Dr Sam Kariuki

Studying drug-resistant pathogens of pandemic potential in One Health

When most people in the global north fall ill with what is often referred to as ‘a stomach bug’ they feel rotten for a few days but quickly return to health without requiring antibiotic treatment. This is not the case in many parts of sub-Saharan Africa, including Kenya, where a bout of something like non-typhoidal Salmonella can be fatal, especially among young children. The question that challenged the young Sam Kariuki was why this was the case – was there something different about the food-borne diseases in Kenya?

This fascination with diseases and how they are transmitted and treated has been a life’s work for Sam Kariuki – a very successful life’s work which has led to him being awarded an honorary degree by LSTM. He came to epidemiology by way of a degree in Veterinary Medicine and a master’s in Pharmacology and Toxicology, both from the University of Nairobi. Early plans to study human medicine were abandoned with the realisation that, “I never like to work at night, and in veterinary medicine nobody would wake me up to go and do clinical duties at night!” Plans to become a vet also disappeared with the realisation that he really wanted to focus on research.

This early exposure to both human and animal medicine gave rise to an understanding in Sam that the two were inextricably linked and fuelled a curiosity to explore that connection. This was at a time when the concept of One Health (the recognition that the health of humans, animals, plants, and the wider environment are interdependent) was not widely held.

He was also driven by a desire to understand how medicines work, what is happening when they do not work, and how we can intervene. His interest in antimicrobial resistance (AMR) - when the organisms that cause infection evolve ways to survive antibiotic treatments – was also born. It is an area of study that has been brought into sharp focus by COVID-19:

“Probably the scariest things facing us are diseases emanating from the animals we interact with. In my institution [KEMRI] we have put an emphasis on pathogen discovery… to be able to detect early and understand the pathogens of pandemic potential. All of this must come from our understanding of how humans, animals and the environment interact.”

Academic success

After securing a post at the Centre for Microbiology Research at KEMRI (Kenya Medical Research Institute) Sam worked with a team looking at AMR and secondary infections in HIV. After three years he had impressed his supervisor enough to receive a call to follow him to LSTM to undertake a PhD.

 And so began a relationship which benefitted – and continues to benefit - both parties but which has had an even greater impact on the people of Kenya and surrounding region.

 Throughout his academic career, Sam has been fascinated by technology and its potential to help tackle certain diseases, particularly those he saw at home in Kenya. He says of his PhD studies:

 “I really wanted to work towards understanding how enteric bacteria, especially salmonella, were causing such severe disease in young children [in Kenya and the region] yet in the western world they were just causing self-limiting diarrhoeal disease.”

His work to address this question - utilising PCR technology and whole genome sequencing - revealed that Kenya was actually dealing with a very specific strain of salmonella typhimurium (ST313) that was different from that which causes disease in developed countries. His paper was published in the Journal of Medical Microbiology and through that study Sam was awarded the Pfizer Award for the Best African Scientist of the Year in 2012. It was the first of many awards and accolades.

Around this time Sam was also successful in securing funding from the Wellcome Trust for a post-doctoral fellowship on invasive non-typhoidal salmonellosis, which is endemic in sub-Saharan Africa. Sam hypothesised that person-to-person, rather than zoonotic transmission (from animals), was playing a major role in the disease’s transmission and, despite scepticism from some scientists, this has proven to be correct.

Since then, his work and reputation have blossomed. Sam has researched and published extensively on the epidemiology and genomics of AMR and the surveillance of food-borne enteric pathogens. This work has contributed extensively to policy change in the treatment and management of those infections and in understanding AMR. His work has undoubtedly helped prevent much illness and saved many lives.

Today, Sam is the Director of Research and Development and Acting Director General at KEMRI, a Fellow of the African Academy of Sciences, an honorary faculty member at the Wellcome Sanger Institute, and a visiting Professor of Tropical Microbiology at the University of Oxford. He is also a World Health Organization consultant providing technical advice around food safety, AMR and infectious disease surveillance.

Mentoring the next generation

Despite these accolades and titles, Sam remains committed to the science and to the young scientists in his charge. He says:

“My motivation was always my desire to be able to mentor young people and to be able to form a core group of scientists that research on antimicrobial resistance and enteric diseases epidemiology... It inspires me that they will probably become a mentor to someone else, and we'll be able to build that critical mass of scientists and really help the country realise its potential in research, but also be a resource for the region.”

Over the years, many students and junior staff having passed through his lab at KEMRI; a facility that the World Health Organization recognises as a centre of excellence. Almost all have gone on to join institutions, either in Kenya or abroad, where they are carrying the scientific baton.

An enduring relationship

 Sam’s time as a PhD student at LSTM was one which he recognises as providing the foundations for his future success:

“That was the beginning of my post-doctoral and research career journey – the genesis of me being more independent in my research. I think my career pathway wouldn't have happened if I hadn’t had a proper grounding at my post-graduate level.”

It also proved to be just the beginning. Before leaving LSTM, Sam and LSTM mentor, the late Professor Tony Hart, secured funding to conduct what proved to be a highly-successful enteric diseases One Health programme in Kenya to better understand livestock and human interactions. That work continues today with funding from the UK Department of Health and is still building capacity in epidemiology and surveillance of AMR.

Looking to future collaborations with LSTM, Samuel hopes that some of the technologies and expertise developed at the School can be transferred to the field in Kenya, improving disease diagnostics, surveillance and management. He also has hopes for the young scientists in both institutions:

“We are looking towards the kind of collaboration where we host the students from LSTM and some of our students can spend time in Liverpool - that would really be enriching for our young scientists in terms of experience and outlook in a global sense.”

 And his advice for those young researchers?

 “If you get the opportunity then come into settings like ours and see field conditions as they are. Understand where diseases originate and how they get transmitted. You can never, ever learn that from books or from lectures. And that enrichment sticks with you forever and it keeps you motivated to be able to do the best research.”