Wellcome Connecting Science Course Run Website Link
Course Time Table
Course Informatics Guide
Implementing genomics is increasingly critical for effective surveillance of antimicrobial resistance (AMR), requiring the development of infrastructure and capacity through intensive training of scientists and healthcare staff.
A Clinically Oriented Antimicrobial Resistance Network (ACORN) is a Wellcome-funded, multi-country project aiming to establish clinical-based AMR surveillance in 15 sites across 9 African and Asian countries. The project focuses on bacteria that are highly prevalent as global AMR pathogens in both community- and hospital-acquired infections, including E. coli, K. pneumoniae, S. aureus, and Acinetobacter spp., the latter due to its rapid acquisition of multi-drug resistance mechanisms. Whole genome sequencing (WGS) offers a comprehensive and precise method for obtaining genetic data needed for accurate subtype classification, improved epidemiological investigations, and effective surveillance.
Building upon the hospital network and genomic infrastructure developed by the project partners, ACORN, in collaboration with Wellcome Connecting Science Learning and Training Programme, and the KEMRI Wellcome Trust Research Programme, introduces a week-long course covering genomics of AMR for bacterial pathogens. This course will include practical laboratory sessions using next-generation sequencing technologies, along with hands-on bioinformatics sessions for downstream data analysis for detecting resistance and identifying transmission patterns. Additionally, the course will dedicate time to capacity development strategies, considering existing and upcoming genomic implementation workflows, identifying gaps, and ensuring sustainability.
This course is strictly by invitation to ACORN members from the various sites of operation nominated for this training, as well as additional delegates from the host institute.
The course will cover the following topics:
The end-to-end pathway of the application of genomics in ACORN sites
- The importance of sampling and storage of isolates (hospital vs community acquired, drug-resistant vs susceptible), and its impact on genomic data
- The use of genomic analysis in outbreaks and AMR, using a real outbreak scenario
- Implementing whole genome sequencing for infection prevention and control
- Performing sequencing and analysis of sequence data for making clinical associations covering both Illumina short read sequencing and Oxford Nanopore long read sequencing.
- Genomic data analysis and quality control from short and long read assembly to detecting resistance
- Utilising tools developed by the Centre for Genomic Pathogen Surveillance (CPGS) such as Pathogen Watch, as well as other freely accessible tools for AMR analysis
- Analysis and visualisation through the generation of phylogenetic trees
- Clinical interpretation of genomic data and how to present results for different audience groups.
- Building genomics capacity for AMR with a specific focus on workflows and sustainability.
The programme will also include a mandatory introductory Linux pre-course module to be completed before the start of the course.
By the end of this course participants will be able to:
- Identify which sequencing techniques are suitable for their specific diagnostic application/laboratory
- Perform DNA extraction and sequencing protocols using both long and short read technologies
- Generate phylogenetic trees for AMR using the relevant data and software
- Analyse and interpret genomic data from clinical isolates for AMR surveillance
- Identify the next steps to incorporate genomic techniques for the continuation of site-specific ACORN projects
Course Instructors
- Trinh Son Tung, Oxford University Clinical Research Unit (OUCRU)
- Patrick Musicha ,Sanger Institute, UK
- Julio Diaz,CPGR, UK
- Anne Amulele,KEMRI Wellcome Trust Research Programme, Kenya
- Rogier Van Doorn,ACORN, Vietnam
- Paul Turner , ACORN, Cambodia
- Iruka Okeke, ACORN, Nigeria
- Arun Decano,University of Oxford, UK
- Rito Mikhari,National Institute for Communicable Diseases, South Africa
- Collins Kigen,Kenya Medical Research Institute
- Agilakumari Pragasam, OUCRU, Vietnam
- Stanford Kwenda, NICD, South Africa
Wellcome Connecting Science Team
- Jorge Batista da Rocha, Education Developer
- Cassandra Soo, Laboratory Courses Manager
- Aaron Dean, Laboratory Technical Officer
- Scarlett Storr, Events Organiser
- Isabela Malta, Assistant Overseas Courses Manager
- Martin Aslett, Informatics Manager
- Vaishnavi Vikas Gangadhar, Informatics Technical Officer
- Alice Matimba, Head of Training and Global Capacity
- Michelle Bishop, Associate Director
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
Take a look what courses are coming up at Wellcome Connecting Science Courses & Conference Website.
For more information or queries, feel free to contact us via the Wellcome Connecting Science website.
Find us on socials Wellcome Connecting Science Linktr