Leveraging on Existing Laboratory Information Management System to Respond to Emerging Public Health Emergencies in East Africa

Background

The Association of Public Health Laboratories (APHL), in collaboration with the Kenya National Public Health Laboratory (NPHL) Information Communication and Technology (ICT) team through Center for Disease, Control and Prevention (CDC) funding, enhanced the already operational Laboratory Information management system (LIMS) at NPHL to support COVID-19 reporting for the entire country. The LIMS was expanded to support both private and public laboratories testing for COVID19 to develop their capacity for submitting results to the national COVID-19 data center. 

Once received, the data were verified and analyzed by teams from the Emergency Operation Center (EOC) and Monitoring and Evaluation. Summarized data were shared with the Ministry of Health including national and county epidemiology and public health surveillance teams. APHL and NPHL ICT teams also worked to ensure appropriate storage of these data in a national data repository at NPHL and further utilization of these data through integration of the repository with external systems. 

Method

APHL and NPHL ICT undertook two significant steps to develop a robust, high quality, accurate national data repository: 1) The teams together developed an Application Programming Interface (API) for testing laboratories to automatically upload their COVID-19 results to the national data center. For laboratories unable to use API capability, the teams developed standardized spreadsheets that, once completed, could be uploaded to a secure portal. 2) the teams developed an API to support Kenya’s border surveillance efforts, enabling the Regional Electronic Cargo & Driver Tracking System (RECTDS) to access COVID-19 results from the data center for drivers responsible for transporting cross border goods. 

The development team carried out needs assessment in the 10 laboratories that were initially testing for COVID-19 assessing their interoperability preparedness at the time. It was evident that a Hybrid system would be the best. Allowing both API and semi-automated (use of Excel) as methods of uploading data to the national repository. 

Results

The COVID-19 national data repository is receiving data from over 500 testing facilities including PCR and AgRDT tests. Of these 60% are in the public sector while the remaining facilities are private institutions. As a result of the APIs and standardized sheets for submitting COVID-19 result data, turn around time decreased from 5 days to less than 24 hours. The integration with the RECDTS system allows truck drivers to efficiently move across Kenya’s borders as their test results could be verified at all border points within twenty-four hours of testing. 

Conclusion

The APHL and NPHL teams developed creative informatics solutions during a global pandemic and were able to leverage the immediate need for test results to demonstrate partnerships and data sharing agreements between public and private laboratories, serving as a role model to other nations. In addition, the establishment of a national data repository for COVID-19 data has validated the need for a centralized platform for laboratory data to further strengthen surveillance and overall preparedness.