GenEpi-BioTrain - Virtual training 21 - Bacterial Strain Taxonomy for Genomic Surveillance

Topic outline

• Welcome to the virtual training on Bacterial strain Taxonomy for Genomic Surveillance!

  Welcome to the virtual training on Bacterial strain Taxonomy for Genomic Surveillance!

  Course description

  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..

  Target audience

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

  Pre-requisites

  For the practical exercises, participants may choose to use web-based (basic) tools or command-line (advanced) tools depending on their comfort and experience. Please see ‘Software requirements’ section below for more information.

  Format

  This virtual training consists of two half-day sessions held in the morning periods on Wednesday, October 22, and Thursday, October 23, from 09:00 to 12:00 (CEST).

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  Aim and Objectives

  Aim and Objectives

  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.

  Upon completing 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).
  • 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.
• Summary of tools and software employed during the training

  Summary of tools and software employed during the training
  While there are no strict requirements to be familiar with all the tools used in this training, having a working knowledge of the following tools will greatly enhance your learning experience and participation:

  
  

  • BIGSdb-Pasteur
  • PubMLST
  • LIN codes
  • PathogenWatch
  • Enterobase
  • ChewBBACA
  • Chewie-NS
  • Mykrobe
  • ReporTree
  • FigTree
  • PopPUNK
• Delivery

  Delivery
  Format

  This virtual training takes place over two sessions that will be held on Wednesday, October 22 and Thursday, October 23 from 9:00 to 12:00 (CET).

  
  

  Outline

  Session 1: Foundations of Genomic Nomenclature

  Part 1: Introduction to Genomic Taxonomy and Nomenclature

  Part 2: MLST and cgMLST: Concepts and Applications

  Part 3: Enterobase and hierarchical clustering

  Part 4: Phylogenetic taxonomies based on whole-genome SNPs (practical)

  
  

  Session 2: Applications of Genomic Nomenclature in Surveillance

  Part 1: ChewBBACA and creation of cgMLST schemes (practical)

  Part 2: ReporTree: Clustering and Visualization for Surveillance (practical)

  Part 3: Kmer-based approach: the example of PopPunk (practical)
• Session 1: Foundations of Genomic Nomenclature

  Session 1: Foundations of Genomic Nomenclature
  • FileAGENDA

    
    

  • Recording

  • Session opening

     

      

  • Part 1: Introduction to Genomic Taxonomy and Nomenclature

  • FileIntroduction to Genomic Taxonomy and Nomenclature
  • Part 2: MLST and cgMLST: Concepts and Applications

  • FileMLST and cgMLST- Concepts and Applications
  • Part 3: Enterobase and hierarchical clustering

  • FileEnterobase and hierarchical clustering
  • Part 4 Phylogenetic taxonomies based on whole-genome SNPs

  • FilePhylogenetic taxonomies based on whole-genome SNPs
  • You completed session 1

    If you see this message, it means that you have either attended session 1 live or watched the recording of session 1. This is pre-requisite to access the certificate

    
    

    Not available unless any of:

    • The activity Online session 1 — Virtual training 21 is marked complete
    • All of:
      • The activity SESSION OPENING  https://learning.ecdc.europa.... is marked complete
      • The activity PART 1: INTRODUCTION TO GENOMIC TAXONOMY AND ... is marked complete
      • The activity PART 2: MLST AND CGMLST: CONCEPTS AND ... is marked complete
      • The activity PART 3: ENTEROBASE AND HIERARCHICAL ... is marked complete
      • The activity PART 4 PHYLOGENETIC TAXONOMIES BASED ON ... is marked complete
• Session 2: Applications of Genomic Nomenclature in Surveillance

  Session 2: Applications of Genomic Nomenclature in Surveillance
  • FileAGENDA

    
    

  • Datasets

  • FileDatasets for ReporTree exercise

    Please download this file containing datasets for ReporTree. Due to the large volume, we recommend downloading them in advance so they’re ready for the exercise.

  • Recording

  • Opening  

    
    

  • Part 1.a: ChewBBACA and creation of cgMLST schemes (presentation)

    
    

  • Part 1.b: ChewBBACA and creation of cgMLST schemes (demo)  

    
    

  • FolderChewBBACA and creation of cgMLST schemes
  • Part 2: Kmer-based approach: the example of PopPunk 

    
    

  • FileKmer-based approach: the example of PopPunk
  • Part 3: ReporTree: Clustering and Visualization for Surveillance 

    
    

  • FileReporTree: Clustering and Visualization for Surveillance
  • You completed session 2

    If you see this message, it means that you have either attended session 2 live or watched the recording of session 2. This is pre-requisite to access the certificate.

    Not available unless any of:

    • The activity Online session 2 — Virtual training 21 is marked complete
    • All of:
      • The activity PART 1.A: CHEWBBACA AND CREATION OF CGMLST ... is marked complete
      • The activity PART 1.B: CHEWBBACA AND CREATION OF CGMLST ... is marked complete
      • The activity PART 2: KMER-BASED APPROACH: THE EXAMPLE OF ... is marked complete
      • The activity PART 3:REPORTREE: CLUSTERING AND VISUALIZATION ... is marked complete
• Evaluation and Certificates

  Evaluation and Certificates
  • The certificate of completion is now available to participants who attended both sessions.

    In case you missed one, you can watch the recording of the session you missed. 

    
    

• Contacts

  Contacts

  For any questions regarding the this webinar series, please use the discussion forum.

  If you have questions regarding other training initiatives please contact: courses@ecdc.europa.eu.

  If you have technical issues please contact ECDC Helpdesk - ICT Front Office ICT.FrontOffice@ecdc.europa.eu.