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Genomics and Clinical Microbiology

18-23 January 2015

Wellcome Trust Genome Campus, Hinxton, Cambridge

Now closed for applications. Please email us 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 course combines practical hands-on laboratory and bioinformatics work with faculty lectures by, and discussions with, leaders in this exciting and expanding 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 in diagnosis treatment monitoring, public health and hospital epidemiology and will examine the application of whole genome sequence analysis to clinical microbiology practice.

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 was approved by the Royal College of Pathologists in 2014. A similar application will be submitted for the 2015 course.


The practical part of the course will provide laboratory and computer sessions that will examine the application of molecular techniques generally 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 bio-informatic 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 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 relative meritsof 'genetics' and 'culture'
Developing a molecular diagnostic service

Course instructors

2015 Guest speakers

  • 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 Sebastien Gagneux (Swiss Tropical and Public Health Institute, Switzerland)
  • 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 was approved by the Royal College of Pathologists in 2014. A similar application will be submitted for the 2015 course.

Feedback from the 2014 course

“Overall fantastic experience-I cannot praise this course highly enough!”
“I enjoyed the course very much and learned many things I hope to apply in my lab in the future. The atmosphere was very friendly and all the staff were very approachable and helpful.”
“Thank you very much - I loved the course!”

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 £730 towards board and lodging for clinical and academic applicants. The fee for commercial (non-academic) applicants is £3200.

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).

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

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

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