SEQAFRICA - Extending whole genome sequencing capacity for AMR Surveillance​

A consortium of sequencing centers

SEQAFRICA has established and currently support a consortium of three regional sequencing centers in:

  • Nigeria (University of Ibadan, UI)
  • Tanzania (Kilimanjaro Clinical Research Institute, KCRI)
  • South Africa (National Institute for Communicable Diseases, NICD)

as well as a national center:

  • Ghana (Noguchi Memorial Institute for Medical Research, NMIMR)

and a COVID-19 response center in:

  • South Africa (NICD Center for Respiratory Diseases and Meningitis (NICD-CRDM))

Bringing WGS into AMR surveillance​

SEQAFRICAs main objective is to develop, expand and support WGS and bioinformatics capacity for antimicrobial resistance (AMR) surveillance across Africa. In addition, we contribute to the global pandemic surveillance efforts of SARS-CoV-2.

Our centers provide WGS and analysis services to surrounding countries in West, East and Southern Africa and support investigations of outbreaks, unusual resistance phenotypes, and/or delineation of the flow of organisms/genes across human, animal, agricultural and aquaqulture sectors. Please find application forms for WGS further down this page.

Building capacity sustainably through training

Improving the surveillance of AMR in Africa does not only require building and expanding existing sequencing capacity through instrumentation, but also call for training in the use of equipment and acquiring necessary skills to analyze the generated data. In-depth training is instrumental to sustain activities beyond the timeframe of the project, and as such SEQAFRICA has developed extensive virtual training for a range of audiences going from novel and non-users to more experienced staff. Please find more information, details and resources for the training below.



(PDF document)​


Introduction to WGS in AMR surveillance

​This course is an introduction to Whole Genome Sequencing (WGS) and its use in AMR surveillance for those who would like to know more about why it is important and how can it can be incorporated.

Click below to read more and find resources for participants

Read more

WGS workflow - from isolate to analysis

​​This course is to be considered a continuation of Introduction to WGS in AMR. Here the entire workflow, from sampled isolate to finished analysis of sequencing data will be covered in lectures and hands-on exercises.

Click below to read more and find resources for participants.

Advanced bioinformatics for AMR surveillance.​

​​This course covers advanced bioinformatics for those who are already using WGS in AMR surveillance and would like to move from using online tools to command line tools to increase analysis throughput.

Click below to read more and find resources for participants

SARS-CoV-2 - whole genome sequencing

​​This course will specifically cover the entire workflow from a SARS-CoV-2 sample to finished analysis of sequencing data. It consists of lectures and hands-on exercises.

Click below to read more and find resources for participants.​

Sequencing service

In SEQAFRICA we provide WGS services of your isolates as well as bioinformatic analysis if desired. To apply for sequencing please download, fill out and send the application form to your regional or national sequencing center which can be found below. 

The primary targets of the project are bacterial isolates of high importance such as Pandrug Resistance (PDR) or Extensive Drug Resistance (XDR) strains, or strains related to an outbreak. Furthermore, isolates as part of Fleming Fund fellowship projects or other research projects, in which sequencing will facilitate an increased knowledge of antimicrobial resistance and circulating emerging clones will be considered. Finally, minor collections of already available nontyphoidal Salmonella and E.coli with an atypical antimicrobial resistance profile, as well as S. Typhi and V. cholera in general are considered.

Application for WGS at UI

(Word document)​​


Application for WGS at KCRI

(Word document)​​


Application for WGS at NICD

(Word document)​​


Application for WGS at NICD

(Word document)​​



Interim meeting


17-18th June 2021

​SEQAFRICA partners and stakeholder will be meeting virtually on the 17th and 18th of June to assess the advancement of the project, address and discuss needs, bottlenecks and challenges. Extensive discussions on sustainability will take place with participation and input from all partners and stakeholders.


Are you in need of more information or have questions, please contact Project Manager Pernille Nilsson or Technical Lead Rene S. Hendriksen.


SEQAFRICA is led by the Research Group for Global Capacity Building at the National Food Institute, Technical University of Denmark and is funded through a Regional Grant by The Fleming Fund. The Fleming Fund is a £265 million UK aid investment to tackle antimicrobial resistance in low- and middle-income countries around the world. The programme is managed by the UK Department of Health and Social Care, in partnership with Mott MacDonald, the Fleming Fund Grants Management Agent for the Country and Regional Grants and Fellowship Programme.


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