Whole Genome Sequencing services

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. Especially pathogens from the WHO GLASS and FAO priority pathogens lists will have precedence*. 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 pathogen collections with an atypical antimicrobial resistance profile, as well as V. cholera in general are considered.

* WHO GLASS priority pathogens include Acinetobacter spp., E. coli, Klebsiella pneumoniae, Neisseria gonorrhoeae, Salmonella spp., Shigella spp., Staphylococcus aureus and Streptococcus pneumoniae. FAO priority pathogens partially overlap with the GLASS priority pathogens but also include Campylobacter spp. and Enterococcus spp.

Please note that the list of mentioned pathogens is not exhaustive, so if you are in doubt as to whether your isolates are within SeqAfrica's scope don't hesitate to contact us!

How to apply for sequencing?

To apply for sequencing, please complete the survey in this link. Your application will be sent to the relevant regional sequencing centre and be reviewed and processed there. In general the relevant site will be the sequencing centre closest to you, but there might be cases where a different sequencing centre is more appropriate. If you have any questions please contact project managers Pernille Nilsson and Christa Twyford Gibson.