About
This workshop aims to provide participants with a comprehensive understanding of bacterial classification and nomenclature approaches used in genomic surveillance. Participants will gain insight into MLST, cgMLST, SNP-based taxonomies, LIN codes, and k-mer-based clustering. The training will focus on how these systems are applied in public health microbiology to classify bacterial pathogens, track outbreaks, and support global surveillance efforts. Participants will also gain practical experience with tools such as BIGSdb, EnteroBase, MyKrobe, and PopPUNK, enabling them to apply bacterial taxonomy tools in genomic surveillance work.
Dates and duration
This webinar takes place over two sessions:
- Session 1 : Foundations of Genomic Nomenclature – October 22, from 9h to 12h
- Session 2 : Applications of Genomic Nomenclature in Surveillance – October 23, from 9h to 12h
Objectives
By the end of the webinar, participants will be able to:
- Explain the principles and differences between MLST, cgMLST, SNP-based taxonomies, LIN codes, and k-mer-based approaches
- Apply genomic nomenclature systems to classify bacterial isolates at various taxonomic levels (species, lineage, down to outbreak strains).
- Use tools such as BIGSdb, GrapeTree, EnteroBase, chewBBACA, ReporTree, and PopPUNK
- Design or adapt cgMLST schemes using chewBBACA for pathogens lacking standardized schemes.
- Understand the role of hierarchical clustering and phylogenetic trees.
- Evaluate the strengths and limitations of different taxonomic and typing approaches in the context of public health microbiology.
Trainers
- Pr Sylvain Brisse, Institut Pasteur, Paris, France
- Dr Keith Jolley, Oxford University, Oxford, UK
- Dr Nigel Dyer, Warwick University, Coventry, UK
- Dr Danielle Ingle, Doherty Institute, Melbourne, Australia
- Pr Mario Ramirez, University of Lisbon, Lisbon, Portugal
- Rafael Mestre Mamede, University of Lisbon, Lisbon, Portugal
- Dr John Lees, Cambridge University, Cambridge, UK
- Dr Veronica Mixao, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
Registration
To access the virtual training sessions, you can register for free on the ECDC Learning Portal. This will also allow you to have access to other webinars organized in this programme.
The webinar “Bacterial strain Taxonomy for Genomic Surveillance” is available here:
GenEpi-BioTrain Programme
This interdisciplinary programme, funded by ECDC, combines lectures and practical sessions delivered by multiple host institutions in order to enhance surveillance, preparedness, and readiness to respond to outbreaks.