A novel international research initiative born out of Biomaker

Rarely does the opportunity arise to translate academic research to positively influence policy and capacity in a developing country. To this end, we developed the UK-Kenya Phytoplasma Research Initiative with the aim of building local capacity in East-Central Africa to mitigate the risks imposed by emerging and re-emerging phytoplasma-associated crop diseases.

Through a successful OpenPlant-Biomaker Challenge bid, we conceived the initiative and built the partnerships required to impact local Kenyan communities while contributing to international research.

[left] Partners of the UK-Kenya Phytoplasma Research Initiative. From left: James Canham (Postgraduate student, John Innes Centre, Norwich, UK), Florence Munguti (Officer-in-charge, KEPHIS, Nairobi, Kenya), Dr Isaac Macharia (Managing Director, KEPHIS, Nairobi, Kenya), Dr Rose Kigathi (Research Scientist, Pwani
University, Kilifi, Kenya). [Top/bottom right] KEPHIS station in Muguga, Kenya.

The Kenya Plant Health Inspectorate Service (KEPHIS) is a government parastatal under the Ministry of Agriculture, Livestock, Fisheries and Irrigation (MoAFI) and the National Plant Protection Organization (NPPO) of Kenya. During a BBSRC PIPs placement at Pwani University, Kenya, I met with officials from KEPHIS as a part of a nationwide exploration of plant health-related research.

During these meetings, KEPHIS staff described several threats they were monitoring, one of
which appeared to be phytoplasma-related. Given that several colleagues in my lab at the John Innes Centre (Hogenhout lab; https://www.jic.ac.uk/people/saskia-hogenhout/) work on phytoplasma, I was aware of associated diseases and our capacity to study this plant pathogen and hence the Phytoplasma Research Initiative was born.

“Our aim is to establish rapid diagnostic and surveillance tools, expertise and capacity and influence agricultural policy based on our findings. We are optimistic that the initiative will enable us to achieve our aim and help address the challenges of emerging pests”.

- Dr Isaac Macharia, Managing Director, KEPHIS

Along with the Pwani University Bioscience laboratory (PUBReC) staff, we identified the OpenPlant-Biomaker Challenge as an excellent platform to help kick-start the initiative and attract more expertise. We recruited researchers at EBI, Cambridge and Cambridge University as well as an entomologist based at the Museum of Wales and research staff at CIRAD, France. With this team, we believe we are very well placed to build the technical capacity required to help local researchers and stakeholders.

KEPHIS staff surveying agricultural and pastoral land in Kenya to assess the occurrence of plant pathogenic phytoplasma.

What has been achieved so far?

Once the partnership was in place, we moved ahead designing and testing workflows. The PUBReC staff and KEPHIS team started to survey crops with disease symptoms along the breadth of the Kenyan coastline. Samples were transported to PUBReC where Prof. Santie de Villiers and her staff would process them.

In order to build long term capacity and impact, Pwani University used the initiative to develop an MSc. project and two undergraduate studentship projects. To support these students, we provided the Kenya-based staff with reagents to perform gold-standard, PCR-based characterisation of isolates as well as share our experience of sample collection, storage and processing. Additionally, we recently won an internal JIC grant that will fully fund a Kenyan PhD student for 9 months to visit the JIC labs to study the molecular basis of phytoplasma-host plant interactions.

Newly recruited students, John and Hesbon working on projects within the initiative at Pwani University, Kilifi, Kenya.

We have discovered that current diagnostic tools may lead to misidentification of the pathogens and are in the process of re-tooling and optimizing protocols to ensure more accurate characterisation going forward.   

What is next for the project?

All partners are now working toward generating whole-genome sequence data which will allow us to further understand how distinct phytoplasma isolates colonise their plant and insect hosts.

Whilst mitigating actions, resulting from our positive identifications may require a hammer, we hope that with a greater understanding of the pathogen, in future, a chisel will suffice.

We have big plans for the initiative, including several grant applications that will allow us to move the project forward. We are deeply grateful to the OpenPlant-Biomaker Challenge for the platform that allowed us to form effective partnerships and promote our project to a broad, interdisciplinary audience.

Watch this space! 

James Canham (PhD student, John innes Centre)