SEQAFRICA Whole Genome Sequencing services​

In SEQAFRICA we provide Whole Genome Sequencing (WGS) services of your isolates as well as the added option of bioinformatic analysis.

Target pathogens​

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. Isolates as part of Fleming Fund Fellowship projects, Fleming Fund Country Grants 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.

Please note that the list of mentioned pathogens is not exhaustive, so if you are in doubt as to wether your isolates are within SEQAFRICAs scope, contact us!

How to apply for sequencing?

To apply for sequencing, please download, fill out, and send the application form to your regional sequencing centre​. In general you should use the sequencing centre closest to you, but there might be cases where a different sequencing centre is more appropriate. If you are unsure please contact project managers Pernille Nilsson and Natasia Thornval.

For Westerns Africa please use application forms for either the sequencing centre based at

  • The University of Ibadan (UI) or
  • The Noguchi Memorial Institute for Medical Research (NMIMR)

For Eastern​ Africa please use the application form for the sequencing centre based at the Kilimanjaro Clinical Research Institute (KCRI).

For Southern Africa please use the application forms for one of the centres based at the National Institute for Communicable Diseases (NICD):

  • ​Centre for Enteric Diseases (CED) - for enteric bacteria such as Salmonella, Shigella, Campylobacter, Listeria and E.coli.
  • Centre for Respiratory Diseases and Meningitis - for respiratory pathogens such as Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis and Group A and B streptococcus.


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Technical University of Denmark, National Food Institute

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