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Genomics and Epidemiological Surveillance of Bacterial Pathogens

1-6 February 2015

Faculty of Microbiology, University of Costa Rica, San José, Costa Rica

Now closed for applications. Please email to join our mailing list.

Please note: The content of this course has been updated (18 August 2014). Please contact us if you have any questions regarding these updates.

Course 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. We have updated the 2015 course to further 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.

The updated programme will build on the previous two courses, increasing the number of 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 will 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 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, The University of Costa Rica and Universidad Nacional of Costa Rica.

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
Bacterial genomic DNA extraction
Real Time PCR (including optimisation and primer design)

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

Course instructors

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)
Caterina Guzman Verri (PIET, Veterinary School, Universidad Nacional, Costa Rica)
Claire Jenkins (Health Protection Agency, UK)
Clare Ling (Health Protection Agency, UK)
Francisco Duarte (Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud [INCIENSA], Costa Rica)
Carlos Quesada (CIET, Faculty of Microbiology, University of Costa Rica, Costa Rica)
Josefina Campos (Centro de Referencia Regional PulseNet AL y C, Argentina)
Steve Baker (Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam)
Matt Holden (Wellcome Trust Sanger Institute, UK)
Simon Harris (Wellcome Trust Sanger Institute, UK)

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).

The course is free to attend for applicants from non-commercial institutes. Bursaries for travel and accommodation costs are also available (see below).

Bursaries are available for non-commercial applicants to cover travel, accommodation and sustenance costs and are awarded on merit. If you would like to apply for a bursary, please complete the bursary section of the online application form (see below for application process).

Now closed for applications. Please email to join our mailing list.

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