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Whole genome sequencing of tuberculosis for routine clinical use in Latvia: evidence-based design and concept evaluation

Project Title: „Whole genome sequencing of tuberculosis for routine clinical use in Latvia: evidence-based design and concept evaluation.”

Funding: European Regional Development Fund (ERDF), Measure 1.1.1.1 “Support for applied research”

Project No.: 1.1.1.1/20/A/046

Period: 1 January 2021 – 30 November 2023

Project costs: 540 540.54 EUR

Principle Investigator: Dr. biol. Renāte Ranka

Cooperation partner: SIA “GenEra” 

 

Project summary:

The aim of this project is to design and evaluate an approach of introducing the whole genome sequencing of M. tuberculosis into routine clinical practice in Latvia.

Tuberculosis remains one of the most devastating diseases affecting people of all ages across the globe. It is among the top 10 causes of death worldwide and has high economic impacts. The widespread transmission and prevalence of drug resistant variants of mycobacteria is one of the major obstacles for successful control of the disease. Patients infected with drug resistant strains are hard or even impossible to be cured, and their treatment is more toxic and expensive. In Latvia, multi-drug resistant tuberculosis remains a serious health problem: in 2017, almost 8% of all TB cases in Latvia were caused by drug-resistant M. tuberculosis strains.

Slow and cumbersome laboratory diagnostics for M. tuberculosis complex risk delayed treatment and poor patient outcomes. Whole-genome sequencing (WGS) could potentially provide a rapid and comprehensive diagnostic solution and is moving from proof-of-concept research into for routine clinical use.

 Information published 04.01.2021.

 

Progress of the project

1 January 2021 – 31 March 2021

The systematization of available DNA samples of M. tuberculosis isolates collected in previous studies was performed, which included checking the availability of phenotypic data and assessing the amount / purity of DNA. The first sample set, which included multidrug-resistant M. tuberculosis strains, was selected. Additional DNA purification was performed on samples with low DNA quality. Development of M. tuberculosis enrichment protocols has begun. Evaluation of available M. tuberculosis resistance mutation databases has been performed.

Information published 31.03.2021.

 

Progress of the project

1 April 2021 – 30 June 2021

Whole genome sequencing and data analysis was performed for the particular DNA sample set of M. tuberculosis isolates collected during the previous studies. The development of M. tuberculosis enrichment protocols has been continued. Evaluation of available M. tuberculosis resistance mutation databases has been continued. The conference thesis was presented and published at the 41st Annual Congress of the European Society of Mycobacteriology: Sadovska et al.,“WGS-based recurrent tuberculosis cause determination for patients involved in local outbreaks in Latvia”.

Information published 30.06.2021.

 

Progress of the project

1 July 2021 – 30 September 2021

We continued the whole genome sequencing and data analysis for the particular DNA sample sets of M. tuberculosis isolates collected during the previous studies. We performed the adaptation and improvement of several bioinformatics pipelines. The development of M. tuberculosis enrichment protocols has been continued. Evaluation of the detected M. tuberculosis resistance mutations in conjunction with phenotypic data has been started.

Information published 30.09.2021.



Mājas lapas izstrādi finansēja ERAF 2.1.1.2. aktivitātes projekts Nr. 2010/0196/2DP/2.1.1.2.0/10/APIA/VIAA/004 "Latvijas biomedicīnas pētījumu integrācija Eiropas zinātnes telpā".