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Molecular and genomic techniques are revolutionising the routine identification and characterisation of pathogens, creating 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 in the clinical setting using worked examples of bacterial pathogens of importance in Africa.
The course is aimed at those primarily trained in culture-based microbiology and combines an understanding of the latest research techniques and theoretical approaches, with practical methods to provide a foundation-level of understanding of the philosophy, methods, and specialist terminology of molecular techniques.
What will you be able to do?
After attending this course, participants 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 sequencing.
- Analyse genomic data using publicly available software tools to identify causative organisms in an infection and to track an outbreak using WGS.
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 genomics sequence data, sequence variation analysis, 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 in the lectures and tutorials and employed during the course practical sessions in the cross-cutting themes of pathogen detection and characterisation, including antimicrobial resistance and the evolution of pathogens, and the application of the data in the improvement of interventions to reduce disease burden.
Course Instructors
- Angeziwa Chunga, Kamuzu University of Health Sciences, Malawi
- Anzaan Dippenaar, University of Antwerp, Belgium
- Brenda Kwambana-Adams, Liverpool School of Tropical Medicine, Malawi
- Chisomo Msefula, Kamuzu University of Health Sciences, Malawi
- Elizabeth (Lizma) Streicher, Stellenbosch University, South Africa
- Keith Jolley, University of Oxford
- Leonard Ndwiga, University of Glasgow
- Martin Maiden, University of Oxford
- Odile Harrison, University of Oxford
- Robert Onsare, Kenya Medical Research Institute
- Sam Kariuki, Kenya Medical Research Institute
Wellcome Connecting Science Team
- Alice Matimba, Head of Training and Global Capacity
- Isabela Malta, Assistant Global Training Manager
- Karon Chappell, Event 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).
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