Genomics and Epidemiological Surveillance of Bacterial Pathogens (Latin America) (Virtual)

25–29 October 2021

Virtual Course

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


PLEASE NOTE: Due to the ongoing Covid-19 pandemic we are no longer able to safely offer this course in a face-to-face format.

We are currently exploring options to deliver the course virtually. Participants will be notified of any changes to the course format shortly.

In collaboration with the Central Laboratory of Public Health, Ministry of Health and the Faculty of Exact and Natural Sciences of the National University of Asunción, Paraguay, we are pleased to announce our latest overseas course in Genomics and Epidemiological Surveillance of Bacterial Pathogens.

This course aims to provide training in the skills required to generate and interpret next generation sequencing data in a public health setting. This year’s course will have a strong emphasis on AMR and pathogens endemic to Latin America, whilst also training participants in the latest laboratory and computational methods for next generation sequence analysis and genomic surveillance.

Course background
This is a focused course that was established in 2013 to build strong links between traditional methods of epidemiological surveillance, modern molecular typing methods and those based on genomics. Although the course is built around genomic surveillance the focus of this course is designed to reflect regional public health priorities, and this year’s course will have a strong emphasis on infections endemic to Latin America. World-wide over the last few years the surveillance community has been 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 debate has now been resolved and 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. 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 that genomic datasets are growing day by day and they offer the context against which to understand local patterns of disease. Secondly these studies also highlight the power gained from public health scientists and academic research scientists working together to better understand infectious disease. 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/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 traditional and molecular typing methods -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:
Laboratory-based practicals: Molecular Sub-typing techniques:

  • Generating Next Generation Sequencing data using Illumina and Nanopore technologies.

Computational practicals: Informatics and Surveillance

  • Practical bioinformatics skills needed to manipulate raw sequence data (some of which will be generated on the course), including: mapping and de novo assemblies, SNP calling, annotation and analysis of genomic information
  • Sequence analysis and comparative genomics of next generation sequencing data using Artemis and ACT
  • 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:

  • Recognize the principles next generation sequencing and how to apply them effectively
  • Sequence genomic bacterial DNA using short- and long-read methods
  • Use sequence analysis tools effectively
  • Explain what a phylogenetic tree is and what it represents
  • Formulate projects using the global surveillance platform Microreact
  • Perform comparative genomics on multiple genome sequences
  • Compare different traditional bacteriological identification methods with modern molecular typing methods and genomics in the context of local and regional resources
  • Explain, using examples, how bacterial pathogens and AMR spread among human populations.

Instructors and speakers

Lead instructors/organisers

Josefina Campos
INEI ANLIS “Dr. Carlos G. Malbrán, Argentina

Matt Holden
University of St Andrews, Scotland

Natalie Weiler Gustafson
Central Laboratory of Public Health Asunción, Paraguay

Course instructors

Silvia Argimon
Wellcome Sanger Institute and Centre for Genomic Pathogen Surveillance, UK

Mathew Beale
Wellcome Sanger Institute, UK

Matthew Dorman
Wellcome Sanger Institute, UK

Caterina Guzman Verri
PIET, Veterinary School, Universidad Nacional, Costa Rica

Nick Thomson
Wellcome Sanger Institute, UK

Maria Veronica Orrego
Central Laboratory of Public Health Asunción, Paraguay

How to apply

Applicants should be clinical/public health molecular biologists or microbiologists working in Latin America and the Caribbean. Applicants should also have training in standard microbiology lab techniques (pipetting, handling of biological samples, etc.).

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

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.


The course is subsidised by Wellcome Genome Campus Advanced Courses and Scientific Conferences and is free to attend for non-commercial applicants. Please contact us for the commercial fee.

A limited number of bursaries are available for each course. These are awarded on merit to cover travel, accommodation and sustenance. The maximum award for travel (economy class) will be £750. 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.


Feedback from the 2019 course:

“The instructors are the soul of the course. You can feel all the work behind the organization and they were very accesible to any questions that we have. I´m very impressed about their professionalism and charisma”.

“Excellent course! Excellent instructors! The organization was great too. The best part was the conceptualization of the course, giving time for networking, discussions, and learning how to teach and work in groups, was amazing! I am thankful for the opportunity to participate in this course”.

“The best aspect of the course was to be able to carry out the complete process of sequencing, from the DNA to the analysis and interpretation of results”.

“Thank you for this wonderful opportunity The professors and course assistants were kind and gave us a great experience. I learned in a week the equivalent of months of training in different courses”.

“The course covered my expectations, I want to thank everyone for the work of all the instructors and assistants”.

Back to top Back to top