Introduction to Molecular Epidemiology of Infectious Diseases in Animal Populations

This course is intended for researchers and professionals who are working with, or planning to work with, genomic data of infectious agents to explore epidemiological questions. As sequencing technology becomes more accessible and affordable, and research funders and publishers increasingly use open access data sharing models, there is a cornucopia of sequence data available, covering an ever-growing number of infectious agents and animal hosts. In parallel, a plethora of sequence data analysis tools and techniques has been developed. This course will introduce you to epidemiological and bioinformatic aspects of the use of pathogen genomic data to inform our understanding of disease transmission and control. It aims to equip participants with the ability to pair epidemiological questions with relevant data and tools, to undertake basic bioinformatic analysis of small datasets, and to read relevant literature with greater understanding and confidence.

Learning outcomes

Course participants will have increased abilities to

1. To understand the relevance of epidemiological data and the importance of model assumptions in the analysis and interpretation of genomic data from infectious agents of animals, with two case studies on a bacterial and a viral infectious disease in animal populations;
2. To acquire, assemble and align sequence data and select evolutionary models in preparation for the construction of trees or networks representing populations of infectious agents;
3. To construct and visualize phylogenetic trees or networks, including the use and visualisation of relevant metadata or features of specific interest such as virulence genes or antimicrobial resistance genes;
4. To evaluate the possibilities and limitations of the use of genomic data in understanding transmission events in infectious diseases;
5. To interpret literature on the topic and to identify approaches and software packages suitable for further analysis of epidemiological questions using pathogen genome sequences.

General Information

Target Group	Postgraduate students, WUR staff and non-WUR participants
Course level	In-depth, postgraduate
Group size	A minimum of 10 and a maximum of 20 participants
Course duration	3 days given once
Prior knowledge	Undergraduate degree in microbiology, epidemiology, genetics, bioinformatics or related field
Homework/self-study	Pre-course requirements include reading of key publications provided by course coordinators.   Participants are expected to use their own computer or work with a buddy on their computer.
Language	English
Credit points	1 ECTS (Note: 1 ECTS is equal to 28 hours of study)
Name lecturer(s)	Chiara Crestani (Institut Pasteur), Don Klinkenberg (IDE, WUR), Ynte Schukken (IDE, WUR), Ruth Zadoks (University of Sydney)
Teaching method	Lectures, computer practicals, discussions
Venue	Wageningen University campus, Wageningen, the Netherlands. Note: Room and building will be communicated to registered and confirmed participants about one week before the start of the course

 

Programme

Day 1

Morning – Introduction to epidemiological and molecular aspects of molecular epidemiology

Afternoon – Retrieving, trimming, assembling and annotating sequence data

Day 2

Morning – alignment, models of evolution, recombination

Afternoon – phylogeny construction and visualisation

Day 3

Morning – identifying and visualising features of interest (GWAS, AMR, virulence genes)

Afternoon – introduction to advanced topics (ancestral state reconstruction, phylodynamics)

Fee

WGS PhDs with TSP	€ 250
Other PhDs, WUR postdocs and WUR academic staff	€ 500
All others	€ 750

 

Cancellation condition

Participants can cancel their registration free of charge 1 month before the course starts. A cancellation fee of 100% applies if a participant cancels his/her registration less than 1 month prior to the start of the course.

The organisers have the right to cancel the course no later than one month before the planned course start date in the case that the number of registrations does not reach the minimum.

 

Information

For more information please contact: Ruth Zadoks (ruth.zadoks@wur.nl)