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The future of microbiological diagnostics and infection epidemiology is increasingly centred on rapid and point of care molecular testing, including the application of nucleotide sequencing technologies. Consequently, practitioners in clinical microbiology and related areas must process and interpret molecular data that are very different from the information generated by familiar culture-based and serological microbiology techniques. The importance of these technologies was dramatically highlighted by the COVID-19 pandemic.
To demystify this crucial, exciting, and expanding area, the Genomics and Clinical Microbiology Advanced Course, presented by leaders in the field, combines hands-on laboratory and bioinformatics work, faculty lectures, and small-group discussions. The course aims to equip consultants, clinical scientists, and specialist registrars, in infection 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 approaches that are likely to enter practice in the near future. Employing a range of practical approaches, the course programme includes: sample collection and preparation; characterization of isolates with a variety of molecular techniques; data interpretation and dissemination; and monitoring treatment responses.
The practical part of the course provides laboratory and computer data analysis sessions that examine the application of molecular, specifically genomic, techniques to clinical practice. Learning is centred on three clinical scenarios that exemplify different challenges and solutions:
- tuberculosis;
- healthcare associated infections;
- encapsulated bacteria
Different methods and approaches will be demonstrated for each of these clinical areas. Importantly, as genome sequencing is increasingly entering clinical practice there will be discussion about how such methodologies can be incorporated into the clinical workflow. Participants will generate their own data and analyse it on the course to make public health, clinical and infection control decisions.
This course is designed for clinical scientists, specialist registrars or consultants in medical microbiology.
The course has been approved for 43 CPD credits by the Royal College of Pathologists.
Having completed the course, participants will have acquired:
- An advanced understanding of the theoretical bases of pathogen genomics, including the application of population genomics to epidemiology and clinical microbiology;
- A wide appreciation of the currently available technologies for whole genome analysis and likely future developments;
- A thorough knowledge of the clinical applications of genomics in developing diagnostics and how these can be deployed and exploited in clinical settings;
- An overview of the latest research and development in the area, informed by state-of-the-art examples.
They will have performed:
- A range of molecular analyses, including whole genome sequencing on diverse platforms;
- A variety of molecular diagnostic techniques that depend on the application of genomics to practice;
- Data analysis using a wide variety of software, including variant mapping and gene-by-gene analysis;
- An investigation of three clinical scenarios that illustrate how the techniques, software, and theoretical approaches covered can be applied in real-world situations.
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.
- Martin Maiden, University of Oxford, UK
- Stephen Gillespie, University of St Andrews, UK
- Katarina Oravcova, University of Glasgow, UK
- Charlene Rodrigues, University of Oxford, UK
- Keith Jolley, University of Oxford, UK
- Natasha Walbaum, University of St Andrews, UK
- Marie Chattaway, UK Health Security Agency, UK
- Alice Matimba, Head of Training and Global Capacity
- 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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