Genomics & Epidemiological Surveillance of Bacterial Pathogens - Latin America and the Caribbean

21–26 July 2024

San José, Costa Rica

Learn how to apply genomics to epidemiological surveillance of bacterial pathogens and public health in Latin America.


In collaboration with the Universidad Nacional and Universidad de Costa Rica, we are pleased to announce our latest overseas course in Genomics and Epidemiological Surveillance of Bacterial Pathogens.

This course will provide training in the latest computational methods for analysis and interpretation of high throughput genome sequence data in a public health setting. Although the course is built around genomic surveillance the focus of this course is designed to reflect regional public health priorities on bacterial pathogens, with a strong emphasis on infections endemic to Latin America.

Course background

Established in 2013, the course provides skills to combine epidemiological, metadata and genomics data analysis, hence contributing to generating the most reliable information available for public health decision making. In the last few years, the COVID-19 pandemic challenge accelerated the introduction of advances in genomics, sequencing technology and our ability to interpret high resolution sequence data for surveillance purposes. 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, contributing to reinforce a One Health approach. 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, genomic datasets are growing day by day and they offer the context against which to understand local patterns of disease. Secondly, these studies highlight the power gained from public health scientists and academic research scientists working together to better understand infectious diseases. 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.

Target audience

The course is targeted at clinical or public health molecular biologists and microbiologists working in Latin America and the Caribbean.

The course is free to attend for non-commercial applicants. Limited travel bursaries are also available.



This course builds upon previous versions, incorporating genomics and problem solving exercises with modules that demonstrate how epidemiological information and phenotyping – in combination with sequence data – can be used:

  1. 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
  2. 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 will include:

  • Practical bioinformatics skills needed to manipulate raw sequence data, including: mapping and de novo assemblies, SNP calling, annotation, antimicrobial resistance calling, and analysis of genomic information
  • 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:

  • Select and apply appropriate tools to analyse genome sequence data effectively
  • Perform comparative genomics on multiple genome sequences
  • Interpret phylogenetics to gain insights into pathogen evolution and epidemiology 
  • Formulate projects using the global surveillance platform Microreact and Epicollect
  • Explain, using examples, how bacterial pathogens and AMR spread among human populations.


Instructors and speakers

Lead instructors

Caterina Guzman Verri
Universidad Nacional, Costa Rica

Josefina Campos
World Health Organization, Switzerland

Matt Holden
University of St Andrews, Scotland


Mathew Beale
Wellcome Sanger Institute, UK

Julio Caballero
Centre for Genomic Pathogen Surveillance, University of Oxford, UK

Matthew Dorman
University of Galway, Ireland

Francisco Duarte-Martínez
INCIENSA, Costa Rica 

Jose Arturo Molina Mora
Universidad de Costa Rica, Costa Rica

María Sol Haim
National Center of Genomics & Bioinformatics - ANLIS-Malbran, Argentina

Tomás Poklepovich
National Center of Genomics & Bioinformatics - ANLIS-Malbran, Argentina

César Rodríguez
Universidad de Costa Rica, Costa Rica

Marcela Suarez
Universidad Nacional, Costa Rica


Alice Matimba
Wellcome Connecting Science

Isabela Malta
Wellcome Connecting Science

Nicola Stevens
Wellcome Connecting Science

Martin Aslett
Wellcome Connecting Science

How to apply

Applicants should be clinical/public health molecular biologists or microbiologists working in Latin America and the Caribbean.

Places are limited and the course will be held in English (with language support provided where necessary by Spanish- and Portuguese-speaking instructors).

*Please note: The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some familiarity with the Linux operating system. This will be essential for participants to fully benefit from the course. A free Introduction to Linux for Biologists online course will be provided free of charge for selected participants to equip them with essential bioinformatics skills for pathogen genomics.

How to Apply
Please click the Apply button above to begin the online application process. Places are limited and will be awarded on merit. If you have any problems with the online application process, please contact us.

Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g. supervisor, line manager 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.

Accommodation services phishing scam – please be vigilant. More information


The course is subsidised by Wellcome Connecting Science and is free to attend.

A limited number of bursaries are available for each course. These are awarded on merit to cover travel, accommodation and sustenance. If you would like to apply for a bursary, please complete the bursary section of the online application form.

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.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.

Accommodation services phishing scam – please be vigilant. More information.

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