Genomics and Clinical Microbiology

17–22 January 2016

Wellcome Genome Campus, Hinxton, UK


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 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.
The aim is to equip clinical scientists, specialist registrars, and
consultants in infection disciplines with 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. The
programme will include sample collection and preparation,
characterization with a variety of molecular techniques, and data
interpretation using a variety of practical bioinformatic

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

Feedback from the 2015 course
“An informative and comprehensive course highly recommended to any
clinical microbiologists or scientists who are interested in microbial
“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!”


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
example clinical problems in
tuberculosis, enteric infections; and encapsulated
bacteria. There will
be demonstrations of the
uses of different approaches in these clinical
areas. Participants will use data generated on the course to make
clinical and infection control

The course will cover a range of cutting-edge diagnostic techniques

  • 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

  • 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 merits of ‘genetics’ and ‘culture’
  • Developing a molecular diagnostic service

CPD Accreditation
CPD accreditation will be sought from the Royal College of

Instructors and speakers

Course instructors
Martin Maiden University of Oxford, UK
Stephen Gillespie University of St Andrews, UK
Cath Arnold Public Health England, UK

Guest speakers
Dag Harmsen University of Münster, Germany
Estee Torok University of Cambridge Department of Medicine, UK
Julian Parkhill Wellcome Trust Sanger Institute, UK
Jon Green Public Health England, UK
Derrick Crook University of Oxford, UK

How to apply

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

course is subsidised by the Wellcome Genome Campus
Advanced Courses and Scientific Conferences Programme. This is a
course and there is a fee of £745 towards board and lodging
for non-commercial applicants. Please contact us for the commercial fee.

Applications for this course can be completed online. 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 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.




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

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

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK

Overseas Courses (held outside of the UK)
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

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

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