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
• 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: Limited bursaries are available for
clinical and academic applicants from anywhere in the world to attend
this course, and are awarded on merit. In addition, CPD
accreditation will be sought from the Royal College of
Pathologists.

Feedback from the 2016 course:

• “This was the best course I have been on, bar none. It was a full schedule but very well paced and with plenty of time and opportunity to get into discussions with instructors/participants”
• “Keep the course, it fills an important gap!”
• “Overall, I thought the course was excellent and gave a real insight into the complexities and advantages of using genomic data and new sequencing approaches in my work. Thanks for the organisation and huge time commitment of the tutors. Also – what a fantastic group of participants! A real pleasure to meet everyone.”
• “I would like to sincerely thank all the organisers of this course for a truly wonderful week.”
• “One of the best courses I have attended – many thanks to all involved!”

The programme will include lecture and practical
laboratory/computer-based sessions covering 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

Areas/issues that will be addressed in practical classes, demonstrations
or lectures will include:

• 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 be able to:

• explain the theoretical bases of pathogen genomics, including the application of population genomics to epidemiology and clinical microbiology
• identify the currently available technologies for whole genome analysis and likely future developments
• describe the clinical applications of genomics in developing diagnostics and evaluate their use in clinical settings
• report on the latest research and development using state-of-the-art examples.

In addition, participants will be able to:

• perform a wide range of molecular analyses (including whole genome sequencing on diverse platforms) and molecular diagnostic techniques utlilising genomics
• demonstrate data analysis using a wide variety of software, including variant mapping and gene-by-gene analysis
• explain how the techniques, software, and theoretical approaches covered can be applied in real-world situations

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

Guest speakers will include:
Xavier
Didelot Imperial College London, UK
Jennifer
Gardy BC Centre for Disease Control, Canada
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 £775 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. Places are limited
and will be awarded on merit. 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

Travel visas
Please contact the
event organiser if you require a letter to support a travel visa
application. Note that letters will be provided to confirmed attendees.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website and information for general visitors and business
visitors.

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 £775 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.