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.