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Genomics and Clinical Microbiology

19-24 January 2014

Wellcome Trust Genome Campus, Hinxton, Cambridge

Now closed for applications. Please email to join our mailing list.

Course summary

The analysis of bacterial genomes is revolutionising clinical microbiology, and the clinical microbiologists of the immediate future will have to process and interpret data very different from that provided by agar-centric clinical microbiology laboratories. This laboratory-based training course combines practical hands-on laboratory and bioinformatics work with faculty lectures by, and discussions with, leaders in this exciting area. The principal aim is to equip clinical scientists, specialist registrars, and consultants in medical microbiology (including joint medical microbiology and infectious diseases) with sufficient understanding of these areas to meet these challenges in the future. The course will concentrate on techniques that are currently practicable and will examine the application of whole genome sequence analysis to clinical microbiology.

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 (45 credits) was approved by the Royal College of Pathologists in 2013. A similar application will be submitted for the 2014 course.


The practical part of the course will provide laboratory and computer sessions that will examine the application of molecular techniques using examples in three areas:(i) Tuberculosis; (ii) enteric infections; and (iii) encapsulated bacteria, with demonstrations of the uses of different techniques applied to real clinical scenarios. Participants will use the data generated to make clinical and disease-control decisions. The course will include sample collection and preparation, characterisation 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
Sequence-based typing
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 sequencing
Technique discrimination – demonstrate how to choose the appropriate technique
Case studies demonstrating the benefits of 'genetics' over 'culture'
Developing a molecular diagnostic service

Course instructors

Guest speakers

  • Dr Sebastien Gagneux (Swiss Tropical & Public Health Institute, Switzerland)
  • Dr Jon Green (Public Health England, UK)
  • Professor Dag Harmsen (University of Münster, Germany)
  • Professor Helen Lee (University of Cambridge, UK)
  • Dr Paul Keim (The Translational Genomics Research Institute, AZ, USA)
  • Dr Xavier Nassif (Unité de Pathogénie des Infections Systématiques, France)
  • Professor Julian Parkhill (Wellcome Trust Sanger Institute, UK)
  • Dr Harold Swerdlow (Wellcome Trust Sanger Institute, UK)
  • Dr John Wain (University of East Anglia Medical School, UK)

CPD Accreditation

CPD accreditation was approved by the Royal College of Pathologists in 2013. A similar application will be submitted for the 2014 course.

Read a review of the course in this BMJ article.

Feedback from the 2013 course
“A very big thank you to the organisers of this course. Despite the increasing need of knowledge and skills in this area in microbiology, there are few courses available for this purpose. I'm extremely grateful for the opportunity to meet and learn from experts in the field.”
“Excellent enjoyable course: thank you to everyone who gave their time to educate me”
“Thank you for a brilliant week!”

How to apply

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

The course is subsidised by the Wellcome Trust. This is a residential course and there is a fee of £695 towards board and lodging for clinical and academic applicants. The fee for commercial (non-academic) applicants is £3050.

Limited bursaries are available for non-commercial applicants (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).

Now closed for applications. Please email to join our mailing list.

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