Genomics and Clinical Microbiology

The future of microbiological diagnostics and infection epidemiology is
increasingly centred on 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
familiar agar-centric clinical microbiology laboratories.

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. The course will concentrate on the
application of cutting-edge molecular and genomic techniques that can be
implemented now and explore new approaches that will enter practice in
the near future. The programme will include sample collection and
preparation, characterization of specimens with a variety of molecular
techniques, and data interpretation using a variety of practical
bioinformatic approaches.

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 decisions.

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.

Feedback from the 2016 course:

• “This was a well run and very worthwhile course. It has completely changed my view and practice regarding genomics.”
• “Genomics and Clinical Microbiology is the best course I have ever participated in. It blends clinical and molecular aspects of infectious disease diagnosis & epidemiology in a very clever way.”
• “Excellent course, highly relevant for clinical microbiologists.”
• “Great balance of practical and theoretical teaching.”
• “It was a wonderful course and please keep running it!”

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

• Design and implementation of real time PCR tests for pathogen detection
• Molecular approaches to detect multiple pathogens
• PCR-based typing
• Whole genome sequencing
• Mycobacterial typing and molecular bacterial load assays
• Sequence-based isolate characterisation
• Bioinformatics and data interpretation
• Outbreak investigation

• Specimen collection and contamination problems
• Biological background to WGS approaches
• Whole genome sequencing platforms and technologies
• Technique discrimination – demonstrate how to choose the appropriate technique
• Case studies demonstrating the relative merits of ‘genetics’ and ‘culture’
• Developing a molecular diagnostic service

Learning outcomes
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
• An extensive 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 extensive overview of the latest research and development in the area, informed by state-of-the-art examples.

In addition, participants will have performed:

• A wide range of molecular analyses, including whole genome sequencing on diverse platforms
• A wide range of molecular diagnostic techniques utlilising genomics
• 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.

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

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

Guest speakers
Xavier
Didelot Imperial College
London, UK
Jennifer
Gardy BC Centre for
Disease Control, Canada
Nick
Loman University of Birmingham, UK
Leila Luheshi PHG Foundation, UK
Julian
Parkhill Wellcome Trust Sanger Institute, UK
Estée
Torok University of Cambridge, UK

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

Cost
The
course is subsidised by the Wellcome Genome Campus Advanced Courses
and Scientific Conferences Programme. This is a residential
course and
there is a fee of £760 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

Additional limited bursaries are available (up to 50%
of the course fee)
and are awarded on merit. Please see the “Bursaries”
tab for details.

Applications
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.

Deadlines
Deadline for Applications: Closed

Cost
The
course is subsidised by the Wellcome Genome Campus Advanced Courses
and
Scientific Conferences Programme. This is a residential
course and
there is a fee of £760 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

Bursaries
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 application
form.

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,
Cambridge)
A
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
courses.

Overseas Courses (held outside of the UK)
A
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.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.