Genomics and Clinical Microbiology

23–28 January 2022

Wellcome Genome Campus, Hinxton

Training in molecular and genomic techniques for microbiological diagnostics and infection epidemiology


(The current plan is to run a face to face course but this will be reviewed prior to selection of participants taking into consideration any Covid pandemic restrictions. A virtual course could be offered as an alternative.)

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; and data interpretation and dissemination and monitoring treatment response.

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; and
  • encapsulated bacteria.

Different methods and approaches will be demonstrated for each of these clinical areas. Participants will generate their own data and analyse it on the course to make public health, clinical and infection control decisions.

CPD accreditation is sought annually for this course from the Royal College of Pathologists.


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;
  • Bioinformatic analysis and data interpretation;
  • Outbreak investigation and public health application;
  • Monitoring response to treatment
  • Data analysis, interpretation, display and dissemination.

Issues 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.

CPD Accreditation
CPD accreditation is being sought from the Royal College of Pathologists.

WTGC Advanced Course ‘Genomics and Clinical Microbiology’ Learning Outcome

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.

Instructors and speakers


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

How to apply

Applicants should be clinical scientists, specialist registrars or consultants in medical microbiology.

Click on the Apply button above to begin the application process. Places are limited and will be awarded on merit. If you have any problems with the online application process, please contact us.

Please note: Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g. supervisor, line manager, or head of department). A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline. Applications without a supporting statement cannot be considered.


*Course fee £820


Advanced Courses are subsidised for non-commercial applicants from anywhere in the world. Additional, limited bursaries are available (up to a 50% reduction of 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.

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

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


Feedback from the 2020 Course

“”Thank you for a very well run, and packed course. I hope I can use all I have learned to drive forward clinical diagnostics.”

“A huge amount of information was covered in the course, all in great detail.”

“The course was organized very well in the sense that there was a good mix of seminars, lab sessions & computational analyses each day.”

“All the staff I encountered during my time on campus were kind and willing to help with any query, I truly thank all involved in the course and hope it continues to evolve and exist for the benefit of future scientists.”

“This was an absolutely incredible course on Infection Genomics and highly valuable for infection trainees. I will be recommending this course to all my infectious disease trainees and colleagues.”

“The course was excellent, all the tutors, assistants, guest lecturers and organisers were really knowledgeable, friendly and made the whole course a really valuable experience. Thanks for giving me the opportunity to attend.”

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