WCS ACORN - Bioinformatics for Antimicrobial Resistance - Virtual

21 May–6 June 2024

Virtual across Africa and Asia

Course Summary

Antimicrobial resistance (AMR) is critical to monitor as it threatens modern medical and public health systems. The Clinically Oriented antimicrobial Resistance Network (ACORN) project is developing an effective AMR surveillance system across nine African and Asian countries.

This course aims to train ACORN team members across nine centres with core bioinformatics skills which can be utilised to analyse and identify resistance from pathogen genome data.

This course is virtual and will run twice a week from 21 May until 6 June 2024


Course Content

This virtual bioinformatics course will offer a series of lectures and practical sessions including the following topics:

  • Pathogen genome assembly
  • Annotation of pathogen genomes
  • Phylogenetics in clinical contexts

Learning Outcomes

At the end of this course, participants will be able to:

  • Apply appropriate tools to analyse WGS data of bacterial genomes
  • Identify sequencing data formats
  • Use pathogen genomic analysis web-tools to process sequence data
  • Execute the basic processes of genome assembly for pathogen species
  • Identify and interrogate antibiotic resistance genes and mutations
  • Implement data workflows and bioinformatic analysis of genomic sequence data, including risk and resistance prediction for bacterial epidemiology and pandemic response
  • Conduct phylogenetic analysis in the context of outbreak and other epidemiological investigations
  • Compare phylogenetic trees for different species and outbreak scenarios


Training Team

Tung Trinh
Oxford University Clinical Research Unit Vietnam

Patrick Musicha 
Sanger Institute, UK

Julio Diaz 

Arun Decano 
University of Oxford, UK

Rito Mikhari 
National Institute for Communicable Diseases, South Africa

Collins Kigen 
Kenya Medical Research Institute

Buhle Ntozini
National Institute for Communicable Diseases, South Africa


Tung Trinh
Oxford University Clinical Research Unit Vietnam

Jorge Batista da Rocha
Wellcome Connecting Science

Vaishnavi Vikas Gangadhar
Wellcome Connecting Science

Isabela Malta
Wellcome Connecting Science

Martin Aslett
Wellcome Connecting Science

Alice Matimba
Wellcome Connecting Science

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