GenEpi-BioTrain - Virtual training 12 - Focus on the Agents of Whooping Cough

Topic outline

• Focus on the agents of Whooping cough (GenEpi-BioTrain — Virtual Training 12)

  Focus on the agents of Whooping cough (GenEpi-BioTrain — Virtual Training 12)

  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 12 held in November 2024, and certificates are only issued to participants who attended the live webinar sessions.

  Welcome to this virtual training space on EVA.

  Below you will see the two online sessions and their support materials.

  In anticipation for the live sessions, we encourage participants to:

  1. Explore the materials available; 

  2. Install the software indicated below;

  3. Suggest topics of interest for future virtual trainings.

  • ForumAnnouncements
  • PagePresenters' biography
  • PageVirtual training organisation credits
  • PageLegal terms and conditions
• Aim and Objectives

  Aim and Objectives

  The aim of this virtual training is to provide participants with an in-depth understanding of whooping cough (pertussis) epidemiology, surveillance, and vaccination strategies. Participants will learn how genomic tools are used for surveillance, examine the epidemiology of recent outbreaks, and explore the public health impacts of vaccination, particularly in the context of pregnancy and early infancy. Additionally, practical sessions will provide hands-on experience in the rapid genotyping of Bordetella pertussis.

  Upon completion of this training, participants will be able to:

  • Understand the global and European epidemiology of whooping cough and the structure of surveillance systems.

  • Describe the genomic evolution of Bordetella pertussis and Bordetella parapertussis under vaccine pressure.

  • Recognize the spatial dynamics of Bordetella pertussis and its fitness changes induced by vaccines.

  • Use genomic tools, including BIGSdb and GrapeTree, for rapid genotyping of B. pertussis to analyze vaccine antigens, antibiotic resistance, and genomic comparisons.

  • Analyze the public health impact of vaccination, particularly maternal vaccination strategies to prevent infant pertussis.
• Delivery

  Delivery

  Format

  This virtual training takes place over two sessions that will be held on the morning of Monday 4th November, from 9:00 to 12:30 (GMT+1) and the morning of Tuesday 5th November from 9:00 to 12:00 (GMT+1).

  
  

  Outline

  Session 1: Whooping Cough Epidemiology and Surveillance
  

  Part 1: Whooping Cough Epidemiology and Surveillance

  Part 2: EU Perspective on Whooping Cough Surveillance

  Part 3: Genomic Evolution of Whooping Cough Pathogens under Vaccine Pressure

  Part 4: Practical Session: Rapid Genotyping of B. pertussis using BIGSdb

  Session 2: Vaccination and Public Health Impact
  

  Part 1: Practical Session: Rapid Genotyping of B. pertussis using BIGSdb (continuation)

  Part 2: Global Spatial Dynamics and Vaccine-Induced Fitness Changes in B. pertussis

  Part 3: Vaccination during Pregnancy to Prevent Early Infant Pertussis 

  
  

  
  

  • PageClick here for a detailed agenda
• Software requirements

  Software requirements

  The following online tools will be used during practical sessions:

  • BIGSdb: https://bigsdb.pasteur.fr/bordetella/
  • GrapeTree: https://github.com/achtman-lab/GrapeTree 

  You need to register on BIGSdb and on the Bordetella database, by following these instructions: https://bigsdb.pasteur.fr/register/
  
• Session 1: Whooping Cough Epidemiology and Surveillance (4 November)

  Session 1: Whooping Cough Epidemiology and Surveillance (4 November)

  1. Whooping Cough Epidemiology and Surveillance (40min) — Sylvain Brisse (Institut Pasteur)

  • Overview of whooping cough epidemiology in the country and across the EU.

  • Discussion of the structure of surveillance systems, including the role of a reference lab (example: NRC for Whooping Cough, Institut Pasteur).

  • Case study: Recent 2024 outbreak.

  
  

  2. EU Perspective on Whooping Cough Surveillance (30min) — Maria Keramarou (ECDC)

  • Examination of the EU's approach to whooping cough surveillance, data collection, and response to outbreaks.

  
  

  3. Genomic Evolution of Whooping Cough Pathogens under Vaccine Pressure (40min) — Valérie Bouchez (Institut Pasteur)

  • Analysis of the genomic evolution of Bordetella pertussis and Bordetella parapertussis in response to vaccine use.

  
  

  4. Practical Session: Rapid Genotyping of B. pertussis Using BIGSdb (30min) — Valérie Bouchez and Martin Rethoret-Pasty (Institut Pasteur)

  • Hands-on session on genotyping B. pertussis, focusing on vaccine antigens, 23S rRNA, and macrolide resistance.

  • Tools used: GrapeTree, BIGSdb.

  • Lectures

  • FolderPresentations
  • URLProtocol_Real-time PCR amplification and genotyping of the 23s rRNA from Bordetella pertussis using the LightCycler 480
  • Practicals

  • FileRapid Genotyping of B. pertussis Using BIGSdb
  • FilePractical exercises to do before Session 2

    Here you can find the practical exercises that should be completed before Session 2. Answers will be given at the beginning of Session 2.

    If you need help, you can refer to the presentation titled 'Rapid Genotyping of B. pertussis Using BIGSdb,' which is available above.

• Session 2: Vaccination and Public Health Impact (5 November)

  Session 2: Vaccination and Public Health Impact (5 November)

  1. Practical Session: Rapid Genotyping of B. pertussis Using BIGSdb (Continuation) (50min) — Valérie Bouchez and Martin Rethoret-Pasty 

  • Correction of the hands-on practice.

  
  

  2. Global Spatial Dynamics and Vaccine-Induced Fitness Changes in B. pertussis (50min) —  Noémie Lefrancq (ETH Zürich)

  • Exploration of the global spatial dynamics of B. pertussis and how vaccine-induced changes affect pathogen fitness.

  
  

  3. Vaccination During Pregnancy to Prevent Early Infant Pertussis (50min) — Helen Campbell (UKHSA)

  
  

  • Exploration of the role of maternal vaccination in reducing the risk of pertussis in newborns and infants.

  • Lectures

  • FolderPresentations
  • Practical

  • FilePractical exercise - Correction
• 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.