Whole Genome Sequencing services
SeqAfrica provides Whole Genome Sequencing (WGS) 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. Pathogens from the WHO GLASS and FAO priority pathogens lists will have precedence*. Isolates for 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 for sequencing. Minor pathogen collections with an atypical antimicrobial resistance profile, as well as V. cholera will be considered.
* WHO GLASS priority pathogens include Acinetobacter spp., E. coli, Klebsiella pneumoniae, Neisseria gonorrhoeae, Salmonella spp., Shigella spp., Staphylococcus aureus and Streptococcus pneumoniae. More information can be found here.
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.
Sample shipping guidance
This guide describes sample preparations and shipping guidelines for clients receiving Whole Genome Sequencing services by SeqAfrica. It covers recommendations and guidance on shipping bacterial isolates or extracted DNA to the sequencing centres for short-read sequencing.
