The objective of this course is to enhance proficiency in the detection of antimicrobial resistance (AMR) and to cultivate expertise in genomic surveillance of AMR. It aims to offer a foundational understanding and hands-on training in laboratory methodologies for detecting AMR in bacteria, encompassing both phenotypic and molecular testing. The curriculum will also delve into theoretical concepts surrounding the evolution and spread of AMR, while exploring the utilisation of whole-genome sequencing and bioinformatics techniques for AMR surveillance and control.
Participants will engage in computational exercises focused on identifying AMR genes, investigating outbreaks, and tracing the transmission of bacterial strains through whole-genome sequence analysis. By providing an end-to-end view of AMR genomics, command-line and web-based analysis tools, the course will empower participants to conduct independent research and apply genomic methodologies in their work. Furthermore, the course will foster collaboration among scientists from diverse regions of Africa, facilitating the establishment of new research networks.
Target audience
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 offer a blend of lectures, seminars, and practical laboratory sessions, focusing on internationally recognised methods for detecting antimicrobial resistance in bacteria. Through this tailored combination of activities, participants will gain a deeper understanding of the importance of quality controls, identification of sources of errors, acquisition of high-quality data, and cultivation of critical thinking skills within the laboratory environment, particularly when employing phenotypic and genomic AMR detection techniques. Moreover, the course aims to provide a comprehensive comprehension of how bacterial genomics (including metagenomics) can be harnessed to elucidate various aspects of AMR, including epidemiology, biology, transmission dynamics, ecological interactions, and diagnostic approaches.
Learning Outcomes
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.
- 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
Shield:
This work is licensed under a Creative Commons Attribution 4.0 International License.
