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Genomics and Epidemiological Surveillance of Bacterial Pathogens

17–22 April 2016

Administracion Nacional De Laboratorios E Institutos De Salud Dr. Carlos G. Malbran, Buenos Aires, Argentina

Application deadline: 20 November 2015

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. 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 (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
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

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)
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)

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).

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 are available for clinical and academic applicants to cover travel, accommodation and sustenance costs and are subject to open competition. Bursaries can be applied for as part of the application process.

Application forms for this course can be completed online. 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: 20 November 2015

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