Periodic Reporting for period 3 - ECOEVODRTB (Linking within-host and between-host evolution of multidrug-resistant Mycobacterium tuberculosis)
Periodo di rendicontazione: 2023-08-01 al 2025-01-31
Antimicrobial resistance (AMR) is a growing public health threat. Multidrug-resistant tuberculosis (MDR-TB) is among the most frequent causes of human death due to AMR. TB is caused by a bacterium called Mycobacterium tuberculosis (Mtb) and is transmitted from human to human via aerosolized droplets, similar to COVID-19. In contrast to COVID-19 however, TB has been affecting humanity for thousands of years. While TB can be treated with a cocktail of antibiotics that need to be taken on a daily basis for many months, the complexities of this treatment, combined with the fact that patients sometimes interrupt their treatment prematurely, can lead to the development of drug resistance. However, the detailed molecular, ecological and evolutionarily basis of these phenomena are not well understood. Moreover, how the development of drug resistance influences the capacity of Mtb to transmit between patients, as well as how this is related to the way Mtb evolves within individual patients during treatment has not been addressed. After many decades of neglect, several new anti-TB drugs have new been approved for the treatment of MDR-TB, and these new treatment regimens are being rolled out in many countries around the world, including in the country of Georgia. Georgia has a high burden of MDR-TB compared to many other countries around the world. Our previous work has shown that one of the reasons of the high MDR-TB incidence in Georgia is the fact that some of the Mtb strains circulating there are very well adapted to drug resistance. As the new treatment regimens are being rolled out, there is real danger that these highly drug-resistant Mtb strains acquire additional resistance to these new drugs. The goal of this project is to take advantage of this natural experiment, and study the within-patient evolution of Mtb during treatment and how this is connected to the spread of these Mtb strains between patients. In addition, we will explore the role of drug tolerance in these processes. The expected results of this project will generate a better understanding of the emergence and spread of AMR in TB and other bacterial infections in general.
This project comprises an epidemiological arm, for which TB patient are prospectively recruited in the country of Georgia, as well as an experimental arm, mainly carried out in our laboratory in Switzerland.
With regards to the epidemiological arm, after an initial delay due to the COVID-19 pandemic, patient recruitment started in January 2021 and is now well underway. In parallel, clinical information and many microbiological samples are being collected from these TB patients as they are being treated and analyzed in the laboratory in Georgia. A subset of these samples are also sent to Switzerland for more in-depth microbiological and genomic analyses. This epidemiological arm of the project also builds on, and further expands our previous work in Georgia, which studied the transmission of MDR-TB in particular. In terms of results so far, our molecular epidemiological investigations revealed that while some drug-resistant Mtb strains circulating in Georgia are less likely to successfully transmit from patient to patient, other Mtb strains that carry so-called compensatory mutations transmit much better, and in some cases equally well as fully drug-susceptible strains. Moreover, our analyses revealed that prisons have played an important role in the epidemiology of MDR-TB in Georgia, as they might serve as incubators for highly drug-resistant and highly transmissible Mtb strains that subsequently can spill over into the general population. Taken together, these findings have important implications for the control of TB, particularly in light of the ongoing roll-out of the new TB treatment regimens against MDR-TB in Georgia and many countries around the world.
Regarding the experimental arm of the project, we have made progress in setting up a new proteomics pipeline to study the gene expression of defined drug-resistant mutants of Mtb as well as clinical Mtb strains from Georgia. The goal of this work is to explore the physiological effects of different drug resistance mutations, alone and in combinations, on the gene (i.e. protein) expression of these Mtb strains. Similarly, we have successfully established a drug tolerance assay to explore the role of this phenomenon in the evolution of drug resistance in Mtb, including during individual patient treatment. We are now in the process of applying these assays to a large number of Mtb mutants and clinical Mtb strains from Georgia.
With regards to the epidemiological arm, after an initial delay due to the COVID-19 pandemic, patient recruitment started in January 2021 and is now well underway. In parallel, clinical information and many microbiological samples are being collected from these TB patients as they are being treated and analyzed in the laboratory in Georgia. A subset of these samples are also sent to Switzerland for more in-depth microbiological and genomic analyses. This epidemiological arm of the project also builds on, and further expands our previous work in Georgia, which studied the transmission of MDR-TB in particular. In terms of results so far, our molecular epidemiological investigations revealed that while some drug-resistant Mtb strains circulating in Georgia are less likely to successfully transmit from patient to patient, other Mtb strains that carry so-called compensatory mutations transmit much better, and in some cases equally well as fully drug-susceptible strains. Moreover, our analyses revealed that prisons have played an important role in the epidemiology of MDR-TB in Georgia, as they might serve as incubators for highly drug-resistant and highly transmissible Mtb strains that subsequently can spill over into the general population. Taken together, these findings have important implications for the control of TB, particularly in light of the ongoing roll-out of the new TB treatment regimens against MDR-TB in Georgia and many countries around the world.
Regarding the experimental arm of the project, we have made progress in setting up a new proteomics pipeline to study the gene expression of defined drug-resistant mutants of Mtb as well as clinical Mtb strains from Georgia. The goal of this work is to explore the physiological effects of different drug resistance mutations, alone and in combinations, on the gene (i.e. protein) expression of these Mtb strains. Similarly, we have successfully established a drug tolerance assay to explore the role of this phenomenon in the evolution of drug resistance in Mtb, including during individual patient treatment. We are now in the process of applying these assays to a large number of Mtb mutants and clinical Mtb strains from Georgia.
Our findings that some highly drug-resistant Mtb strains are equally transmissible than fully drug-susceptible Mtb strains in Georgia have been generated using cutting-edge phylodynamic modelling, which is a method that in this form had never been applied to Mtb. Moreover, our study is the first to have used a nation-wide approach that included all available Mtb samples collected over multiple years in a country with a high burden of MDR-TB. Our additional expected results will link a detailed understanding of how Mtb strains evolve inside patients undergoing TB treatment to how these strains transmit between patients. Moreover, our findings will show if and how phenotypic drug tolerance contributes to the evolution of drug resistance in Mtb, including in the context of the new anti-TB drugs that are being rolled-out in Georgia and across the world.