Genomics and Clinical Microbiology

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; and
• 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.

Who should attend this course?

This course is designed primarily for clinical scientists, specialist registrars, or consultants in medical microbiology and related disciplines including public health and infection control.

CPD Accreditation
This course has been accredited for 42 CPD points  by the Royal College of Pathologists.

Bursaries

Available for clinical and academic applicants from anywhere in the world to attend this course. Please see the “Cost and financial support” tab below for more information.

What will you achieve?

 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.

This residential course will start at approximately 12.00 on Sunday 2 February 2025 and close at approximately 17:00 on Friday 7 February 2025. All times are in GMT.

 The course will cover a range of techniques including:

• Design, implementation, and interpretation of real-time PCR tests for pathogen detection;
• Molecular approaches to detect multiple pathogens;
• Whole genome sequencing (WGS) using short-read (Illumina) and long-read (Nanopore) techniques;
• PCR and sequence-based isolate characterisation;
• Bioinformatic 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:

• Concepts for modernising and developing a molecular diagnostic service;
• Theoretical bases 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.

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

Training team

Pre-requisites

Bioinformatics training will include the use of Linux/UNIX command line. Though participants learn to use the command line during the course, familiarity with these resources is recommended. ‘Introduction to Linux for biologists’ pre-course module will be provided for completion prior to the course. 

How to Apply

1. Start the application
   • Click on the “Apply” button above to start your application. Please note that places are limited and will be awarded based on merit.
2. Demonstrate the course’s relevance to your project/role
   • Our courses are highly subscribed, so it is essential to clearly show how the skills you will learn in the course will be directly applicable and beneficial to your current role/project and how do you plan to disseminate the knowledge after the course.
   • Preference will be given to applicants who are currently working on related projects or soon will be.
3. Letter of recommendation
   • Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g., supervisor, line manager, or head of department). Ensure that your sponsor provides a tailored supporting statement by the application deadline. This statement must be uploaded as a PDF document to the registration system within your application. Applications without a supporting statement will not be considered.
4. Need help?
   • If you encounter any problems with the online application process, please contact us courses@wellcomeconnectingscience.org for assistance.

Application deadline: 21 October 2024

Travel visas

Citizens of many countries can travel to the UK to attend a course or conference without needing a visa. Please check the UK government website for visitor information: https://www.gov.uk/standard-visitor.

Confirmed attendees requiring a letter to support a visa application should contact us courses@wellcomeconnectingscience.org.

*The course fee is subsidised by Wellcome Connecting Science and applies to non-commercial applicants. Please contact us for the commercial fee.

Payment will be requested once acceptance is confirmed.

Bursaries

Limited bursaries are available (up to 50% reduction on the course fee) and are awarded on merit. If you would like to apply for a bursary, please complete the bursary section of the online application form, explaining why you would benefit from funding.

Bursaries can be applied for as part of the course application form. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. The decision of the selection committee is final.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.

Deadline: 29 October 2024

Additional funding opportunities
Visit our support page for additional financial support currently available.

Extra accommodation
If you wish to book onsite accommodation either side of the course dates, please contact Hinxton Hall Conference Centre directly.

Accommodation services phishing scam – please be vigilant. More information.

Feedback from the 2024 Course

“The course was excellent, all the trainers, assistants, lectures and organisers were really
friendly. Thanks for the valuable experience through lab work, data analysis and discussion.”

“Everyone was friendly and willing to help. The accomodation and meals were of a very high standard and made the stay enjoyable…especially during this very cold weather. The facilities were great.”

“The opportunity to do both the lab work and then the downstream bioinformatics in such a supportive and structured way. And meeting a great bunch of people.”