Дайджест о выполнении проекта «Роль регион-специфичных полиморфизмов генов вирулентности в формировании лекарственной устойчивости Mycobacterium tuberculosis»
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BRICS STI Project «The role of region-specific SNPs in virulence genes in Mycobacterium tuberculosis drug resistance» digest
We had a long journey prior to the preparation of our BRICS application. Back in 2010 Dr. Gail Cassel from Harvard University launched an international collaboration that resulted in the establishment of the TBResist consortium. TBResist brought together researchers from 20 countries and aimed to analyze Mycobacterium tuberculosis whole-genomic sequences from all over the world to discover novel mechanisms of drug resistance. Research groups from Russia, China and South Africa (countries with high tuberculosis burden, accounting for almost 13% of global tuberculosis cases). Thus it was a logical step for the leading researchers from these three countries (Prof. Valery Danilenko from Vavilov Institute of General Genetics RAS, Prof. Martie Van der Walt from the TB Platform of the South African Medical Research Council and Dr. Lingyun Shao from Fudan University) to join their efforts and submit an application as soon as the first BRICS STI grant call was announced.
Dr. Dmitry Maslov (key participant, Russia), Prof. Martie Van der Walt (PI, South Africa) and Prof. Valery Danilenko (PI, Russia); Dr. Ligyun Shao (PI, China)
Currently, it is known that the clinical manifestations and epidemiology of tuberculosis largely depend on the balance between the host's immune system and the pathogen's virulence systems. The causative agent of tuberculosis in the human body is often in a latent form, and the key factor affecting the transition to active is a decrease in immunity, which can be caused by various reasons, including the presence of concomitant diseases that lead to a decrease in immunity (HIV, type II diabetes, metabolic syndrome, hepatitis B). Also the M. tuberculosis genome includes more than three hundred virulence genes, whose products are involved in various stages of the infectious process and allow colonization of the host's mucosa, infiltrate cells, avoid the immune system response, survive adverse conditions, etc. Different lines of M. tuberculosis are characterized by variations in pathogenicity genes, which can lead to changes in protein properties, and, as a result, to changes in the virulence profile.
This multifactorial evolution of MTB lead to a spread of “successful” clones in different geographic locations, such as the Beijing B0/W-148 in Russia, Beijing modern in China and F15/LAM4/KZN in South Africa. The emergence of new sublineages within the “successful” clones, which are associated with drug-resistant phenotypes and harbor a number of specific mutations in virulence-associated genes, is observed lately. Enhanced virulence may be linked to drug resistance. One of the main examples of genes involved in both aspects is WhiB7, which controls the expression of a regular containing genes responsible as for intrinsic drug resistance, as well as for virulence. Other examples may include ecc5 type VII excretion system and toxin-antitoxin systems.
Our project aimed to identify SNPs in virulence-associated genes, associated with drug-resistant phenotype of M. tuberculosis belonging to geographical-specific lineages that emerged in the era of antibiotics. Each partner analyzed a collection of clinical MTB isolates derived from their respective country to fulfill the aim.
To support the international collaboration, several exchange visits were made. These include the visit of the Russian group members to Cape Town in 2017, the group from South Africa visited Moscow in May-June 2018 to participate in the All-Russian Scientific Practical Conference with International Participation «An Actual Issues of ТВ Care in the Russian Federation: Consolidation of Efforts for ТВ Control», group members from South Africa and China visited Vavilov Institute of General Genetics in May 2019 to discuss the project results, Russian researchers visited Fudan University in Shanghai in October 2019 and participated in the 6th International Forum on Clinical Microbiology and Infectious Disease, and researchers from South Africa visited Moscow in December 2019. Dr. Lesibana Malinga and Dr. Awelani Mutshembele also took a month-long training in molecular genetics in the laboratory of bacterial genetics VIGG RAS in 2018 and 2019 respectively.
The project implementation led to the detection of mutations in M. tuberculosis virulence genes specific to Russia. Mutations in two genes (pe_pgrs54, pks15) associated with immunocompromised conditions of patients formed the basis for the development of a diagnostic kit (together with the industrial partner "DNA Technology") for the detection of these epidemiologically dangerous strains. Another one (in the mce3F gene) is able to provide resistance of mycobacteria to streptomycin.
Analysis of a collection of isolates from China revealed genes that can provide new mechanisms of resistance to PASC (mutation in the metH gene) and tolerance to rifampicin (mutation in the small RNA B11 gene).
An important result of the collaboration was the training of researchers from South Africa in the VIGG RAS laboratory of bacterial genetics, aimed at mastering the methods of molecular genetic manipulation of mycobacteria.
The work that is currently carried after the project’s ending is focused on a general phylogenetic analysis of all sequenced genomes from Russia, China and South Africa in order to identify common SNPs that potentially characterize the common path of evolution of epidemiologically dangerous strains. We believe that this work will lead to a high-impact joint publication.
The implementation of this BRICS project has also stimulated the creation of the Russian tuberculosis consortium, which includes circa 20 Institutes and organizations in Russia, and has also given a start to new areas of collaboration in the field of tuberculosis research with other groups in China and South Africa.
Today the World has met a new challenge in the face of COVID-19, and our team is working on preparing a joint proposal for the new BRICS-STI call, entitled “Development of new adjuvant formulations for second-generation anti-COVID-19 recombinant protein vaccine”. New groups from India and Brazil are joining the teams from Vavilov Institute of General Genetics (Russia) and Fudan University (China) in this effort.
Group photo at VIGG RAS (Dr. Dmitry Maslov, Prof. Valery Danilenko, Dr. Lesibana Malinga, Dr. Kirill Shur), Moscow, 2018
Dr. Lesibana Malinga, Prof. Martie Van der Walt, Dr. Aleksey Vatlin, Moscow, 2018
Group photo at the DNA Technology headquarters, Moscow, May 2019
Dr. Kirill Shur at a seminar in Shanghai, presenting BRICS project results. Shanghai, October 2019
Prof. Valery Danilenko giving his speech at the 6th International Forum on Clinical Microbiology and Infectious Diseases & 3rd Prevention and Control of MDR Summit, October 2019
Group photo at the 6th International Forum on Clinical Microbiology and Infectious Diseases & 3rd Prevention and Control of MDR Summit, October 2019
Group photo at the Huashan Hospital, Fudan University, October 2019
Group photo from Moscow, 2018. (Prof. Valery Danilenko, Prof. Martie Van der Walt, Dr. Lesibana Malinga)
Dr. Awelani Mutshembele during her molecular genetics training in the laboratory of bacterial genetics VIGG RAS, Moscow, 2019