Genomics and Epidemiological Surveillance of Bacterial Pathogens (San Jose, Costa Rica)

09 - 14 July 2017San Jose, Costa Rica
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    Course aim
    This course aims to provide training in the skills required to generate
    and interpret next generation sequencing data in a public health setting.

    This year’s course will have a strong emphasis on Antimicrobial
    Resistance
    (AMR) and
    its spread, whilst also training
    participants in the latest laboratory and computational methods for
    next
    generation sequence analysis and genomic surveillance.

    Course background
    This is a focused course that was established in 2013 to build strong
    links between traditional methods of epidemiological surveillance, modern
    molecular typing methods and those based on genomics. Although the course
    is built around genomic surveillance the focus of this course is designed
    to reflect regional public health priorities, and this year’s course will
    have a strong emphasis on AMR.

    World-wide over the last few years the surveillance community has been 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 debate has now been resolved and we are now seeing a shift
    from the use of molecular typing data for epidemiological surveillance
    and public health investigations of infectious disease to using whole
    Genome Sequencing (WGS) for this purpose. In some settings WGS is now
    being used to define outbreaks and trace infection sources in humans,
    animals and the environment. This approach also offers enormous promise
    for predicting antimicrobial resistance phenotypes.

    Existing studies that have used genomics for mapping the spread of
    pathogens have highlighted two things, firstly that genomic datasets are
    growing day by day and they offer the context against which to understand
    local patterns of disease. Secondly these studies also highlight the
    power gained from public health scientists and academic research
    scientists working together to better understand infectious disease. This
    is the foundation of this course and expert instructors have been
    assembled from a wide range of settings in Latin America and Europe,
    including national and international public health organisations and
    front line high-profile genomic research organisations. We recognise the
    synergy between academic research and public health and this is your
    opportunity to strengthen this effort by attending the course.

    We also have a strong focus on “Train the Trainer” and there will be
    opportunities to develop your teaching skills and feedback on how these
    courses can be improved to facilitate participants teaching the skills
    they have learnt back in their own countries.

    Target audience
    The course is targeted at clinical molecular biologists
    and
    microbiologists working in resource-limited countries in Latin
    America
    and the Caribbean. Please note: The course is free to attend for
    non-commercial applicants.
     

    Applicants should 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).

    Venue
    The 2017 course will be hosted by the Microbiology Faculty and the
    Research Center for Molecular and Cell Biology at the main campus of the
    University of Costa Rica in San José.

  • Programme

    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:
    a) for 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, and
    b) to understand the fine detail of new and emerging infections, the risk
    to public health and the management of infectious diseases.

    The week-long programme includes:

    Laboratory-based practicals: Molecular Sub-typing
    techniques:

    • Running and interpreting real-time PCR assays (including optimisation and primer design)
    • Generating Next Generation Sequencing data

    Computational practicals: Informatics and Surveillance

    • Practical bioinformatics skills needed to manipulate raw sequence data (some of which will be generated on the course), including: mapping and de novo assemblies, SNP calling, annotation and analysis of genomic information
    • Sequence analysis and comparative genomics of next generation sequencing data using Artemis and ACT
    • Principles of phylogeny and construction of accurate phylogenies
    • Group exercises designed to teach everyday skills required to work in genomic surveillance
    • Practical exercises for using GPS to map cases of infectious disease and phenotypes (such as AMR) across the world

    Learning outcomes
    After attending the course, participants should be able to:

    • Recognize the principles of real time PCR and next generation sequencing (including primer design) and how to apply them effectively
    • Sequence genomic bacterial DNA 
    • Use sequence analysis tools effectively
    • Explain what a phylogenetic tree is and what it represents
    • Formulate projects using the global surveillance platform Microreact
    • Perform comparative genomics on multiple genome sequences
    • Compare different traditional bacteriological identification methods with modern molecular typing methods and genomics in the context of local and regional resources
    • Explain, using examples, how AMR is spread among bacterial pathogens
  • Instructors / Speakers

    Course Instructors

    Caterina Guzman Verri PIET, Veterinary School, Universidad
    Nacional, Costa Rica
    Josefina Campos Centro de Referencia Regional PulseNet
    AL y C, Argentina
    Claire Jenkins Public Health England, UK
    Matt Holden University of St Andrews, UK
    Nick Thomson Wellcome Trust Sanger Institute, UK
    David Aanensen Wellcome Trust Sanger Institute, UK
    Silvia Argimon Wellcome Trust Sanger Institute, UK
    Leonor Sanchez Buso Wellcome Trust Sanger Institute, UK


    Guest Speakers

    Enrique Perez-Gutiérrez Pan American Health
    Organisation
    Foodborne Diseases

    Marcelo Galas Pan American Health Organisation
    Antimicrobial Resistance

  • How to Apply

    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.
    Limited bursaries to cover travel, accommodation and
    sustenance costs
    are also available and are awarded on merit. More information on
    bursaries can be found under the “Cost / Bursaries” tab

    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 / Bursaries

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

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