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Genomics and Clinical Microbiology

17-22 January 2016

Wellcome Trust Genome Campus, Hinxton, Cambridge

Deadline for applications: 9 October 2015

Course summary

The future of microbiological diagnostics and infection epidemiology is increasingly centred around rapid molecular testing and the application of sequencing technology. Practitioners in these disciplines will have to process and interpret data such data which is very different from the agar-centric clinical microbiology laboratories of the past.The Genomics and Clinical Microbiology course combines practical hands-on laboratory and bioinformatics work with faculty lectures by, and discussions with, leaders in this crucial, exciting, and expanding area. Theaim is to equip clinical scientists, specialist registrars, and consultants in infection disciplineswith sufficient understanding of these areas to meet these challenges in the future. The course will concentrate on the application of cutting edge molecular and genomic techniques that could be implemented today and explore new approaches that will enter practice in the coming few years.

PLEASE NOTE: bursaries are available for clinical and academic applicants from anywhere in the world to attend this course, see below for details. This includes bursaries for UK registrars. In addition, CPD accreditation will be sought from the Royal College of Pathologists.


The practical part of the course will provide laboratory and computer sessions that will examine the application of molecular and specifically genomic techniques to three clinical problems in tuberculosis, enteric infections; and encapsulated bacteria that will serve as examples.There will be demonstrations of the uses of different approaches in these clinical area. Participants will generate and use data generated to make clinical and infection control decisions. The course will include sample collection and preparation, characterization with a variety of molecular techniques, and data interpretation using a variety of practical bioinformatic approaches.

The course will cover a range of cutting edge diagnostic techniques including:

Design of real time PCR tests for pathogen detection
Real time PCR to detect multiple pathogens
Whole genome sequencing (WGS)
Mycobacterial typing methodologies
Molecular bacterial load assays
Sequence-based isolate characterisation
PCR-based typing
Bioinformatics and data interpretation

Areas/issues that will be addressed in practicals, demonstrations or lectures:

Specimen collection and contamination problems
Biological background to WGS approaches
Next generation and third generation sequencing
Technique discrimination – demonstrate how to choose the appropriate technique
Case studies demonstrating the relative meritsof 'genetics' and 'culture'
Developing a molecular diagnostic service

Course instructors

Guest speakers

  • Professor Dag Harmsen (University of Münster, Germany)
  • Dr Paul Keim (The Translational Genomics Research Institute, AZ, USA)
  • Professor Julian Parkhill (Wellcome Trust Sanger Institute, UK)
  • Dr Jon Green (Public Health England, UK)
  • Dr Estee Torok (University of Cambridge, UK)
  • Professor Derrick Crook (University of Oxford, UK)

CPD Accreditation

CPD accreditation will be sought from the Royal College of Pathologists.

Feedback from the 2015 course

“An informative and comprehensive course highly recommended to any clinical microbiologists or scientists who are interested in microbial genomics”
“Thank you for all your effort. Everyone was kind and helpful. I am using the knowledge to promote a service redesign in our large laboratory”
“Thank you for an excellent opportunity and great teaching. I left feeling inspired and educated!”
“Thanks so much for a truly fantastic course!”

How to apply

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

The course tuition fees are subsidised by The Wellcome Trust for researchers and clinicians based in non-commercial institutions anywhere in the world. This is a residential course and there is a fee of £745 towards board and lodging for non-commercial applicants. Commercial applicants should contact us for the commercial fee.

Limited bursaries are available for non-commercial applicants (up to 50 per cent of fee) and are subject to open competition. If you would like to apply for a bursary, please complete the bursary section of the online application form (see below for application process).

Application forms for this course can now be completed online. If you have any problems with the online application process, please email us.

Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your supervisor 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.

Application deadline: 9 October 2015

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