Molecular and Genomic Approaches to Clinical Microbiology in Africa

Molecular and genomic techniques are revolutionising the routine identification and characterisation of pathogens, opening new opportunities and challenges in all areas of clinical microbiology from clinical diagnostics to fundamental research. This course will examine the impact of these approaches using region-specific clinical scenarios. 

The week-long training course will be held at, and in collaboration, with the MRC Unit in The Gambia and feature an intensive programme delivered by field experts providing clinical microbiologists and laboratory scientists with a concise yet comprehensive overview of the latest research and best practice in this essential area.

What will this course cover?

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

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 in the foreseeable future, including whole genome sequencing (WGS) using portable devices
• of value to participants in interpreting the literature and assessing the likely utility of new technologies as they are developed

The course content will be delivered in English.

Who should attend this course?

This course is open only to applicants based in Africa.

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

What will you achieve?

 After completing this course, you will be able to:

• Assess the strengths, weaknesses and limitations of different methodologies and approaches in clinical microbiology.
• Appreciate the utility of molecular techniques in clinical laboratory and bacteriological methods and their transferability to other applications.
• Apply a range of genomic methods including real-time PCR and conventional sequencing.
• Create sequence data using next generation single molecule 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 09.00 on Saturday 13 September 2025 and end at approximately 15:00 on Friday 19 September 2025.

Teaching will be based around three themes, chosen to represent three of the most pressing clinical imperatives in clinical bacteriology throughout the continent:

• Mycobacterium tuberculosis
• Enteric bacteria and antimicrobial resistance
• Encapsulated bacteria and vaccination

For each of these themes the following approaches will be covered:

• Fundamental molecular biology techniques including preparing, handling, and storing DNA.
• PCR, including real-time PCR, with an emphasis on methods, applications and data interpretation.
• 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.
• An overview of future technologies, and their potential for application in clinical microbiology.

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

Training team

Kanny Diallo
Centre Suisse de Recherche Scientifique

Brenda Kwambana-Adams
Liverpool School of Tropical Medicine and the Malawi-Liverpool-Wellcome Clinical Research Programme

Martin Maiden
University of Oxford

Elizabeth Streicher
University of Stellenbosch

Dam Khan
London School of Hygiene and Tropical Medicine

Keith Jolley
University of Oxford

Leonard Ndwiga 
University of Glasgow

Anzaan Diepenaar 
University of Antwerp

Connecting Science team

Alice Matimba
Head of Training and Global Capacity

Cassandra Claire Soo
Laboratory Courses Manager

Martin Aslett
Informatics ManagerMartin 

Isabela Malta
Assistant Overseas Courses Manager

Karon Chappell
Event Organiser

Aaron Dean
Laboratory Technical Officer

Vaishnavi Vikas Gangadhar 
Informatics Technical Officer

Prerequisites:

Applicants are required to have demonstrable experience in a relevant field, e.g. microbiology and be based in Africa.

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. 

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. 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}
3. 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.
4. Need help?
   • If you encounter any problems with the online application process, please contact us at globaltraining@wellcomeconnectingscience.org for assistance.

Application deadline: 6 May 2025

Travel visas
Depending on your citizenship, you may require either a visa, clearance, or both a visa and clearance. Please check The Gambia Tourism Board website for visitor information: https://visitthegambia.com/?page_id=4935

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

This course is subsidised by Wellcome Connecting Science, and is free to attend.

Bursaries
A number of bursaries are available for each course. These are awarded on merit to cover travel, accommodation and sustenance.

Bursaries may be applied for as part of the course 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.

Testimonials from the 2024 course

‘The training offered me an opportunity to meet people in the field of research similar to my interest. My expectations were mainly on Bioinformatics but this training delved deep into molecular approaches such as comparing platforms to allow for an informed decision on which platforms to use based on the research question. The trainer to participant ratio is very good that it allow as one on one interaction.’

‘Bioinformatics was awesome! Never knew it could help my research this way! R platform has taught me alot. My current research work will definitely be analysed using R With WGS, My patient management skills will be improved The problems of Antimicrobial resistance in Nigeria and the globe will get to near eradication is not complete eradication if the principles of WGS, Bioinformatics and other applications are known by health workers’