"To understand why bacteria behaves in a particular way, you need genomics..."
The human genome was fully sequenced for the first time nearly 20 years ago and has consequentially resulted in remarkable medical and scientific discoveries. Since 2003, whole genome sequencing (WGS) has been used to help stop the spread of infections, develop cures to rare diseases, support surveillance programmes and identify signs of genetic disease transmission.
Since 2019, the Fleming Fund has been investing in building sequencing capacity across Africa through a consortium of grantees including several African laboratories and academics at the Danish Technical University. The aim of the programme is to use sequencing to improve antimicrobial resistance (AMR) surveillance and to invest in training African scientists who can help spread sequencing technologies across the continent.
In brief, sequencing is done by extracting DNA from a cell and then identifying the unique pattern or sequence of the DNA strand’s four nucleic acids (cytosine [C], guanine [G], adenine [A] or thymine [T]); every organism’s pattern is different. The DNA sequence is then compared against a database of sequencing information, helping to determine the organism’s type, its resistance to treatments and other key characteristics.
Iruka Okeke, Professor at the University of Ibadan and member of the Fleming Fund sequencing consortium said “I’m really interested in microbiology and I really like bacteria. They look pretty and they do cool things. Typical microbiology techniques can help you understand what bacteria is doing, but if you wanted to understand why bacteria behaves in a particular way you need genomics.”
Typical microbiology techniques can help you understand what bacteria is doing, but if you wanted to understand why bacteria behaves in a particular way you need genomics.
Understanding bacterial behaviour is critical in surveillance and in making accurate epidemiological predictions. For example, identifying identical genomic sequences in pathogens from humans and animals is a sign there has been disease transmission between the two. Similarly, clusters of identical pathogens within a particular geographic area signal an outbreak.
Sequencing facilities in the consortium from Nigeria, Tanzania and South Africa are using genomics to identify AMR transmission patterns, and more recently, trace COVID-19 outbreaks. Rene Hendriksen, Professor and Researcher at the Danish Technical University says using genomics for current outbreaks (like COVID-19) demonstrates the real power of sequencing. “You can see if the continent has been infected with different clones [mutations of COVID-19] or the same clone and then track those to the point of entry.” Understanding the point of entry is the key to curbing the spread of disease.
Genomics for Public Health
Iruka hopes that demonstrating the power of genomics in predicting and controlling the spread of disease, will act as a catalyst to encourage other African countries to leverage sequencing at home. Support from the Fleming Fund will allow Iruka and her team to sequence isolates from across the continent and provide ministries of health with concrete examples of sequencing’s power and efficiency. “We hope [genomics will help] our public health agencies make better decisions around antimicrobial resistance, discover outbreaks sooner, understand where resistance is coming from and how it’s being transmitted,” she said.
We hope [genomics will help] our public health agencies make better decisions around antimicrobial resistance, discover outbreaks sooner, understand where resistance is coming from and how it’s being transmitted.
The grant is also supporting training and training of trainers within Nigeria, Tanzania and South Africa and beyond. For Iruka, who has lived, taught and studied across the US, UK and Nigeria, supporting and training African scientists is a one of the main reasons she is in Nigeria. “I returned to Nigeria because I wanted to provide excellent instruction in Nigeria. I studied here originally, and I’ve had excellent teachers over the years. I wanted to be that for my students."
“Since Fleming Fund has come along, we’ve been able to broaden the number of people we are training which is important for sustainability. When I was a graduate student it was difficult to get support to do research for surveillance. But now there is much more support – I’m so grateful that funders have taken an interest in building these capacities in Africa. Its enriching to my students and more importantly it’s giving us skills we need for the future so thank you.”