Bacterial Genomic Surveillance - Ireland and Northern Ireland

In the last few years, the introduction of advances in genomics, sequencing technologies, and our ability to interpret high resolution sequencing data for surveillance purposes – both regionally and internationally – lead to a shift from the use of molecular typing data to using Whole Genome Sequencing (WGS) for epidemiological surveillance and public health investigations of infectious disease. In some settings WGS is now being used to define outbreaks and trace infection sources in humans, animals and the environment, contributing to One Health approaches and better prediction of antimicrobial resistance (AMR) phenotypes, for instance.

This course is built on a strong foundation, bringing together experts from both academic and public health organisations from different regions of the world. It highlights the synergy between research and infectious disease surveillance, and of international collaboration, providing a unique learning opportunity.

The programme will provide training in the latest computational methods for analysis and interpretation of high throughput genome sequencing 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. The skills developed in this course, combine epidemiological, metadata and genomics data analysis, hence contributing to generating the most reliable information available for public health decision making. 

What Will You Learn?

• How genomic data is revolutionising the tracking and understanding of bacterial pathogen spread, providing valuable context for local disease patterns.
• Examples of how genomics has been successfully applied to bacterial pathogen surveillance internationally, and the roles played by clinical, academic, and public health personnel in those examples. 
• The power of collaboration and insights from public health experts and academic researchers involved in advancing infectious disease control.
• The critical link between research and public health and how you can play a role in strengthening this connection.

Target audience

The course is targeted at clinical or public health molecular biologists and microbiologists working in Ireland and Northern Ireland who are actively engaged in, or soon to commence related research or work in bacterial pathogen genomics and epidemiology. 

What will you be able to do?

After attending the course, participants should be able to:

• Select and apply appropriate tools and workflows to analyse pathogen genome sequence data effectively.
• Perform comparative genomics across multiple genome sequences.
• Interpret phylogenetic trees and genomic clustering results to infer pathogen evolution, outbreak dynamics, and epidemiology links.
• Design and communicate genomic surveillance projects using global platforms for data collection and visualisation. 
• Explain, with real-world examples, how bacterial pathogens and AMR determinants spread within and between human populations.

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 to understand the fine detail of new and emerging infections. The content of the course also highlights how to identify risks to public health, and contribute to the management of infectious diseases, including the application of georeferencing (also known as ‘phylogeography’) where the location of disease causing strains are mapped with detailed genetic and phenotypic data (for example AMR patterns) to look for regional patterns of disease.

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 develop everyday skills required to work in genomic surveillance.
• Practical exercises for using GPS to map cases of infectious disease and phenotypes (such as AMR) locally, regionally, and across the world.

Computer Requirements

Selected participants will need to install software on their personal laptops before or during the course. Participants must ensure they have administrator rights to install software and access to a Google account.

For the practical sessions, participants are encouraged to bring a laptop with the following recommended specifications:

• Processor: Intel Core i5/i7 or equivalent
• Memory: Minimum 8 GB RAM (16 GB recommended)
• Storage: approximately 70 GB 
• Operating system: Windows 11 or a recent Windows version
• Software: Google Chrome or Mozilla Firefox, office software (e.g. Microsoft Office or equivalent), and Oracle Java

These specifications are recommended to ensure smooth participation in the practical exercises. Laptops with different configurations may present performance limitations or software compatibility issues which may reduce the benefit participants gain from some hands-on sessions.

Trainers

Caterina Guzman
Centro de Investigación Enfermedades Tropicales, Costa Rica

César Rodríguez
Centro de Investigación Enfermedades Tropicales, Costa Rica

Julio Diaz Caballero
Ellison Institute of Technology Oxford, United Kingdom

Marcela Suarez Esquivel
Universidad Nacional, Costa Rica

Matthew Dorman
Trinity College Dublin, Ireland

Sabrina Di Gregorio
Universidad de Buenos Aires, Argentina

Tomás Caride Poklepovich
Administración Nacional de Laboratorios e Institutos de Salud, Argentina

Wellcome Connecting Science

Liã Bárbara Arruda – Education developer

Lucy Esmond – Event logistics

Prerequisites

This course prioritises applicants currently based in Ireland and Northern Ireland.  Applicants should be postdoctoral scientists, PhD students, junior faculty members or clinicians/ healthcare professionals actively engaged in or soon to commence research involving the topics of the course.

How to Apply

1. Start your application 
   • Click on the “Apply” button above to start your application. Please note that places are limited and will be awarded based on merit.
2. Demonstrate the course’s relevance to your work
   
   • Our courses are in high demand. Please provide an outline of your work (research project(s) and/ or clinical/ healthcare activities). It is essential to clearly explain how the skills you will acquire from the course are directly relevant to your current role and beneficial to your work, research, or organisation. Preference will be given to applicants who have genomic sequence data to analyse.
3. Letter of recommendation
   • Applications must be supported by a letter of recommendation from a sponsor or professional referee such as supervisor, line manager, or head of department. The statement should be tailored to indicate their  support of your application and how the course could be of benefit. This statement must be uploaded as a PDF document to the online registration system by the application deadline. Applications without a supporting statement will not be considered.
4. Need Help?
   • If you have any questions or encounter any problems with the online application process, please contact us for assistance.

Course fee: 300.00 Euros

The fee will be requested once acceptance is confirmed.

Participants are responsible for arranging and covering their own travel and accommodation costs. Lunch and coffee breaks will be provided during the course. Breakfast and dinner are not included, and participants should make their own arrangements. The course organisers are unable to provide financial support for these expenses.

Bursaries

We are unable to provide bursaries for this course.