The aim of this virtual training workshop is 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: 22 and 23 october 2025. 

 Duration: Two half-days 09:00-12:00 CEST. 

Location: Online - Find the link after enrolment. 

Audience: Public health microbiologists, epidemiologists, or bioinformaticians interested in learning about Bacterial strain Taxonomy for Genomic Surveillance.

Objectives:  

Upon completion of this workshop, 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.

Participation: This course is open for public enrolment.