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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

Application deadline: 3 October 2014

Course summary

Now in its third year the aim of this free course is to forge a strong link between traditional methods of epidemiological surveillance, the latest molecular sub-typing techniques and the ability to use, analyse and interpret whole genome sequence data for the same purpose. 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).


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 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 the PFGE-based 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. There are 20 places available and the course will be held in English.


Molecular Sub-typing techniques
Bacterial genomic DNA extraction
Real Time PCR (including optimisation and primer design)

Pulsed Field Gel Electrophoresis (PFGE)
Wet-lab based practical experience of PFGE and training in the use of Bionumerics software for data analysis

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

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 Vietnam.

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.

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).

Application forms for this workshop can now be completed online. Please click here to be redirected to the application portal. If you have any problems with the online application process, please email us.

Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your 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.

Application deadline: 3 October 2014

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