Whole genome sequencing (WGS) technology is currently revolutionizing genetic research all over the world. However, low-income countries in Africa are still lagging behind even though the current advances suit their unique needs more than ever before. Through Next generation sequencing (NGS), genomic research has been fundamentally transformed and the continually emerging new developments are significantly reducing the cost of sequencing to affordable levels. For clinical microbiology applications, the NGS technology is beginning to show extreme potential for ultra-fast and accurate molecular typing and diagnosis. The combination of low cost and rapid turnaround time offered by the current and the emerging desk-top sequencers, makes pathogen WGS the key to accurate diagnostic tool and the ultimate epidemiological typing method with the digital, portable, and universally applicable capabilities. Compared to the current diagnostic methods, microbial clinical sequencing is by far more informative and capable of distinguishing very closely related strains. Furthermore, microbial genome sequencing is transforming our understanding of the evolution of pathogen virulence factors and the molecular basis that leads to the development and spread of antimicrobial resistance.
Given the complex nature of microbial infection is Sub-Saharan Africa (SSA) where cases of multiple pathogen infection are common, a universal diagnostic approach offered by whole genome sequencing in the context of metagenomics approach, provides the most effective solution to accurate diagnosis and pathogen typing. Setting a genomic pathogen diagnostic and epidemiology platform in SSA will help: 1) develop methods for epidemiological typing to define transmission pathways and support outbreak investigations; 2) develop methods for drug susceptibility testing using known markers for antibiotic resistance especially for slow-growing bacteria such M. tuberculosis complex and also for viral genotyping; 3) develop local resources for capacity building in genomics that will enable Africans to contribute to the global genomics research arena. For the countries in SSA to benefit from the current genomic revolution, there is a need to strengthen research capacity, training, and collaborations that will enable the continent to contribute fully to global health improvement. Although SSA is still poorly resourced in terms of healthcare funding, the universality of pathogen sequencing, means that a single sequencing machine can offer a wider diagnostic repertoire bridging the gap left by the different generic diagnostic methods. Thus, improve efficiency, accuracy and cost reduction. As both research and a clinical tool, WGS platform is valuable in providing genomic information of known and unknown pathogens upon which individual pathogen-specific diagnostic tools can be developed that is sensitive and compatible with the local strains and genotypes.