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Genomics and infectious disease transmission

Genomics and infectious disease transmission


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Research Description:

Our vision is to use genomic tools 

  1. to describe the transmission of infectious disease in order to inform infectious outbreak control policy
  2. to provide an immediate view of the evolution of resistance to host immunity and drug pressure

We are well placed to deliver insights in this area given the availability of samples over 25 years of continuous sampling with detailed clinical and spatial data; international partners providing availability to geographically diverse samples; bioinformatics and sequencing technology within Kilifi; and established collaborations with the Wellcome Trust Sanger Institute to enable high-throughput sequencing. 


The Kilifi Health and Demographic Surveillance system has been running since 2002, and is distinctive as a DSS in that from inception its primary role was to support health related research. Currently a population of 279,158 are under surveillance within an area of 900km2 centred on Kilifi County hospital. 

The long term demographic surveillance provides information on trends in mortality and dynamics of mobility, age-structure, household occupancy and spatial distribution that are of intrinsic interest. Data on cause of death are obtained from linked surveillance to the wards of the county hospital and also through Verbal Autopsy undertaken for all deaths. 

Hospital admissions can be linked to person years residency to provide highly detailed denominator based incidences of admissions due to disease syndromes (pneumonia, diarrhea, malnutrition) and specific aetiologies (eg malaria, S.pneumoniae, rotavirus). 

Similarly, denominators and geographic data are linked to maternity study data (eg KIPMAT) and vaccine records in health facilities throughout the HDSS (PCVIS). This also enables studies on the spatial distribution of diseases (eg malaria hotspots), health interventions (eg H. influenzae type B, S. pneumoniae), and post-discharge mortality or readmission (eg severe malnutrition cases). 

The HDSS provides the frame for sampling, for example, to identify controls for cases-control studies and participants for household or social epidemiology research, also for evaluation of vaccine intervention (PCVIS and rotavirus vaccination), public health data (eg bednet usage, water and sanitation), and large-scale sampling for prevalence estimation (eg neurological disorders). The KHDSS is part of the INDEPTH network. 

In addition to the hospital-based surveillance we also conduct surveillance at two primary healthcare facilities, in the sickle cell outpatient clinic, and we intensively follow two cohorts of 300 children for malaria episodes and diarrhoea episodes with weekly visits and fieldworkers resident in the relevant villages to capture episodes occurring out-of-hours. These cohorts include some children aged 15 where complete life histories of weekly surveillance have been documented. 

Investigators :