Antimicrobial Resistance of Bacterial Pathogens - Africa 

Antimicrobial resistance (AMR) is a global public health emergency and threatens the safe delivery of modern medical care. A recent study estimated that there were 4.95 million deaths associated with AMR bacterial infections in 2019. Global projections of the negative impact of AMR predict the loss of nearly 10 million lives per year, and a cumulative loss of global production up to 100 trillion US dollars by 2050. AMR requires immediate, concerted, international, collaborative action to monitor its prevalence and spread throughout the world. 

The importance of this has been recognised both by the United Nations, and by the World Health Organisation; the latter has published a list of priority pathogens and a global strategy for AMR surveillance.

In collaboration with the National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Services, Johannesburg, South Africa, we are pleased to announce our 2026 global training course in AMR of bacterial pathogens in Africa. This course aims to address regionally specific AMR-associated challenges through knowledge transfer and skills development by global experts.  

What will this course cover?

This week-long course will include an introduction to AMR with hands-on laboratory practicals for AMR detection through molecular and phenotypic testing accompanied by theoretical training on the evolution and spread of AMR and utilisation of whole-genome sequencing and bioinformatics analysis methods for AMR surveillance and control. 

It will also provide an opportunity for participants to network and potentially build a regional AMR community to support long-term partnerships and collaborations.

Who is this course for?

This course is open to applicants based in Africa only, who are actively engaged in, or soon to commence related research or work. This may include diagnostic stewardship, antimicrobial stewardship, infection prevention and control, or generate policies related to AMR in bacteria. Applicants should be PhD students, clinical trainees, or specialists in medical microbiology or bioinformatics, postdoctoral scientists, senior technicians, or research assistants with a Master’s degree.

What will you achieve?

 After completing this course, you will be able to:

• Carry out standard laboratory methods for antimicrobial susceptibility testing (e.g. disc diffusion testing and MIC determination)
• Describe the principles and practice of quality assurance and control in AMR surveillance techniques, antimicrobial susceptibility testing and reporting.
• Discuss the range of control strategies for AMR in human and veterinary medicine (e.g. antimicrobial stewardship, infection control and policies).
• Use appropriate software tools to analyse WGS data for assembly of bacterial genomes, detect resistant variants and conduct phylogenetic analysis.
• Analyse and interpret genomics data for AMR surveillance.

The course will consist of a series of lectures and hands-on laboratory and computational practicals. Participants will learn standard international methods for the detection of antimicrobial resistance in bacteria and explore multi-pathogen approaches for limited resource settings. They will also complete computational practicals covering the investigation, tracking, and understanding AMR in bacteria.

Topics will include:

• Epidemiology of AMR pathogens and national surveillance programmes
• Clinical importance of AMR
• Causes and biological mechanisms of resistance in Gram-positive and Gram-negative bacteria
• Antimicrobial susceptibility testing (AST) methods e.g. disc diffusion testing, automated systems, and E-test
• Understanding of  breakpoints and AST reporting, QC/QA
• Antibiotic policies and stewardship
• Tackling AMR using a One Health Approach
• Whole genome sequencing (WGS)
• Web-based and command line tools for pathogen genomics analysis
• Genomic surveillance of AMR

Training team

Beth Blane
University of Cambridge, United Kingdom

Vindana  Chibabhai
Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), National Institute for Communicable Diseases (NICD), South Africa

Francesc Coll I Cerezo
Instituto de Biomedicina de Valencia, Spain

Ewan Harrison
Wellcome Sanger Institute, United Kingdom

Fahad Khokar
University of Cambridge, United Kingdom

Collins Kigen
Kenya Medical Research Institute(KEMRI)/WRAIR-Africa MicroHub Lab, Kenya

Cebile Lekhuleni
National Institute for Communicable Diseases (NICD), South Africa

Caroline Maluleka
Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), National Institute for Communicable Diseases (NICD), South Africa

Fahima Moosa
National Institute for Communicable Diseases (NICD), South Africa

Anthony Smith
National Institute for Communicable Diseases (NICD), South Africa

Pre-requisites:

Laboratory experience: The laboratory practical sessions will require basic microbiological and laboratory skills. This will be essential for participants to fully benefit from the course.

Computer Proficiency: Bioinformatic training will include the use of Linux/UNIX command line. Though 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. 

The course will be taught in English.

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
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 courses@wellcomeconnectingscience.org for assistance.

Application deadline: 3 November 2025

Travel visas
Depending on your citizenship, you may require either a visa to enter South Africa. Please check The South African Government official information and services website for visitor information: https://www.gov.za/services/temporary-residence/visa

Confirmed attendees requiring a letter to support a visa application should contact us at courses@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.

Feedback from the 2024 course:

“The exposure to various tools for analysis has been immensely beneficial, providing me with a comprehensive understanding of the resources available for my research. Moreover, the opportunity to connect with esteemed professionals and experts in the field has been invaluable.”

The course exceeded my expectations. It was well-organized, course material was shared well ahead of time, the trainers were patient and always willing to assist. Concepts and tools were introduced sequentially and paced accurately.”

“The course provided me with the relevant, knowledge, skills and networking opportunity which is much needed to carry out bioinformatics analysis in my ongoing and new projects.”