Uncovering the molecular epidemiology of Clostridioides difficile in Africa to guide treatment and inform vaccine efficacy

The overarching aims of this study are to assess the contribution of Clostridioides difficile to diarrhoeal disease burden in African and identify potential circulating hypervirulent strains to guide treatment and inform potential vaccine development in this region. C. difficile remains one of the top five multi-drug resistant pathogens considered to pose an urgent threat to public health by the US Centers for Disease Control. In this study, I aim to better understand the molecular epidemiology of C. difficile infection (CDI) in the African region, focussing initially in Kenya and then broadening the approach to include other countries (Nigeria, South Africa, Malawi, South Sudan). I will conduct a cross-sectional study in Kenya and through collaborative networks obtain stool specimens and bacteria isolates from other Africa countries which will be used to investigate resistomes and key virulence loci. The expected outcome of this work is a comprehensive understanding of CDI in Africa, which will inform resistance-guided treatment and infection prevention activities. As most curated African referencing resources focus on aerobic bacteria, this study will also help to develop a reference gene catalogue for anaerobic bacteria that can be used to improve existing databases and compared with other geographically distinct isolates.