GenEpi-BioTrain - Virtual training 19 - Genomic Tools in Outbreak Investigations - Case Study Cholera Outbreak This two-half-day training explores the use of genomic tools in outbreak investigations, using the 2010 Haitian cholera outbreak as a case study (DOI: 10.1128/mBio.00157-11).
Through guided analysis of molecular and genomic data, participants will compare traditional typing methods (e.g., Pulsed-field gel electrophoresis-PFGE) with modern approaches like Whole-Genome Sequencing-Based Typing (WGST), and develop skills in interpreting phylogenetic relationships, antimicrobial resistance (AMR), and virulence profiles, and genomic epidemiology in a real-world context. The course includes a simulation exercise to reinforce practical understanding.
Dates: 27 August and 3 September 2025.
Duration: Two half-days 09:00-12:30 CEST.
Location: Online - Find the link after enrolment.
Audience: Audience: Bioinformaticians, Microbiologists, Epidemiologists, and Clinicians with basic Bioinformatics skills.
The practical exercise in this webinar has several prerequisites and requires software installation. Please follow the 'Prerequisites' and 'Software Requirements' sections carefully.
Objectives
Upon completion of this workshop, participants will be able to:
- Describe the epidemiological context of the 2010 Haitian cholera outbreak.
- Explain the differences in resolution and applicability between PFGE and WGST.
- Use simple bioinformatics tools to infer phylogenies from genomic data.
- Analyze and interpret Single Nucleotide Polymorphism (SNP) matrices and maximum parsimony trees.
- Correlate antimicrobial resistance, and virulence profiles with epidemiological data.
- Assess evidence to infer outbreak sources using genomic data.
- Communicate findings from genomic investigations in a structured report.
- Critically evaluate the role of genomics in global health surveillance.
Participation: This course is open for public enrolment.