TB Genomic Surveillance

Surveillance of drug resistant M. tuberculosis complex strains by Whole Genome Sequencing 

Our overarching aim is to establish a multi-country integrated genomic surveillance of drug resistant M. tuberculosis complex (MTBC) strains in Africa. 

Objectives: 

The key objectives of this WP are to: 

1. Establish standardized core genome multi locus sequence typing approach (cgMLST) for population structure, transmission and outbreak analysis.
2. Develop and provide tools for NGS/WGS based resistance prediction.
3. Develop a framework for structured collections of MTBC strains and metadata (clinical, microbiological and epidemiological) in the African setting.
4. Test the cgMLST approach in pilot studies in partner countries and generate pilot data on populations structure, transmission dynamics, and resistance profiles of DR MTBC strains in Africa.
5. Develop a prototype for a web-based database for a combined analysis of cgMLST data generated in different countries to detect cross-border transmission.

The established publicly available NGS/WGS databases in combination with metadata will create a versatile platform for surveillance of DR MTBC strains in Africa and throughout. The established tools for resistance prediction and transmission will allow for better treatment of individual patients, improved epidemiological risk management and better infection control. 

Specific tasks of the WP are: 

1. TB case recruiting and MTBC isolation utilizing standardized SOPs 
2. Establishing of cgMLST in partner countries 
3. Proof of concept pilot studies 
4. Establishing a central cgMLST database 
5. WGS and NGS-based resistance conferring mutation analyses and interpretation 
6. Confirmation of resistance-conferring mutations using MICs 

We heavily collaborate with the training WP to build capacity in all of the above. 

WP Leaders: Prof. Stefan Niemann, Prof. Dorothy Yeboah-Manu, Dr. Prince Asare and Dr. Margo Diricks 

All 16 partner sites are involved in this WP.