Wellcome Connecting Science Course Run Website
Course Time Table
In collaboration with the National Institute for Communicable Diseases (NICD), South Africa, we are pleased to announce the Antimicrobial Resistance of Bacterial Pathogens course.
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 with the majority of deaths occurring in sub-Saharan Africa (Murray et al, 2022). 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.
The challenges of controlling AMR in Africa are considerable for a number of reasons, including overuse and misuse of antibiotics, lack of antimicrobial policies or stewardship programmes, limitations in data infrastructure and information sharing on antimicrobial prescription, consumption. Workforce capacity challenges and resources are major factors impacting on quality of data and subsequent care. In addition, there is limited knowledge of pathogen strains and AMR gene carriage due to lack of consistent and comprehensive AMR surveillance, making it difficult to track transmission, evaluate risks, detect and control outbreaks in hospitals and communities. To develop capacity for effective control of AMR, multi-disciplinary approaches are needed. Technologies such as whole genome sequencing, bioinformatics and data science tools are revolutionising routine diagnostics and surveillance of disease causing pathogens.
The aim of this course is to improve skills for effective AMR detection and develop capacity for genomic surveillance of AMR. It will provide a basic introduction and practical training in the laboratory aspects of AMR detection (phenotypic and molecular testing) in bacteria. The course will integrate theoretical aspects on the evolution and spread of AMR and explore the use of whole-genome sequencing and bioinformatics analysis and methods for AMR surveillance and control.
This week-long course is designed for scientists based in Africa who are actively involved in, or preparing to embark on, research or professional work within antimicrobial resistance (AMR) related fields. This includes individuals working in diagnostic stewardship, antimicrobial stewardship, infection prevention and control, or involved in the development of policies related to AMR.
The course will consist of lectures, seminars and hands-on laboratory approaches covering international standard methods for the detection of antimicrobial resistance in bacteria.
The tailored combination of course activities will reinforce the importance of quality controls, sources of errors, high-quality data and critical thinking in the laboratory when undertaking phenotypic and genomic AMR detection methods. The course will also provide a comprehensive understanding of how bacterial genomics (and metagenomics) can be used to understand AMR: (1) epidemiology, (2) biology, (3) transmission, (4) ecology and (5) diagnosis
Participants will complete computational practicals covering the identification of AMR genes, investigation of outbreaks and tracking transmission of bacterial strains using whole genome sequence analysis. By providing an end-to-end view of AMR genomics, command-line and web-based analysis tools, participants will be empowered to conduct their own research and apply genomics techniques in their work. The course will bring together scientists from across Africa and create new research networks.
After attending this course, participants will be able to:
- Carry out standard laboratory methods for the detection of antimicrobial resistance in bacteria.
- 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, identify and interrogate antibiotic resistance genes and mutations.
- Conduct phylogenetic analysis in the context of outbreak and other epidemiological investigations.
- Interpret genomics data for AMR diagnosis and surveillance.
Course Instructors
- Ewan Harrison, Wellcome Sanger Institute, UK
- Sabelle Jallow, NICD, South Africa
- Stanford Kwenda, NICD, South Africa
- Beth Blane, University of Cambridge, UK
- Collins Kigen, KEMRI, Kenya
- Fahad Khokhar, University of Cambridge, UK
- Francesc Coll, London School of Hygiene & Tropical Medicine, UK
- Lillian Musila, KEMRI, Kenya
- Narender Kumar, Wellcome Sanger Institute, UK
Wellcome Connecting Science Team
- Alice Matimba, Head of Training and Global Capacity
- Karon Chapell, Events Organiser
- Cassandra Soo, Laboratory Courses Manager
- Aaron Dean, Laboratory Technical Officer
- Christopher Adamson, Laboratory Operations Officer
- Martin Asltett, Informatics Manager
- Vaishnavi Vikas Gangadhar, Informatics Technical Officer
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
Take a look what courses are coming up at Wellcome Connecting Science Courses & Conference Website.
For more information or queries, feel free to contact us via the Wellcome Connecting Science website.
Find us on socials Wellcome Connecting Science Linktr