Genomics and Epidemiological Surveillance of Bacterial Pathogens
3-8 February 2013
Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
Now closed for applications. To be kept updated on future course dates, please email us.
Course summary
The aim of this 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.
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 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 new 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.
Programme
Molecular Sub-typing techniques
Bacterial genomic DNA extraction
Real Time PCR (including optimisation and primer design)
SNP-typing (Single Nucleotide Polymorphism)
Pulsed Field Gel Electrophoresis (PFGE)
Wet-lab based practical experience of PFGE and training in the use of Bionumerics software for data analysis
Informatics
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
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)
How to apply
Prerequisites
Applicants should be clinical molecular biologists or microbiologists working in resource-limited 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.
Cost
There is no course fee for academics/clinicians as all course costs will be met by The Wellcome Trust. Commercial applicants should contact us for the commercial course fee.
Bursaries
Bursaries are available for clinical and academic applicants to cover travel, accommodation and sustenance costs and are subject to open competition.
Deadlines
Now closed for applications.