AMR Bioinformatics - Africa (Virtual)

In collaboration with the National Institute of Communicable Diseases (NICD), South Africa , we are pleased to announce the AMR Bioinformatics course as part of the SAGESA network aimed at training and building capacity for genomic surveillance of AMR in Africa.

Antimicrobial resistance (AMR) is a global public health emergency and threatens the safe delivery of modern medical care. Global projections of the negative impact of AMR predict the loss of nearly 10 million lives and a cumulative loss of global production up to 100 trillion US dollars by 2050. AMR requires immediate, concerted, international, collaborative action to monitor its prevalence and spread throughout the world. The importance of this has been recognised both by the United Nations and by the World Health Organisation; the latter has published a list of priority pathogens and a global strategy for AMR surveillance.

The challenges of controlling AMR in low- and middle-income countries (LMICs) may be considerable for several reasons. Firstly, antibiotics may be available for human and animal use without a prescription, resulting in unregulated use. Secondly, accurate data on antimicrobial prescription or consumption may not be readily available. Thirdly, there may be limited knowledge about the appropriate use of antibiotics and a lack of antimicrobial policies or stewardship programmes. Finally, there may be limitations in healthcare facilities and laboratory capacity for the detection and management of AMR.

This 3-day workshop aims to address some of these challenges by improving the knowledge and skills of individuals interested in antimicrobial resistance in bacterial pathogens in Africa. It will contain hands-on WGS-based bacterial typing methods such as AMR detection, cgMLST, MLST, core genome SNP based phylogenetic analysis. 

Target audience

This workshop is free to attend and open to SAGESA network members based in Africa who are actively engaged in, or soon to commence, research, clinical practice, provision of clinical services, or policy development related to AMR in bacteria. To join the network please click on this link.

Learning outcomes:

• Implement data workflows and bioinformatic analysis of genomic sequence data, including risk and resistance prediction for bacterial epi and pandemic response
• Explain Genomic surveillance and linking epidemiological data, outbreak analyses and global contexts, geographical contexts
• Demonstrate interpretation and application in public health and epidemic/pandemic response

Content overview:

• Module themes
  • Genomic data analysis
  • Application – Interpretation for various uses
  • Training support mentorship and networking

Lead instructors/organisers

Stanford Kwenda
NICD, South Africa

Joconiah Chirenda
University of Zimbabwe, Zimbabwe

Instructors and Speakers

Annie Chan
NICD, South Africa

Arun Decano
St. Andrews University, UK

Erkison Odih
University of Ibadan, Nigeria

Lavania Joseph
NICD, South Africa

Michelle Lowe
NICD, South Africa

Narender Kumar
Wellcome Sanger Institute, UK

Pimlapas Leekitcharoenphon (Shinny) 
National Food Institute, Denmark

Sabelle Jallow
NICD, South Africa

Zamantungwa Khumalo
ClinVet, South Africa

This workshop is free to attend and open to SAGESA network members based in Africa who are actively engaged in, or soon to commence, research, clinical practice, provision of clinical services, or policy development related to AMR in bacteria.

Prerequisites

1. Familiarity with Linux command-line

There are numerous online introductory tutorials to the UNIX/Linux operating system and command line, including:

http://www.ee.surrey.ac.uk/Teaching/Unix

http://swcarpentry.github.io/shell-novice/

2. Should have some sequenced data or planning to do some bacterial WGS

How to Apply
Please click the Apply button above to begin the online application process. Places are limited and will be awarded on merit. If you have any problems with the online application process, please contact us.