Genomics and Epidemiological Surveillance of Bacterial Pathogens (Lima, Peru)

3–8 March 2019

Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru

Learn how genomics is being applied to epidemiological surveillance and public health in Latin America.


In collaboration with the Faculty of Sciences and the ‘Alexander von Humboldt’ Institute for Tropical Medicine at the main UPCH campus in Lima, Peru, 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 Peru and 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.


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:

  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

Course instructors

Pablo Tsukayama
Universidad Peruana Cayetano Heredia, Peru

David Aanensen
Wellcome Sanger Institute and Centre for Genomic Pathogen Surveillance, UK

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

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

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

Matt Holden
University of St Andrews, UK

Nicholas Thomson
Wellcome Sanger Institute, UK

The course will also feature seminars from distinguished regional guest speakers.

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 complete the online application form. Places are limited and will be awarded on merit. If you have any problems with the online application process, please contact us.

Please note: 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 2017 course:

“I would like to congratulate the instructors team for the great work and effort they made to carry out the course, personally it was a very enriching experience in all aspects and a great opportunity to learn more about AMR and new technologies for the epidemiological surveillance that will undoubtedly will apply in our researchs, but above all, to interact with many experts from different countries and share points of view. Congratulations to everyone and thank you very much!”
“Excellent course, More than excellent teachers.”
“Thank you to the lecturers and organizers. This was a fantastic learning experience.”
“Participating in the course was a very valuable opportunity. All the learning I got in a week was greater than all the knowledge I had after years of courses in my country. Having contact with people from my continent and being able to develop a project together with the support of the Wellcome Trust Sanger Institute will be amazing. I just have to thank the organization and instructors for the great experience I had.”

Back to top Back to top