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.
Progress of the project
1 October 2021 – 31 December 2021
Full genome sequencing and data analysis of DNA samples from several M. tuberculosis isolate collections has been continued during the reporting period. Significant differences in the quantity and quality of DNA have been identified due to the use of different DNA isolation methods for M. tuberculosis isolates from solid and liquid media. As a result, the adaptation of DNA purification and concentration protocols to the needs of the WGS has begun.
Information published 30.12.2021.
Progress of the project
1 January 2022 – 31 March 2022
Full genome sequencing and data analysis of several M. tuberculosis isolate sample sets collected in previous studies was continued. M. tuberculosis DNA samples obtained in a hospital laboratory using various DNA extraction methods have been evaluated and compared. Due to the very low concentration of M. tuberculosis DNA in some samples, which makes the use of NGS / WGS technologies very difficult, the workflows have been further adapted and refined. The aim, tasks and progress of the project were reported at the meeting of the Latvian Association of Tuberculosis and Lung Diseases Physicians (March 23, 2022).
Information published 31.03.2022.
Progress of the project
1 April 2022 – 30 June 2022
Summarising of the full genome sequencing data of several M. tuberculosis DNA sample sets has been carried out during the reporting period. An evaluation and in-depth analysis of the current sequencing results has been performed. Special attention was paid to the evaluation of the significance of the applied bioinformatics methods and data for the identification of M. tuberculosis resistance, as well as the tracking of epidemiological links. The work on the preparation of the scientific publication has been started. A student research thesis was defended in connection with the project topic.
Information published 30.06.2022.
Progress of the project
1 July 2022 – 30 September 2022
During this period, the evaluation and in-depth analysis of the current sequencing results has been continued. Based on the obtained results, a manuscript was prepared and submitted to the scientific journal. Two conference theses were also prepared. The results of the project were presented during the 46th FEBS Congress ‘The Biochemistry Global Summit”. Full genome sequencing of additional M. tuberculosis isolate sample sets has been started. Work has been started on the second activity of the project – design of the protocol.
Information published 30.09.2022.
Progress of the project
1 October 2022 – 31 December 2022
During the reporting period, a contract with RAKUS has been concluded and the collection of new samples, which is essential for the progress of the project, has started. A new sample set of M. tuberculosis has been obtained and work has begun to analyze it. Work on the development of the protocol was continued. Corrections of the scientific article have been made according to the recommendations of the reviewers. The preparation of the new article has started.
Information published 30.12.2022.
Progress of the project
1 January 2023 – 31 March 2023
During the reporting period, a set of new M. tuberculosis samples has been received, which is necessary to achieve the results of the project. Appropriate sample processing has been performed. Protocol development has continued and data analysis has been performed. A scientific article has been published in the OpenAccess journal during the reporting period: Sadovska et al. 2023. “Advantages of analyzing both pairwise SNV-distance and differing SNVs between Mycobacterium tuberculosis isolates for recurrent tuberculosis cause determination”. The results obtained in the project were presented at an international conference within the “Research week 2023” of Riga Stradiņš University
Information published 31.03.2023.
Progress of the project
1 April 2023 – 30 June 2023
During the reported period, extensive WGS analysis of the M. tuberculosis samples was performed. Protocol development has been successfully continued and new samples have been included in the workflow. The in-house M. tuberculosis WGS workflow was used to delineate the transmission network of six local TB outbreaks caused by LAM M. tuberculosis strains that occurred in distinct Latvian counties. The genetic distances between M. tuberculosis isolates were assessed. This work highlights the application of WGS in the assessment of M. tuberculosis strain transmission and for public health epidemiology needs.
The results were presented during 43rd Annual Meeting of the European Society of Mycobacteriology (Albania, 25-28 June 2023): Sadovska et al. “WGS-based genetic diversity assessment of LAM genotype M. tuberculosis strains among the tuberculosis outbreaks in distant Latvian counties”.
Information published 30.06.2023.
Progress of the project
1 July 2023 – 30 September 2023
During the reported period, the work has been continued to reach the goals of all research activities. NGS analysis of sputum samples was performed and the protocol development has been successfully continued based on the obtained results. Research article was published: Vīksna et al. Genotypic and phenotypic comparison of drug resistance profiles of clinical multidrug-resistant Mycobacterium tuberculosis isolates using whole genome sequencing in Latvia. BMC Infect Dis 23, 638 (2023). https://doi.org/10.1186/s12879-023-08629-7. The research tasks for the last phase of the project were planned. The project aim and the importance of tuberculosis research studies were highlighted during the Researchers` Night 2023 activities (September 29, 2023).
Information published 02.10.2023.
Progress of the project
1 October 2023 – 30 November 2023
During the last time period of the project, all tasks and activities have been finalised. All results have been summarised. The WGS workflow has been finalised. The M. tuberculosis Whole genome sequencing utility report has been amended and finalised. The final report has been prepared.
Information published 30.11.2023.