Whole Genome Based Diagnostics and Investigations of Infectious Diseases

Start date
January 1, 2013
End date
December 31, 2018
Project code
12-007DTU
Countries
Total grant
8,759,400
Contact person
Frank Møller Aarestrup
Description

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

Midterm report 2017:

The project had the following expected outcomes:

1. Education of 2 PhD-students in sequencing technology.
ONGOING WITH EXPECTED DEFENCE IN OCTOBER 2018.
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 shortcommings of traditional approaches for diagnostics.
WE HAVE IDENTIFIED A NUMBER OF GAPS, INCLUDING SPECIES IDENTIFICATION, SUSCEPTIBILITY TESTING AND TRANSMISSION EVENTS. ALL ISSUES WILL NOT BE SOLVED WITHIN THIS PROJECT.