Train the Trainer: Capacity building for genomic surveillance of AMR in low- and middle-income countries

In collaboration with the NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance (Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, UK), we are pleased to announce this new course Train the Trainer: Capacity building for genomic surveillance of AMR in Low and Middle Income Countries

The increasing prevalence of antimicrobial resistance threatens healthcare at every level and is now a major international threat to public health. Training and capacity building in whole genome sequencing (WGS) and its interpretation (bioinformatics) to provide rapid detection and assessment of newly emerging antibiotic resistant bacteria in low- and middle-income countries (LMICs) is crucial; as is equipping regional public health scientists and programmes with the tools and techniques to be able to transfer these skills within their own countries.

This new train-the-trainer course aims to develop a cohort of instructors that can deliver onward training in the use of genomic technologies for the surveillance of AMR. Trainers will be equipped with the skill sets to establish and build capacity in:

1. Laboratory workflows – AST testing and DNA extraction for genomic sequencing
2. Data flow and bioinformatic analyses for sequence data, including resistance prediction and linking epidemiological data (outbreak analyses and global context)
3. Quality Assurance – internal and external testing for both laboratory and bioinformatics

The course is designed around surveillance of the current WHO bug-drug priority pathogens for the development of new antibiotics. Participants will enhance their current skill sets with teaching methodologies to train others and to enable the establishment of capacity and expertise in their own laboratory settings.This will be achieved through a combination of specialised, hands-on training along with pedagogical theory to enable participants to effectively teach these skills to a mixed audience (e.g. lab-based, epidemiologists, computer scientists, etc.) as part of either new or existing genomic surveillance programmes in their home countries.

Target audience
The course is aimed at bioinformaticians and laboratory scientists based in national, regional and local laboratories and regional surveillance centres in LMICs. Applicants should have existing experience of WGS laboratory techniques or WGS data analysis methods, together with a strong interest in, and opportunities for, training others in these skills.

There is no course fee and limited bursaries are available to cover travel expenses. All accommodation and meals will be provided free of charge at the Wellcome Genome Campus for the duration of the course.

The course programme will combine parallel sessions (laboratory-based WGS or bioinformatics) with joint sessions in training and learning methodologies. Topics will include:

Assembling a WGS laboratory for surveillance (parallel sessions for laboratory scientists)

1. How to communicate genome sequencing to a mixed audience

• A brief history of sequencing
• The value of communicating a public health case for genome sequencing

2. Building a genomics lab for surveillance of infectious disease from the ground up, and transferring this knowledge to new facilities:

• Planning a long-term blueprint
• Identifying and building an optimal lab technology suite
• Constructing a robust lab process
• Scaling operations and long-term sustainability

Bioinformatics (parallel sessions for bioinformaticians):

• How to communicate genome sequencing to a mixed audience
• Implementation of bioinformatics pipelines for producing and analysing whole genome data for the purpose of surveillance of AMR
• Transferring bioinformatics knowledge and skills to a novice audience

Interpretation of WGS data (joint sessions for all participants):

• Interpretation of examples of genomic data at different geographical scales

Training and learning methodologies (joint sessions for all participants):

• Education and training practice
• Training others in Bioinformatics and lab practices

Learning outcomes
After attending the course, participants will be able to:

• Identify and apply effective methods for training others in bioinformatics and laboratory techniques required for genomic surveillance of AMR
• Describe the components involved in the setup of a new genomic surveillance lab for AMR
• Explain the building blocks of genomic surveillance of AMR to local public health scientists including microbiologists and bioinformaticians
• Demonstrate how to implement laboratory and bioinformatics procedures for producing and analysing whole genome data for the purpose of surveillance of AMR
• Interpret examples of genomic data at different geographical scales
• Recognise the importance of genomic surveillance of AMR at a local, national, and international level

Course instructors

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

Pamela Black
Education Lead, Welcome Genome Campus Advanced Courses, UK

Anthony Underwood
Wellcome Sanger Institute and Centre for Genomic Pathogen Surveillance, UK

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

Mihir Kekre
Wellcome Sanger Institute and Centre for Genomic Pathogen Surveillance, UK

Monica Abrudan
Wellcome Sanger Institute and Centre for Genomic Pathogen Surveillance, UK

Harry Harste
Wellcome Sanger Institute and Centre for Genomic Pathogen Surveillance, UK

Matthew Holden
University of St Andrews, UK

Prerequisites
Applicants should be bioinformaticians or laboratory scientists based in national, regional and local laboratories and regional surveillance centres in LMICs. Applicants should have existing experience of WGS laboratory techniques or WGS data analysis methods, together with a strong interest in, and opportunities for, training others in these skills.

How to Apply
Please click on the Apply button above to begin the application process. 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.

Travel visas
Successful applicants will be provided with a support letter for their visa application, if required.

Please visit the following websites for further information on visiting the UK:

• UK Border Agency website
• Information for general visitors and business visitors

Cost
The course is subsidised by Wellcome Genome Campus Advanced Courses and Scientific Conferences in collaboration with the NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistanceand and is free to attend.

All accommodation and meals will be provided free of charge at the Wellcome Genome Campus for the duration of the course.

Travel bursaries
Limited travel bursaries are available and are awarded on merit. If you would like to apply for a bursary, please complete the bursary section of the online 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.

Additional funding opportunities
Visit our support page for additional financial support currently available.

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