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Microbial Diversity, Ecology and Pathogenicity

    1. What is the underlying genetic epidemiology of key pathogens of importance to human health in Africa?
    2. How does genotype (human and pathogen) influence disease severity?
    3. Can reverse vaccinology methodologies translate and ultimately fast track potential targets into viable vaccine targets?
    4. How can we utilise pathogen core and accessory genomes to develop broad based and targeted interventions?
  • The ultimate aim of the MiDEP group is to define how a pathogen interacts with its environment. A pathogens environment can refer its host niche, including co-colonizing organisms within that niche or the pathogens discrete population, whether in country, across a region, continent or even globally. Defining pathogen behavior in each of these contexts and how this influences the ability of pathogens to switch from causing asymptomatic carriage to disease is key to identifying potential intervention measures.
    To underpin this the MiDEP group are developing a regional genomics hub to expand our collaborative research to regional neighbours including Zimbabwe, Mozambique, Mauritius and Botswana. Such a facility is currently severely lacking within East Africa.
    • Develop a robust surveillance platform/cohort for respiratory pathogens as a basis to inform the group’s key questions.
    • Undertake longitudinal genomic analyses across a range of major respiratory pathogens (Streptococcus pneumoniae, Group A Streptococcus, influenza virus and Staphylococcus) to identify targets for vaccine interventions.
    • Test the effectiveness of common vaccine targets identified in animal and human models.
  • MiDEP is one of only three groups within Africa to have secured a $6 million CDC co-operative agreement to study the epidemiology of respiratory pathogens. MiDEP acts as the only low-income Africa country involved in this study.

    Our Pneumococcal African Genomics (PAGe) paper published in the inaugural edition of Microbial Genomics, reported the genetic epidemiology of the highly invasive S. penumoniae serotype 1 globally and provided novel evidence that serotype 1 in Africa commonly recombines and acquires antibiotic resistance genes (Cornick et al., 2015).

    Reporting the trends in bacterial meningitis in Malawi during the era of ART role out and in introduction of the HiB vaccine (Wall et al., 2014).