Dana Auganova

The high antibiotic resistance of Bacteroides fragilis and its ability to combine symbiosis with pathogenicity in the human body make this species a key model for studying the bacterial stress response. Outer membrane vesicles (OMVs), secreted by Gram-negative bacteria, play a key role in intercellular communication, pathogenesis, and adaptation to antibiotics. In this study, we performed a proteomic analysis of B. fragilis OMVs exposed to meropenem using LC-MS/MS and label-free quantification (LFQ). Nineteen differentially expressed proteins were identified, belonging to the main functional groups: enzymes of amino acid and carbohydrate metabolism, antioxidant defense proteins, replication and translation factors, and methyltransferases. Taken together, these changes reflect a redistribution of metabolic fluxes toward maintaining energy balance and antioxidant defense under antibiotic stress. Thus, the proteomic profile of B. fragilis OMVs demonstrates their significant role in the mechanisms of bacterial survival and resistance, and also highlights their potential involvement in pathogenesis.

Yellow fever virus is a mosquito-borne flavivirus responsible for severe human disease. Flaviviruses cause an estimated 400 million infections annually worldwide and are transmitted between animals and humans via arthropod vectors. Viral RNA replication is mediated by non-structural proteins that assemble into membrane-associated replication complexes (RC). Among these, the NS1 protein plays a critical role in replication complex formation and function. In this study, we investigated the replication complex of Yellow fever virus using sucrose density gradient ultracentrifugation. An NS1–GFP replicon system was constructed and employed to isolate and fractionate RC-associated components. This approach enables characterization of the molecular composition and organization of the replication complex and provides insights into the mechanisms underlying RNA replication in flaviviruses.

Background: Radon exposure is the second most important risk factor for lung cancer after tobacco smoking and represents a significant but often underestimated public health problem. Due to the absence of specific clinical manifestations at early stages, the identification of molecular biomarkers reflecting early radon-induced carcinogenic processes is of particular importance. The aim of this study was to identify protein biomarkers associated with radon exposure in lung cancer patients residing in settlements of the Akmola and North Kazakhstan regions of Kazakhstan. Methods: Indoor radon exposure was assessed using CR-39 detectors to measure radon concentrations in residential dwellings during summer and autumn periods. The study included 57 lung cancer patients and 73 control subjects residing in areas characterized by varying levels of radon exposure. Plasma samples were collected and analyzed using liquid chromatography–tandem mass spectrometry (LC–MS/MS) to identify differentially expressed proteins associated with lung cancer and radon exposure. Statistical analyses were performed to evaluate differences between groups and associations between radon exposure and molecular biomarkers. Results: Seasonal variability in indoor radon concentrations was observed, with several settlements demonstrating levels exceeding international reference values. Proteomic analysis identified multiple proteins differentially expressed between lung cancer patients and controls, as well as between radon-exposed and non-exposed lung cancer patients. Several proteins involved in inflammation, lipid metabolism, oxidative stress, and immune regulation pathways demonstrated significant differences in expression levels, suggesting potential associations with radon-induced carcinogenic mechanisms. LC–MS/MS proteomic profiling identified multiple differentially expressed proteins associated with lung cancer and radon exposure after false discovery rate correction. Proteins involved in inflammation, oxidative stress, immune regulation, and lipid metabolism, including ORM2, AZGP1, PRDX2, IRF7, and APOC3, demonstrated significant expression differences between radon-exposed and low-exposure groups. Conclusions: The identified protein biomarkers demonstrated significant associations with both radon exposure and lung cancer status, indicating their potential relevance for early detection and risk assessment of radon-induced lung cancer. The integration of environmental exposure assessment with proteomic profiling may provide new insights into the molecular mechanisms of radon-associated carcinogenesis and support the development of preventive strategies.

