Wellcome Connecting Science Course Run Website
Course Time Table 2025
Course Informatics Guide
Training in molecular and genomic techniques for bacteriological diagnostics, molecular epidemiology, and infection control
The future of bacteriological diagnostics, molecular epidemiology, and infection control is increasingly centred on rapid and point of care molecular testing, including the application of sequencing technologies. Consequently, practitioners in clinical microbiology and related disciplines must process and interpret molecular data that are very different from the information generated by culture-based and serological techniques that have been cornerstone paradigms for over 100 years.
To demystify this crucial, exciting, and expanding area, the Genomics and Clinical Microbiology Course, presented by leaders in the field, aims to equip those in clinical microbiology and related disciplines with sufficient understanding of these areas to meet these challenges. There is an emphasis on the application of molecular and genomic techniques that are currently being implemented, but the course also explores the theoretical foundations of these techniques and approaches that are likely to enter practice in the near future.
What will this course cover?
Employing a range of practical approaches, the course programme includes: sample collection and preparation; characterisation of specimens with a variety of molecular techniques; data interpretation and dissemination of data; and monitoring treatment responses.
Hands-on laboratory and computer data analysis sessions will examine the application of genomic techniques to clinical practice. Learning is centred on three clinical scenarios that exemplify different challenges and solutions:
- tuberculosis;
- healthcare associated infections;
- encapsulated bacteria
A variety of methods and approaches will be demonstrated for each of these clinical areas and there will be discussion about how such methodologies can be incorporated into the routine clinical workflow. Participants will generate their own data and analyse it on the course to simulate making clinical, infection control, and public health decisions.
This course is designed primarily for clinical scientists, specialist registrars, or consultants in medical microbiology and related disciplines including public health and infection control.
The course has been approved for 43 CPD credits by the Royal College of Pathologists.
After completing this course, you will be able to:
- Perform a variety of genomic techniques and be able to identify which technique is applicable to the epidemiological or clinical query
- Appreciate the strengths and weaknesses of currently available technologies and future developments in the field
- Utilise online tools and available software for variant mapping, gene-by-gene analysis, and short-and long-read genome sequence analysis
- Discuss how genomics is used in diagnostics and how these technologies may be deployed in clinical scenarios.
The course will cover a range of diagnostic techniques including:
- Design, implementation, and interpretation of real-time PCR tests for pathogen detection;
- Molecular approaches to detect multiple pathogens;
- Whole genome sequencing (WGS);
- PCR and sequence-based isolate characterisation;
- Bioinformatics analysis and data interpretation;
- Outbreak investigation and public health application;
- Monitoring response to treatment
- Data analysis, interpretation, display and dissemination.
Topics included in practical classes, demonstrations, and/or lectures:
- Theoretical concepts for modernising and developing a molecular diagnostic service;
- Conceptual basis and background to microbial phylogenetic analysis and population biology;
- Specimen collection and contamination problems;
- Whole genome sequencing technologies and clinical applications
- Technique discrimination – identifying the question and choosing the appropriate technique;
- Case studies demonstrating the relative merits of different approaches;
- Presenting molecular data in the context of clinical scenarios.
Course Organisers
- Stephen Gillespie, University of St Andrews, UK
- Martin Maiden, University of Oxford, UK
- Katarina Oravcova, University of Glasgow, UK
- Charlene Rodrigues, London School of Hygiene and Tropical Medicine and UK Health Security Agency, UK
Course Instructors
- Marie Chattaway, UK Health Security Agency, UK
- Chiara Crestani, Institut Pasteur, France
- Jonathan Hubb, UK Health Security Agency, UK
- Keith Jolley, University of Oxford, UK
- Krisna Made, University of Oxford, UK
- Benjamin Parcell, University of Dundee, UK
- Kasia Parfitt, University of Oxford, UK
- Wilber Sabiiti, University of St Andrews, UK
- Natasha Walbaum, University of St Andrews, UK
Wellcome Connecting Science Team
- Martin Aslett, Informatics Manager
- Vaishnavi Vikas Gangadhar, Informatics Technical Officer
- Cassandra Soo, Laboratory Courses Manager
- Aaron Dean, Laboratory Technical Officer
- Christopher Adamson, Laboratory Operations Officer
- Nicola Stevens, Events Organiser
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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