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Molecular Epidemiology of Infectious Diseases

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NOVA PhD course of 3 ECTS, organised by Professor Päivi Rajala-Schultz, University of Helsinki - Faculty of Veterinary Medicine.
Course dates and location: 28 Aug. -1 Sept. 2017 in Finland.

Course Description
The exponential growth of advanced molecular methods and the use of next generation sequencing (NGS) have revolutionized our understanding of the epidemiology of infectious diseases. However, the complexity of data-generation and analysis with advanced molecular methods sometimes obscures the importance of the underlying epidemiological investigation. This course will introduce molecular methods and NGS as applied to infectious agents for the sake of epidemiological investigation. Human and veterinary pathogens will be discussed, including bacteria, parasites and viruses, with emphasis on zoonotic bacteria.

Programme Outline
Draft schedule (course times ca. 9:00 to 16:30 hrs)

  • Day 1 – Introduction
    • AM – lectures
      • What is molecular epidemiology?
      • Basic principles of genetic diversity
      • Basic principles of molecular typing
    • PM - exercise
      • Databases for molecular data
  • Day 2 – Clockspeed, Trees and Networks
    • AM – lectures
      • Molecular clockspeed and spatio-temporal scale
      • Principles of phylogenetics
      • Trees vs. Networks – Dealing with recombination
    • PM – exercise
      • Phylogenetic analysis

  • Day 3 – Genomic Epidemiology
    • AM – lectures
      • Introduction to genomic epidemiology
      • From sample to sequence
      • Analysing sequence data
    • PM – exercise or journal club
      • Sequence data analysis (exercise)
      • Molecular epidemiology of anthrax (journal club)
  • Day 4 – Applications of Molecular Epidemiology
    • AM - Lectures
      • Surveillance
      • Outbreak investigations
      • Heterogeneity problem
    • PM – Preparation time for participant presentations

  • Day 5 – Miscellaneous Topics
    • AM – Selected topics
      • Molecular epidemiology of antimicrobial resistance
      • Host adaptation of pathogens
      • Molecular epidemiology of protozoa and macroparasites
    • PM – Participant presentations

Pre-/Post-Campus Assignments
Course participants will be assigned pre-course readings and they are expected to successfully complete a quiz related to the material prior to the start of the course.

Learning Outcomes
At the end of this course, participants will

  • Understand the molecular basis of comparative and universal strain typing methods
  • Understand how molecular clock speed relates to the spatio-temporal scale of epidemiological investigations
  • Be able to construct and interpret simple phylogenetic trees from genomic data
  • Appreciate the value and limitations of molecular methods in demonstration of causal associations and direction of pathogen transmission
  • Be familiar with epidemiological applications of molecular methods, including use in outbreak investigation, pathogenesis and vaccine studies, risk factor identification, and mathematical modelling
  • Be aware of pitfalls and limitations of public databases
  • Understand benefits and limitations of next generation sequencing

Evaluation Elements
Pass/fail evaluation will be based on: (i) satisfactory completion of a quiz in advance of campus course based on pre-assigned readings; (ii) active participation during the campus course (iii) completion of participant’s own presentation on the last day of the course.

Pedagogical Approach
Theoretical and practical aspects of molecular methods will be covered in a mixture of lectures, exercises and journal discussions, with a focus on the underlying epidemiological processes, study design or interpretation. Applicants will be asked to prepare a short presentation on a proposed or ongoing molecular epidemiology investigation.

Estimated Workload

  • 5 hours seminar / discussions
  • 15 hours lecture (every morning)
  • 15 hours other (exercises/computer practicals)
  • 15 hours independent work during the course
  • 40 hours independent work, pre-course readings and assignments

Prerequisite Knowledge
Basic knowledge of epidemiology

Admission
Admission for NOVA courses is handled by the course organiser/ the NOVA member institution organising the course. Please see the links in the margin for more information.

Published 19. December 2016 - 10:59 - Updated 7. February 2017 - 13:22

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