Genomics and Epidemiological Surveillance of Bacterial Pathogens (Buenos Aires, Argentina)

This popular course was established in 2013 to build strong links between
traditional methods of epidemiological surveillance, modern molecular
typing methods and those based on genomics.

World-wide, the surveillance community is at a crossroads; deciding
whether to continue with traditional methods or to embrace the
unprecedented advances in genomics, sequencing technology and our ability
to interpret high resolution sequence data for surveillance purposes.
This course aims to address the issues that are at the forefront of the
minds of those trying to make the decision as to whether to change their
strategy to implement new sequence based technologies, stay with
traditional methods or combine both approaches.

Each course builds upon previous versions, incorporating genomics and
problem solving exercises with modules that demonstrate how traditional
and molecular typing methods -in combination with sequence data – can be
used for a) passive surveillance and b) georeferencing (also known as
‘phylogeography’) where the location of disease causing strains are
mapped with detailed genetic and phenotypic data (for example antibiotic
resistance patterns) to look for regional patterns of disease. We also
include a module showing how sequence data can be used to understand the
fine detail of new and emerging infections, the risk to public health and
the management of infectious diseases.

The 2016 course will be hosted by the Administracion Nacional De
Laboratorios E Institutos De Salud in Buenos Aires and will for the first
time provide participants with hands-on experience of Next Generation
Sequencing methodologies.

The course will aim to highlight and generate discussion on the strengths
and weaknesses of traditional, molecular and sequence-based approaches
for bacterial disease surveillance.

Background
In Central and South America, as in many parts of the world, Pulsed Field
Gel Electrophoresis (PFGE) is considered a gold standard in
epidemiological surveillance of bacterial pathogens. Since the terms of
reference for on-going and historical knowledge regarding the occurrence
and spread of pathogenic bacteria is via PFGE and other classical
bacteriological phenotyping methods, we felt that there was a need to
link these surveillance efforts to data generated through genomics,
showing the benefits and drawbacks of all techniques and where they can
be used in synergy. Since many regional centres in Latin American and
Caribbean countries are being encouraged to buy next-generation
sequencing machines, this will ensure that epidemiological surveillance
communities are in a strong position to benefit from new discoveries and
advances offered by whole genome sequence data.

This course is a collaboration between Wellcome Trust Advanced Courses,
The Wellcome Trust Sanger Institute Pathogen Genomics Group, The PulseNet
Latin America & Caribbean Network, and the Administracion Nacional De
Laboratorios E Institutos De Salud Dr. Carlos G. Malbran.

The course is targeted at clinical molecular biologists and
microbiologists working in resource-limited countries in Latin America
and the Caribbean and will focus on human, animal and food-borne
bacterial diseases. The programme will combine practical,
laboratory-based training with hands-on, computational data analysis
(informatics).

There are 20 places available and the course will be held in English
(with language support provided where necessary by Spanish- and
Portuguese-speaking instructors).

Laboratory-based practicals: Molecular Sub-typing techniques

• Real Time PCR (including optimisation and primer design)
• Next Generation Sequencing

Computational practicals: Informatics and Surveillance Exercises

• General Web-based bioinformatics (BLAST, FASTA)
• Manipulation of raw sequence data: mapping and de novo assemblies, SNP calling, annotation and analysis of genomic information
• Sequence analysis and comparative genomics software tools (Artemis, ACT)
• Principles of phylogenetics
• Passive surveillance practical exercises
• Georeferencing (phylogeography) practical exercises

The course instructors are a multidisciplinary team, all actively working
on genomics, molecular biology and surveillance of bacterial pathogens in
labs and institutes in the UK, Latin America and SE Asia.

Nick Thomson Wellcome Trust Sanger Institute, UK
Josefina Campos Centro de Referencia Regional PulseNet
AL y C, Argentina
Caterina Guzman Verri PIET, Veterinary School,
Universidad Nacional, Costa Rica
Steve Baker Oxford University Clinical Research Unit, Ho
Chi Minh City, Vietnam
Matt Holden University of St Andrews, UK
Kate Baker Wellcome Trust Sanger Institute, UK
David Aanensen Wellcome Trust Sanger Institute, UK

Guest speaker
Dr Enrique Perez Gutierrez
PAHO/WHO
Department of Communicable Diseases and Health Analysis
Unit of Epidemic Alert and Response and Waterborne Diseases
Washington DC, USA

Prerequisites
Applicants should be clinical molecular biologists or microbiologists
working in Latin American or Caribbean countries. Applicants should also
have training in standard microbiology lab techniques (pipetting,
handling of biological samples, etc.). There are 20 places available and
the course will be held in English (with language support provided where
necessary by Spanish- and Portuguese-speaking instructors).

Cost
Overseas courses are free to attend for non-commercial applicants. Please
contact us for the commercial fee.

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

Bursaries
Overseas courses are free to attend for non-commercial
applicants. Limited bursaries to cover travel, accommodation and
sustenance costs are available 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.