Categories: Sanger Science3 April 20236 min read

African researchers training to develop large-scale genomics projects

Caroline Tigoi has had a passion for biology from a young age. She grew up in Kenya, where she pursued a science degree in microbiology after finishing school, completed masters’ degrees in virology and project management, and took the first steps in her professional science career.

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In 2016 she joined the Childhood Acute Illness and Nutrition Network (CHAIN), based at KEMRI Wellcome Trust in Nairobi. CHAIN’s mission is to identify the biological mechanisms and socio-economic factors that determine a child’s risk of mortality. A big part of this involves following young children for six months after hospitalisation for acute illness to try to determine what biological and social factors underpin high rates of mortality. As Laboratory Lead for CHAIN, Caroline’s role was to coordinate sample collection and storage across nine international sites, as well as standardising laboratory procedures across the Network. In April 2021, Caroline won a competitive DPhil. scholarship at the Nuffield Department of Clinical Medicine, University of Oxford, which she currently pursuing.

It was via CHAIN that Caroline met Sanger Faculty, Trevor Lawley, who is now supervising her doctoral research together with Prof. Jay Berkley (KEMRI Kenya) and Dr. Nicole Stoesser (Oxford University) on carriage and acquisition of antimicrobial resistance (AMR) in gram-negative bacteria such as Escherichia coli among vulnerable children in Kenya. Caroline is also on the organising committee for a microbiome retreat funded by Wellcome Connecting Science and the Gates Foundation to be held later in April on the Wellcome Genome Campus. This invitation only event is bringing together 40 experts from 22 countries to identify ways to increase microbiome research in children in low- and middle-income countries.

“In Kenya, as in many countries around the world, antimicrobial resistance is a serious and growing public health problem. There hasn’t been a lot of research into the bacterial genes responsible for AMR in Kenya and this is something I wanted to change,” said Caroline. “But understanding what is driving AMR is difficult without genome sequencing. We see a lot of outbreaks and transmission within hospitals, but we’re not yet sure whether this is this is acquired from the hospital environment, other sick patients or whether it is linked to the use of antibiotics during hospitalisation. This is one of the key questions I hope to answer in my doctoral research.”

“I’m so grateful for the opportunity to study at Sanger and Oxford University. It has been a steep learning curve, trying to master everything from whole genome sequencing to bioinformatics, but the training here at Sanger with Dr. Lawley’s team has been really good and will allow me to work independently back in Kenya. My aim is to continue using genomics to study infectious diseases and, hopefully in a few years, set up a research group of my own.”

Bonface Gichuki has also been interested in science since he was a child, an interest that has seen him carve his own path and become the first person in his family to attend university, where he graduated with a degree in Biochemistry in 2018. He went on to win a Wellcome International Masters fellowship in 2020 where he worked with Dr. Alan Walker  at the University of Aberdeen and graduated as the best student in 2022. He is currently working within Dr. Lawley’s lab studying the gut microbiome of children readmitted to hospital in Africa and South Asia and recently secured a place on the joint Sanger/University of Cambridge 4-year PhD Programme.

Like Caroline, Bonface had also previously worked with CHAIN and connected with Trevor Lawley through a shared interest in gut microbiomes of children in Africa and South Asia.

“One of the challenges for researchers in Africa is access, whether this is to collaborators, expertise, funding or even the supplies required to conduct sequencing projects. Collaborations like CHAIN are a really important catalyst for genomic research in Africa.”

Though Kenya is advanced in terms of sequencing compared to some African nations, Bonface says there are still barriers to running genomic research projects independently. “We’re lucky in that we can generate genomic data in Kenya, but we do need to develop our expertise in analysing that data so that it can be applied to public health problems. Having the opportunity to study and train at Sanger is perfect because here I can learn everything that I need to be able to run genomics projects back in Kenya, from sample collection to bioinformatics. Every stage of the genome sequencing pipeline is covered.”

Bonface’s ambition is to one day start his own research group, applying the knowledge he has gained at Sanger to areas such as the microbiome, nutrition, immune development and infectious diseases.

“I think you need to take a holistic approach to these health issues, because they are connected. We’re beginning to understand how the microbiome affects everything, from how severe an illness is to how well humans absorb nutrients. Intervention is also a big focus for me. I want to be able to put the knowledge we acquire to good use, we need to translate research findings into improved outcomes for patients – particularly for children.”

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