Molecular and Genomic Approaches: Bacterial Meningitis Diagnosis and Survelliance in Africa

Molecular and genomic techniques have revolutionised the routine identification and characterisation of bacterial meningitis. This has led to both opportunities and challenges from sample collection, to diagnosis, surveillance, data sharing, and public health policy. 

This week-long training course, led by a team from Centre Suisse de Recherches Scientifiques (CSRS) en Côte d’Ivoire in collaboration with the Meningitis Research Foundation (MRF) and the Global Meningitis Genomic Partnership (GMGP) is funded by Wellcome, with support from the Wellcome Sanger Institute. The course will examine the impact of molecular and genomic approaches using regionally relevant clinical scenarios.

Participants will be guided through an intensive programme delivered by field experts providing a clear and comprehensive overview of the meningitis genomic workflow, with hands-on sequencing and data and bioinformatic analysis. They will also be introduced to different bioinformatic tools for sequence analysis including a new PUBMLST platform (AMERT) designed for African reference laboratories to  store and analyse meningitis sequence data.

What will this course cover?

This course seeks to strengthen capacity by emphasising how techniques may be applied in regional settings and encouraging knowledge exchange through networking opportunities. 

It will cover sequencing and bioinformatic analysis of meningitis associated pathogens like Neisseria meningitidis; Haemophilus influenzae; GBS and Streptococcus pneumoniae

The programme will be delivered as a combination of lectures, interactive tutorials, and hands-on laboratory and computer practical sessions which cover approaches which are:

• currently applicable in clinical and diagnostic microbiology labs
• likely to be applicable and widely used in the foreseeable future, including whole genome sequencing (WGS) using portable devices and use of web-based platforms for surveillance
• of value to participants in interpreting and assessing the likely utility of these resources

The course content will be delivered in English with additional support for French speakers

Who should attend this course?

This course is open only to applicants based in Africa and priority will be given to those within the African Meningitis belt or those working within national meningitis surveillance.

Applicants should have demonstrable experience in a relevant field (microbiology, specifically bacteriology) and be clinical trainees or specialists in medical microbiology; . Clinically qualified applicants or those in positions to influence training, policy, and postdoctoral scientists; senior technicians; or research assistants with a Master’s degree implementation are especially encouraged to apply.

What will you achieve?

 After completing this course, you will be able to:

• Appreciate the utility of molecular techniques in clinical laboratory and bacteriological methods and their transferability to other applications.
• Apply relevant QC methods to ensure sample quality for downstream applications
• Generate sequence data using next generation sequencing.
• Analyse genomic data using publicly available software tools to identify causative organisms in an infection and to track an outbreak using WGS.

This course will start at approximately 8.00 on Monday 28 September 2026 and end at approximately 18:00 on Friday 2 October 2026.

 Teaching will be based on bacterial meningitis workflows and include:

• Fundamental molecular biology techniques including preparing, handling, and storing DNA.
• Sample quality control
• Generating genomic sequence data, sequence variation analysis, and its visualisation and interpretation
• Bioinformatic analysis of molecular and genomic data, particularly the exploitation of web-based tools and using R.

These techniques will be explored and employed during the course in the cross-cutting themes of pathogen detection and characterisation, including antimicrobial resistance, and the application of data in the improvement of interventions to reduce disease burden.

Training team

Kanny Diallo
Centre Suisse de Recherche Scientifique

Tiemele Laurent Simon Amoikon
Centre Suisse de Recherche Scientifique

Jolynne Mokaya
Wellcome Sanger Institute

Martin Maiden
University of Oxford

Keith Jolley
University of Oxford

Leonard Ndwiga 
University of Glasgow

Prerequisites:

Applicants are required to have demonstrable experience in a relevant field and ideally be working within national meningitis surveillance 

Bioinformatic training will include the use of Linux/UNIX command line. Although participants learn to use the command line during the course, familiarity with these resources is recommended. ‘Introduction to Linux for biologists’ pre-course module will be provided for completion prior to the course. 

Participants are required to bring a personal laptop suitable for bioinformatics analyses, with the following minimum specifications:

• 8–16 GB RAM (16 GB recommended)
• At least 100 GB of available disk space
• A recent operating system (Windows, macOS, or Linux), with the ability to run a Linux environment (e.g., via virtual machine or subsystem)
• Administrative rights to install required software

Please consult with your institution’s IT support team if you are selected and we will contact you with additional information if you are selected.

How to Apply

1. Start the application
   • Click on the “Apply” button above to start your application. Please note that places are limited and will be awarded based on merit.
2. Answer required questions
   • Please answer either “yes” or “no” to these questions.
3. Demonstrate the course’s relevance to your project/role
   • Our courses are highly subscribed, so it is essential to clearly show how the skills you will learn in the course will be directly applicable and beneficial to your current role/project and how do you plan to disseminate the knowledge after the course.
   • Preference will be given to applicants who are currently working on related projects or soon will be.
   • Add any other relevant information {delete if not necessary}
4. Letter of recommendation
   • Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g., supervisor, line manager, or head of department). Ensure that your sponsor provides a tailored supporting statement by the application deadline. This statement must be uploaded as a PDF document to the registration system within your application. Applications without a supporting statement will not be considered.
5. Need help?
   • If you encounter any problems with the online application process, please contact us at globaltraining@wellcomeconnectingscience.org for assistance.

Application deadline: 15 June 2026

Travel visas
Depending on your citizenship, you may require either a visa. Please check Abidjan Aeroport webpage: https://www.aeroport-abidjan.com/visa_on_arrival_ivory_coast.php

Confirmed attendees requiring a letter to support a visa application should contact us at: globaltraining@wellcomeconnectingscience.org.

The course is subsidised by Wellcome  and is free to attend for selected participants.

A limited number of bursaries are available for this course. These are awarded on merit for travel and accommodation. If you would like to apply for a bursary, please complete the bursary section of the online application form.

Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. The decision of the selection committee is final.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.