GenEpi-BioTrain - Virtual training 20 - Klebsiella pneumoniae genomic epidemiology and antimicrobial resistance

Topic outline

• Klebsiella pneumoniae genomic epidemiology and antimicrobial resistance (GenEpi-BioTrain — Virtual Training 20)

  Klebsiella pneumoniae genomic epidemiology and antimicrobial resistance (GenEpi-BioTrain — Virtual Training 20)

  ℹ️ Please Note

  You are welcome to explore the available resources and video recordings. Please note that the resources in this course come from the Virtual Training 20 held in August–September 2025, and certificates are only issued to participants who attended the live webinar sessions.

  Welcome to the virtual training on Klebsiella pneumoniae genomic epidemiology and antimicrobial resistance!

  Course description

  The aim of this virtual training workshop is to provide participants with an in-depth understanding of the population biology, genomics, capsular diversity and antimicrobial resistance of Klebsiella pneumoniae, and how their study informs public health action against this prominent ESKAPE pathogen, including vaccine-based strategies. The virtual training will also introduce the use of Life Identification Number (LIN) codes for strain-level classification, studies in the One Health context, and highlight international initiatives such as KlebNet.

  Target audience

  Public health microbiologists, epidemiologists, or bioinformaticians interested in learning about K. pneumoniae genomic epidemiology and antimicrobial resistance.

  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 on Tuesday, September 9, and Thursday, September 11, from 9:00 AM to 12:00 PM (CEST).

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  Aim and Objectives

  Aim and Objectives

  The aim of this virtual training workshop is to provide participants with an in-depth understanding of the population biology, genomics, capsular diversity and antimicrobial resistance of Klebsiella pneumoniae, and how their study informs public health action against this prominent ESKAPE pathogen, including vaccine-based strategies. The virtual training will also introduce the use of LIN codes for strain-level classification, studies in the One Health context, and highlight international initiatives such as KlebNet.

  Upon completing this workshop, participants will be able to:

  • Understand strain diversity and main resistance mechanisms in K. pneumoniae.

  • Understand capsular diversity, its links with virulence factors, and vaccine implications.

  • Use LIN codes for precise strain-level classification.

  • Analyze genomic data for AMR determinants and outbreak investigations.

  • Be aware of current global surveillance collaborative initiatives and how to contribute.
• Software Requirements

  Software Requirements

  For the practical exercises, you will need to access the websites below:

  • BIGSdb-Pasteur: https://bigsdb.pasteur.fr/klebsiella/

    You need to register on BIGSdb-Pasteur AND on the Klebsiella database by following these instructions: https://bigsdb.pasteur.fr/register/

  • Kleborate is available on the PathogenWatch platform: https://pathogen.watch/  

    You need to register on the platform to be able to upload datasets: https://pathogen.watch/sign-in?redirect=/upload 

    The Kleborate v3 software will also be presented. If you're interested in its use and comfortable with Python command-line interfaces, please refer to the 'Go further' section below.

  • Kaptive has a web version of the software available here.  Additionally, Kaptive is also available on the PathogenWatch platform: https://pathogen.watch/ 

    
    

    The Kaptive 3 software will also be presented. If you're interested in its use and comfortable with Python command-line interfaces, please refer to the 'Go further' section below. 

  • ___________________________________________________________________________________________

  • Go further

    • Kleborate v3 (how to install? click here)

    We also recommend consulting the Kleborate tutorial: click here to watch the video and here to read the documentation. 

    • Kaptive 3 (how to install? click here)

    We also recommend consulting the Kaptive tutorial: click here to watch the video and here to read the documentation. 

• Delivery

  Delivery
  Format

  This virtual training takes place over two sessions that will be held on Tuesday, September 9 and Thursday, September 11 from 9:00 to 12:00 (CET).

  
  

  Outline

  Session 1: Genomics, Diversity, Resistance Elements, and Tools

  Part 1: Introduction to Klebsiella pneumoniae

  Part 2: Strain Taxonomy using LIN codes (practical exercise with BIGSdb-Pasteur)

  Part 3: Capsule (K) and outer-lipopolysaccharide (O) genetics and typing with Kaptive (practical exercise with Kaptive)

  Part 4: Klebsiella pneumoniae genome analysis with Kleborate (practical exercise with Kleborate)

  
  

  Session 2: Epidemiology, Vaccines, and Global Surveillance

  Part 1: Convergence of virulence and antimicrobial resistance

  Part 2: Seroepidemiology of Klebsiella

  Part 3: One Health genomic surveillance of K. pneumoniae

  Part 4: EURGen-Net CRE surveillance: focus on K. pneumoniae
• Session 1: Genomics, Diversity, Resistance Elements, and Tools

  Session 1: Genomics, Diversity, Resistance Elements, and Tools
  • FileAGENDA

    
    

  • Recording

  • Session opening

  • Part 1: Introduction to Klebsiella pneumoniae

  • FileIntroduction to Klebsiella pneumoniae
  • Part 2: Strain Taxonomy using LIN codes (practical exercise with BIGSdb-Pasteur)

  • FileStrain taxonomy using LIN codes
  • Part 3: Capsule (K) and outer-lipopolysaccharide (O) genetics and typing with Kaptive (practical exercise with Kaptive)

  • FileCapsule (K) and outer-lipopolysaccharide (O) genetics and typing with Kaptive (practical exercise with Kaptive)
  • Part 4: Klebsiella pneumoniae genome analysis with Kleborate (practical exercise with Kleborate)

  • FileKlebsiella pneumoniae genome analysis with Kleborate (practical exercise with Kleborate)
• Live Session 1

  Live Session 1
  Not available unless: You belong to learner enrolled in the live sessions
• Session 2: Epidemiology, Vaccines, and Global Surveillance

  Session 2: Epidemiology, Vaccines, and Global Surveillance
  • FileAGENDA

    
    

  • Recording

  • Opening

  • Part 1: Convergence of virulence and antimicrobial resistance

  • FileConvergence of virulence and antimicrobial resistance
  • Part 2: Seroepidemiology of Klebsiella

  • FileSeroepidemiology of Klebsiella
  • Part 3: One Health genomic surveillance of K. pneumoniae

  • FileOne Health genomic surveillance of K. pneumoniae
  • Part 4: EURGen-Net CRE surveillance: focus on K. pneumoniae

  • FileEURGen-Net CRE surveillance: focus on K. pneumoniae
• 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.