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

17 - 22 April 2016Buenos Aires, Argentina
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    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.

    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

    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).

  • Programme

    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
  • Instructors / Speakers

    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
    Department of Communicable Diseases and Health Analysis
    Unit of Epidemic Alert and Response and Waterborne Diseases
    Washington DC, USA

  • How to Apply

    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).

    Overseas courses are free to attend 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.

    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

    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