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Explore antimicrobial susceptibility testing techniques and how genomics can be applied to AMR surveillance
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 Runs
| Course Date | Course Title | Location | Citation DOI |
|---|---|---|---|
| 9–14 March 2024 | Antimicrobial Resistance in Bacterial Pathogens - Africa | National Institute for Communicable Diseases (NICD) - South Africa |  |
| 2–7 February 2025 | Antimicrobial Resistance in Bacterial Pathogens - Asia | - | Citation DOI |
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).
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