Bacterial Strain Taxonomy for Genomic Surveillance
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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.
Why attend this training?
This training will provide participants an 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 enabling them to apply bacterial taxonomy in genomic surveillance work.
Who is the training for?
This training is designed primarily for bioinformaticians. Public health microbiologists and epidemiologists might find it useful as well. After participating in this course, 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).
- 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.
How long is the training?
Two live sessions will take place on two consecutive days Wednesday and Thursday, 22-23 October, both from 09:00 to 12:00 (CEST).
- Session 1: Foundations of Genomic Nomenclature
- Session 2: Applications of Genomic Nomenclature in Surveillance
Will the training be recorded?
Yes, when you enrol in the training, you will also get access to the recordings after the live sessions.
Can I get a certificate?
To get a certificate of participation, you need to attend at least one live session and watch the recording of the other session you were not able to attend.
What are the software requirements?
There is no software requirement to follow this course. However, to take the most out of it, check the course page for information on how to install/access the software used (BIGSdb-Pasteur; PubMLST; LIN codes; PathogenWatch; Enterobase; ChewBBACA; Chewie-NS; Mykrobe; ReporTree; FigTree and PopPUNK).
How can I enroll?
You can access the webinar for free, thanks to EU funding. Log in to the Learning Portal and enrol in the course.