation in the weekly discussion sessions as well as responses to the weekly short reflections. The structure of the weekly discussion sessions will vary by module, but will be organized around engaging more fully with the content of that week’s lessons. The weekly short reflections are short-answer questions/polls/reflections on the content of the videos that follow the week’s video. Response to these on the course website is required.ScheduleThe primary mode of instruction will be through on-line recorded lectures. For these recorded lectures, each week will include two Lessons, and each Lesson will comprise 3 – 5 short (< 12 minute) videos. The catalog of topics for the Lessons is below. In addition to these core lecture videos, Lessons may also include either of 2 additional types of videos: “Epi-torials”: These tutorials in epidemiologic methods will demonstrate a variety of fundamental data collection procedures that are used in field studies.Guest interviews: These curated interviews with experts in Lesson content will complement the video concepts with real-world field and clinical experience.Aside from on-line recorded lectures, a weekly discussion session will be held Thursday mornings via WebEx. It is expected that all students will have completed the on-line lectures, the required readings, and the weekly quiz prior to this session.Lessons:Lesson 0:Introductions & Course Overview(Taylor)MODULE I: FOUNDATIONS IN INFECTIOUS DISEASE EPIDEMIOLOGY (O’Meara)Week 1 Introduction and fundamentals of infectious disease epidemiology Lesson 1: Hosts and PathogensLesson 2: Measuring infectious disease burden Week 2 Ecology and dynamics of transmissionLesson 3: Basics of ecology and driving forces of epidemics Lesson 4:Modes of transmission, reservoirs, vectors, and contact networksWeek 3 Pathogen emergence, pathogen evolution, and vector-borne infectionsLesson 5:Epidemiology of vector borne and zoonotic infections: malaria and EbolaLesson 6:Emergence and evolution of pathogensWeek 4 Principles for disease-prevention interventionsLesson 7:Non-pharmaceutical interventions for infectious diseasesLesson 8: Vaccination – individual protection, herd immunity and eradicationMODULE II: DISEASE SURVEILLANCE & PREVENTION(Tillekeratne)Week 5: Introduction to infectious disease surveillanceLesson 9: Principles of surveillance: the example of SARSLesson 10: Conducting outbreak investigations: CDC case study of typhoidWeek 6: Challenges to infectious disease surveillance and novel solutionsLesson 11: Surveillance in resource-limited settingsLesson 12: Novel technologies for surveillance Week 7: Infectious disease prevention: focus on vector-borne diseasesLesson 13: Principles of infectious disease prevention: vaccination as an exampleLesson 14: The One Health model and environmental interventions for preventing vector-borne diseasesWeek 8: Infection prevention in the context of antimicrobial resistanceLesson 15: Epidemiology of antimicrobial resistance in the global settingLesson 16: Strategies for preventing antimicrobial resistance: antimicrobial stewardship and infection controlMODULE III: BEYOND THE “BIG 3”: FRONTIERS IN INFECTIOUS DISEASE EPIDEMIOLOGY (Taylor) Week 9 Beyond Tuberculosis: Pneumonia and other syndromesLesson 17: Epidemiology and burden of pneumonia and diarrheaLesson 18:Approaches to controlling pneumonia and diarrheaWeek 10Beyond HIV: Other sexually-transmitted infections and hepatitisLesson 19: HIV and other STIs: Measuring burden and targeting control measuresLesson 20:Viral Hepatitis: Approaches to control, from A to EWeek 11 Beyond malaria: Other parasites including the Neglected Tropical Diseases (NTDs)Lesson 21:Mass Treatment Campaigns for Disease Mitigation: Soil-Transmitted Helminths, Trachoma, and OthersLesson 22:NTD Elimination & Eradication: Programmatic PerspectivesWeek 12The modern epidemiology toolkit: Advances in infectious disease epidemiology Lesson 23:Molecular epidemiologyLesson 24: Digital epidemiologyExpectationsStatement on Disability: Any student with a documented disability that necessitates academic adjustments or accommodations is requested to speak with Dr. Taylor during the first two weeks of the class. All discussions will remain confidential. Students with disabilities will also need to contact the Student Disability Office. Communication:The course instructors will attempt to respond to questions or concerns communicated by email within 24 hours during the week (questions posed over the weekend will be addressed the next working day). Please be mindful of the time differences between North Carolina, Kenya and Sri Lanka.For emails, please include GH777 in the subject line. For complex issues that require more than a couple of sentences to explain, it’s probably best to simply and directly request a time to speak with the relevant instructor.Ethical Considerations and the Duke Community Standard: Students are expected to uphold the Duke Community Standard in all aspects of the course. This Standard is summarized thusly:Duke University is a community dedicated to scholarship, leadership, and service and to the principles of honesty, fairness, respect, and accountability. Citizens of this community commit to reflect upon and uphold these principles in all academic and non-academic endeavors, and to protect and promote a culture of integrity. To uphold the Duke Community Standard, students pledge: oI will not lie, cheat, or steal in my academic endeavorsoI will conduct myself honorably in all my endeavors; andoI will act if the Standard is compromised. Adherence to this Standard is essential not only as a student at Duke but also as a future global health professional.Plagiarism:Plagiarism, of any kind, is not acceptable. Plagiarism will result in an automatic failure and possibly additional disciplinary action. See Duke University guidelines for plagiarism: Attendance Policy:Attendance is mandatory. Professionalism:Students are expected to always act professionally and respectfully in all matters of classroom and course conduct. This includes adequate preparation for discussion sessions, and respectful communication with classmates, teaching assistant and instructors. In addition, during discussion sessions, students will need to silence pagers, cell phones and other devices. There is certainly a time to use these devices, but that time is plainly not during the once-weekly discussion session. Refusal to adhere to this request – as evidenced by writing or checking emails, attending to other work, unrelated web-browsing or dawdling on social media – will impact the Class Participation grade component of the course in a decidedly negative fashion.GradingThe final course grade will be calculated as follows:PercentGrade98-100 A+93-97.9A90-92.9A-88-89.9B+83-87.9B80-82.9B-78-79.9C+73-77.9C70-72.9C- ................
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