Whole Genome Based Diagnostics and Investigations of Infectious Diseases

Project summary

The advancement of genome technologies holds great promise for improving the quality and speed of public health laboratory investigations, and for decreasing their cost. The latest genome DNA sequencers are now suitable for routine use in public health laboratories and may replace conventional culture-based and molecular bacterial methods for laboratory diagnosis. Especially in low income areas this might create new options, and enable laboratories in developing countries to “leapfrog”, avoiding the development of very costly and often insufficient laboratory systems similar to those that are implemented in OECD countries where separate specialist testing capacities exist for each of the many microbiological families.

The problem is the need of very specialized knowledge, computation and tools to analyze the data generated in a standardized and comparable way and provide plain language reports to the primary care users. Such tools are developed or under development in a web-accessible format at DTU.

We propose a pilot-project, where the latest sequencing technology is made available in a diagnostic laboratory in Tanzania and combined with analytic facilities at one of the world’s largest bioinformatic centers at DTU. Two PhD-students from Tanzania will be educated in sequencing technology and use this on routine diagnostic samples. To ensure dissemination to other countries in the region and provide building KCRI will be used as a focal point for WHO GFN training courses.

Outputs

Project completion report:

The project had the following expected outcomes:

1. Education of 2 PhD-students in sequencing technology.
BOTH SUCCESSFULLY DEFENDED IN 31st May 2019.

2. Implementation of the most recent diagnostic technology at a laboratory in Tanzania.
COMPLETED.

3. Description of the population structure of the most important human pathogens in Tanzania.
DONE

4. Detailed knowledge on shortcomings of traditional approaches for diagnostics.
WE HAVE IDENTIFIED A NUMBER OF GAPS, INCLUDING SPECIES IDENTIFICATION, SUSCEPTIBILITY TESTING AND TRANSMISSION EVENTS. ALL THE ISSUES WILL NOT BE SOLVED WITHIN THIS PROJECT.

5. New knowledge on the epidemiology of infectious diseases in Tanzania.
WE HAVE WITH THE 10 PUBLICATIONS PROVIDED MUCH NOVEL INSIGHT INTO MULTIPLE SPECIES.

6. Capacity building though education of researchers and medical doctors in different countries in the East African Region
TEACHING IS DONE IN COLLABORATION WITH THE KCMC COLLEGE AND TRAINING HAS BEEN CONDUCTED AND FURTHER IS PLANNED IN COLLABORATION WITH THE BSU INITIATIVE.

Brief popularized abstract:

The main purpose of this capacity building project was to establish and show the usefulness of whole genome sequencing (WGS) for bacterial isolates in Moshi, Tanzania. The sequencing platform including subsequent analyses of the data have been successfully implemented and used to study the epidemiology of a number of different bacterial species. We have provided novel insight into the local epidemiology of several of the main pathogens at the local hospital and shown the power of WGS of elucidating bacterial outbreaks. the platform has also been extended into analyzing virus and parasites and determine the complete composition of fecal samples. The main challenge of the project has been to transfer the large amount of data through the internet, which have made it necessary to increase the local IT-capacity. The successful implementation has led to a number of novel research projects, which likely will continue enabling KCMC as one of the regional sequencing facilities for Eastern Africa. In the future this will allow Africa to study their own bacterial, viral and in general biological diversity without the involvement of other countries or regions.