Background/Objectives: Citalopram is a selective serotonin reuptake inhibitor that is prescribed to relieve anxiety and depression. Widespread use has led to the contamination of freshwater systems downstream of wastewater treatment facilitates. Few studies have investigated the impact of citalopram on early embryonic development in humans or other species, despite the prevalence of intentional or unintentional exposure. Danio rerio (zebrafish) is a model organism for investigating effects of environmental exposure to xenobiotics on developmental outcomes in vertebrates. Methods: In this study, we examined the metabolome of developing zebrafish embryos exposed to citalopram hydrobromide concentrations (0.03–250 ng/mL) spanning environmental to therapeutic doses during the first 24 h post-fertilization. Exposure was followed by 24 h exposure-free development before harvest at 48 h. Results: Gross morphology of the embryos was normal, although changes were observed in the heart rates of citalopram-exposed embryos. Untargeted metabolomic and multivariate analyses revealed significant, nonlinear changes in the metabolome in response to citalopram exposure. Arginine and proline metabolism was significantly altered, potentially reflecting changes in serotonin signaling, nitric oxide metabolism, and polyamine synthesis. Conclusions: Together, these data demonstrate that transient exposure to citalopram can induce long-lasting metabolomic changes during development, including dose-dependent changes that include aberrant metabolic processes in the developing metabolome. As a result, this work reveals potential biomarkers for early developmental exposure.

The flavivirus NS1 protein is a component of the viral replication complex and plays diverse, yet poorly understood, roles in the viral life cycle. To enable real-time visualization of the developing replication organelle and biochemical analysis of tagged NS1 and its interacting partners, we engineered a replication-competent yellow fever virus (YFV) replicon encoding a C-terminal fusion of NS1 with green fluorescent protein (NS1-GFP). The initial variant was non-viable in the absence of trans-complementation with wild-type NS1; however, viability was partially restored through the introduction of co-adaptive mutations in GFP (Q204R/A206V) and NS4A (M108L). Subsequent cell culture adaptation generated a 17-nucleotide frameshift within the NS1-GFP linker, resulting in a more flexible and less hydrophobic linker sequence. The optimized genome, in the form of a replicon, replicates in packaging cells that produce YFV structural proteins, as well as in naive BHK-21 cells. In the packaging cells, the adapted NS1-GFP replicon produces titers of infectious particles of approximately 10⁶ FFU/mL and is genetically stable over five passages. The expressed NS1-GFP fusion protein localizes to the endoplasmic reticulum and co-fractionates with detergent-resistant heavy membranes, a hallmark of flavivirus replication organelles. This NS1-GFP replicon provides a novel platform for studying NS1 functions and can be further adapted for proximity-labeling strategies aimed at identifying the still-unknown protease responsible for NS1-NS2A cleavage.

Background/Objectives: Multidrug-resistant tuberculosis remains a critical public health challenge in Kazakhstan, yet the genomic determinants contributing to its emergence are still insufficiently understood. Although the quantity of genomic studies from Central Asia and the wider post-Soviet region has increased in recent years, the involvement of DNA repair and genome maintenance pathways in the development of resistance within Kazakhstan has not been comprehensively explored. Methods: In this study, we performed whole-genome analysis of 175 Mycobacterium tuberculosis clinical isolates collected across Kazakhstan between 2010 and 2022 to evaluate the contribution of single-nucleotide polymorphisms in DNA replication, repair, and recombination (3R) genes to the evolution of drug resistance. Results: Alongside well-established resistance mutations in gyrA, we identified recurrent variants in 3R-associated loci (genes involved in DNA replication, repair, and recombination)—including polA, uvrC and ligC—that were enriched among drug-resistant isolates, suggesting a broader role for genome maintenance pathways in facilitating resistance evolution under treatment pressure. Conclusions: These findings provide the first region-specific genomic insights into 3R gene variation in Kazakhstani M. tuberculosis isolates.

