Whole Genome Sequence Based Diagnostics and Investigations


Partner Institution(s): 
Kilimanjaro Christian Research Institute (KCRI - KCMC)
University of Copenhagen, Department of International Health, Immunology and Microbiology
Start Date: 
January 1, 2013
End Date: 
December 31, 2018
Project Code: 
12-007DTU
Total grant: 
DKK 8,759,400
Contact : 
Frank Møller Aarestrup
Countries: 
Tanzania
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.

Output: 

Midterm report 2015
The most important output is a proof-of-concept of global real-time collaboration
combining state-of-the-art technology at point of care with global analysis. In addition, the project will provide the following:

1. Education of 2 PhD-students in a novel scientific field spanning from sequencing
technology, to bioinfomatics and microbiology.

CURRENTLY ONGOING ACCORDING TO PLANS

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.

THE ANALYSIS OF THE FIRST ROUND OF COLLECTION IS ONGOING

4. Detailed knowledge on shortcommings of traditional approaches for diagnostics.

TO BE COMPLETED

5. New knowledge on the epidemiology of infectious diseases in Tanzania.

ONGOIONG. WE HAVE ALREADY IDENTIFIED TRANSMISSION EVENTS.

6. Capacity building though education of researchers and medical doctors in different countries in the East African Region

TO BE COMPLETED. TRAINING IS PLANNED IN COLLABORATION WITH THE BSU INITIATIVE.

This page was last modified on 21 September 2017

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