Microbes & Pathogens

pathogen and microbes

Pathogen richness and prevalence vary dramatically among geographic regions in the world. Africa is the region that has the highest number of human, animal and plant pathogens and microbes. The reasons for this are unclear and are probably caused by a multitude of factors. For example, Africa has suffered and still suffer from low spending on disease control. Poverty and basic sanitation remain a problem. The disease prevalence of pathogens may also be elevated because of enhanced susceptibility owing to the high incidence of human immunodeficiency virus (HIV) or the presence of a greater number of more closely related primates. In spite of the high burden of disease, Africa still lacks genomic facilities that are commonly used around the world to characterise the spread of pathogens, identify better treatments and derive public health interventions.

Genomics Africa is a not-for-profit initiative that makes genomic technologies affordable in Africa to better characterize pathogens. Some of the technologies available that we can use to sequence microbes include:

Long-read technology: PACBIO and Oxford Nanopore Technology 

Short-read technology: BGISEQ, Illumina (Hiseq, NextSeq, Miseq), TFS S5 (S5Ion, S5Prime)

Sanger technology: ABI3730xl (96 capillaries, see Sanger promotion at KRISP), ABI3500xl, ABI3500

Genomics Africa has worked with key collaborators and industrial players to decrease the cost of pathogen sequencing in Africa. Our technology, turn-around time and price are now internationally competitive. For example: 

  • HIV-1 drug resistance testing (TFS/CDC protocol) – $55
  • Bacterial 16S sequencing (Illumina) – $67
  • HIV-1 whole genomes (Illumina) – $135 
  • TB whole genomes (Illumina) – $220

In addition to the previously mentioned pathogens, we have also protocols to sequence many other viruses (e.g. Hepatitis A, B and C, Chikungunya, Dengue, Yellow Fever Virus, etc.) and bacteria (e.g. Listeria monocytogenes, Chlamydia, Gonorrhoea, E-coli, Syphilis, etc.). If a pathogen is not known, We have metagenomics protocols running on Illumina and Nanopre sequencers and qPCR pathogen panels for Sexually Transmitted Infections (STI) (12 pathogens), Gastrointestinal infections (38 pathogens) and Respiratory infections (34 pathogens).

Researchers, clinicians and public health officials can already use our affordable DNA sequencing services. They can also contact us for help to design/fund research projects such as the ones that have already been funded by the NIH in Botswana, Kenya and South Africa. In addition, Genomics Africa and KRISP have a professional grants management unit that can help collaborators to write competitive grant applications. We would also like to encourage funders, companies and philanthropists to adopt a genomics pathogen project in Africa such as the rapid, reliable and cost effective HIV-1 drug resistance testing that was funded by KRISP and Thermo Fisher Scientific.

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