Tuberculosis remains a highly contagious infection, with an estimated annual transmission of about 10 million people globally, as reported in the latest Global Tuberculosis Report by the World Health Organization (WHO). The primary objective of this research is to determine the geographical distribution and drug resistance profiles of Mycobacterium tuberculosis lineage 2, which is predominant in Kazakhstan. A total of over 200 clinical isolates of M. tuberculosis complex (MTBC) were collected from regional phthisiopulmonology centers across all regions of Kazakhstan between 2012 and 2024. Clinical isolates were genotyped using a PCR assay targeting the dnaA-dnaN:IS6110 region, specific for the modern Beijing genotype. Subsequently, selected samples were sequenced using the Illumina MiSeq platform. The TB-Profiler prediction tool was utilized to identify resistance against anti-tubercular drugs and to genotype the lineages. A total of 102 clinical isolates belonging to the L2 modern Beijing genotype were selected for whole-genome sequencing (WGS). The L2.2.1 genetic cluster was identified as the only sublineage present, according to Coll et al.'s classification. More than half of the specimens were found to be multidrug-resistant (n=60, 59%). Among the analyzed samples, monoresistance to isoniazid (IHN) was detected in 17 (16%) cases, while 14 (14%) cases were drug-susceptible TB. Additionally, 7 (7%) cases were identified as Pre-XDR (resistant to rifampicin, isoniazid, and either fluoroquinolones or second-line injectable drugs), 3 (3%) cases were monoresistant to streptomycin, and 1 (1%) case exhibited resistance to rifampicin only. Regional distribution of samples is as follows: Aktau and Kostanay are 14% (n=13/102), Kyzylorda (n=12/102), Taldykourgan (n=11/102), Pavlodar, Karaganda, and Atyrau are at 6% (6/102); Semey is 10% (n=9/102), Almaty and Taraz at 4%, and Shymkent city is 1% (n=1/102). This ongoing research is focused on resistance patterns, genotypes, and transmission dynamics among different regions of Kazakhstan using next-generation sequencing, followed by bioinformatics analysis and interpretation of the data.

According to the World Health Organization, Kazakhstan takes a leading position in the number of cases of multidrug-resistant tuberculosis. This work is aimed at studying clinical isolates of Mycobacterium tuberculosis circulating in Astana in 2021–2022. Among 198 M. tuberculosis isolates collected, 175 (88.38%) belonged to the L2/Beijing family, and the remaining 23 samples (11.62%) belonged to the L4 family. During the research used genotyping aimed at determining the genetic family of M. tuberculosis, as well as whole-genome sequencing of selected 24 L2/Beijing isolates with their subsequent bioinformatics analysis. According to the analysis results, 62.5% of isolates were assigned to the Central Asia Outbreak genotype. The remaining genotypes were represented by Central Asia (20.8%), B0/W148 (12.5%) and Clade A (4.2%). Besides that, phenotypic and genotypic characterization of the resistance of selected isolates to anti-tuberculosis drugs was carried out. One of the possible reasons for the spread of resistant forms of tuberculosis in the country is the predominance of the Central Asia Outbreak genetic cluster associated with MDR-TB.

Kazakhstan ranks among the countries with the highest number of MDR-TB patients per 100,000 population worldwide. The successful transmission of local MDR strains of Mycobacterium tuberculosis (Mtb) poses a significant threat to disease control. In this study, we employed whole-genome sequencing to examine drug resistance, compensatory mutations, population structure, and transmission patterns in a sample of 24 clinical isolates of L2/Beijing Mtb collected in Astana, Kazakhstan between 2021 and 2022. The genotypic prediction of Mtb susceptibility to anti-TB agents was consistent with the phenotypic susceptibility, except for bedaquiline. An analysis of resistance-associated genes characterized most of the isolates as pre-extensively drug-resistant tuberculosis (pre-XDR-TB) (n = 15; 62.5%). The phylogenetic analysis grouped the isolates into four transmission clusters; the dominant cluster was assigned to the “aggressive” Central Asia outbreak (CAO) clade of L2/Beijing (n = 15; 62.5%). Thirteen mutations with putative compensatory effects were observed exclusively in Mtb isolates containing the rpoB S450L mutation. The putative compensatory mutations had a stabilizing effect on RpoABC protein stability and dynamics. The high prevalence of the CAO clade in the population structure of Mtb may explain the rapid spread of MDR-TB in Kazakhstan.

Gram-positive bacteria of Mycobacterium tuberculosis complex (MTBC) are causative agents of tuberculosis disease. According to the report of the World Health Organization, tuberculosis is one of the leading causes of mortality worldwide. Moreover, epidemiological data shows that due to the COVID-19 pandemic tuberculosis mortality has risen in comparison with previous years. Drug resistance is another threatening issue when the resistance to antitubercular (anti-TB) drugs makes therapy less effective. Furthermore, drug resistance is often burdened with compensatory mechanisms that overcome fitness defects related to drug-resistant mutations. This review discusses the drug resistance and compensatory mutations in Mycobacterium tuberculosis and the current situation with anti-TB drug resistance in the Republic of Kazakhstan.