SOME FEATURES OF GENOME STRUCTURE AND EVOLUTION OF MYCOBACTERIUM TUBERCULOSIS

Abstract. Mycobacterium tuberculosis complex includes both human pathogens (M. tuberculosis, M. africanum and M. canettii), rodent paghogens (M. microti), as well as Mycobacterium bovis with wide range of hosts and related M. caprae and M. pinnipedii. In spite of phenotypic and host differences these species present a highly homogeneous genospecies with 99.7–99.9% of genome homology and extremely low level of horizontal gene transfer. Recent genetic research in the last decade permitted to revisit and revise old and new dogmas about genome and evolution of M. tuberculosis. In particular, a classical theory about bovine origin of human tuberculosis during domestication process was rejected. It was demonstrated that genomes of the related species of M. tuberculosis complex evolved through large unidirectional deletions leading to origin of M. tuberculosis sensu stricto, M. bovis and other species (M. canettii, M. microti, M. pinnipedii, M. caprae) from the same progenitor species. Large deletions influence the pathogenic potential of different clonal lineages within M. tuberculosis. At the same time, genetic variation within the short time frames is achieved via changes in the repetitive DNA and transposition of the insertion sequences IS6110 across the genome. Furthermore, M. tuberculosis may adapt to the selective pressure of the host immune system and antituberculosis drugs via specific point mutations. In the last few years a higher level of SNP variation between closely related strains was demonstrated with opens new perspectives for full-genome and multilocus sequence typing of M. tuberculosis

METHODOLOGICAL APPROACHES TO MYCOBACTERIUM TUBERCULOSIS GENOTYPING FOR EVOLUTIONARY AND EPIDEMIOLOGICAL RESEARCH

Abstract. Current genome evolution of Mycobacterium tuberculosis is marked by virtual absence of the lateral gene transfer leading to the clonal population of this species consisting of separate genetic families. Standard typing method of M. tuberculosis (IS6110-RFLP, spoligo- and VNTR-typing) are based on variation of mobile and repetitive elements and provide sufficient strain discrimination for epidemiological purposes such as, estimation of recent transmission versus reactivation of latent tuberculosis, laboratory contamination, mixed infection. At the same time, rapid evolution of some markers may lead to emergence of identical profiles in the non-related strains (homoplasy) due to convergent evolution. Use of different independent markers may help solve this problem. Regularly updated databases are available for global and local analysis and are also important for standardised terminology and designation of the genotypes. Some of the M. tuberculosis genetic families continue to circulate in the limited areas while other families have become omnipresent due to their likely increased transmissibility and pathogeneicity (e.g., Beijing and LAM). The most frequently isolated Russian subvariant Beijing B0/W148 is marked by significantly higher population growth compared to the Russian Beijing population as a whole and hence may be defined as a successful clone in Russia. Recent years revealed higher than previously thought level of genome variation in M. tuberculosis even between related isolates. The whole-genome sequencing may become a useful typing method if its cost is reduced to be similar to that of the traditional typing methods. Accumulation of the data on old and new markers, development and use of new algorithms of their analysis will help to refine our knowledge about evolution of M. tuberculosis and its families, will provide better tools for epidemiological monitoring of the circulating strains on local and global scale

Spoligotype database of Mycobacterium tuberculosis: biogeographic distribution of shared types and epidemiologic and phylogenetic perspectives.

We give an update on the worldwide spoligotype database, which now contains 3,319 spoligotype patterns of Mycobacterium tuberculosis in 47 countries, with 259 shared types, i.e., identical spoligotypes shared by two or more patient isolates. The 259 shared types contained a total of 2,779 (84%) of all the isolates. Seven major genetic groups represented 37% of all clustered isolates. Two types (119 and 137) were found almost exclusively in the USA and accounted for 9% of clustered isolates. The remaining 1,517 isolates were scattered into 252 different spoligotypes. This database constitutes a tool for pattern comparison of M. tuberculosis clinical isolates for global epidemiologic studies and phylogenetic purposes

Epidemiological manifestations of tuberculosis infection in the Omsk region: dynamics and trends

Background. Tuberculosis (TB) infection remains relevant as one of the leading public health problems in Russia.The aim. To characterize the dynamics and trends of epidemiological manifestations of TB infection in the Omsk region.Materials and methods. An observational descriptive-evaluative epidemiological study was carried out in the Omsk region from 2009 to 2021. The data available in the Federal statistical observation forms NN 7, 8, and 33, and results of the bacteriological study of patients with respiratory TB were analyzed.Results. In the Omsk region, an improvement in the epidemiological situation was observed from 2009 to 2021. It was associated with a decrease in TB prevalence by 3.7 times (from 325.6 to 86.7), mortality – by 5.8 times (from 21.1 to 3.6), incidence – by 2.7 times (from 130.7 to 48.4 per 100,000). At the same time, proportion of microscopy/culture-positive patients infected with multidrug-resistant Mycobacterium tuberculosis strains increased from 9.2 to 29.8 % among all patients, and from 15.5 to 30.6 % among newly diagnosed patients. There was a trend towards an increase in the number of cases with primary extensive drug resistance of M. tuberculosis. The incidence of tuberculosis associated with HIV infection has increased 10 times and reached 15.6 per 100,000 population.Conclusions. In the Omsk region, there is a change in the structure of M. tuberculosis strains with a predominance of multiple and extensive drug resistance along with decrease in TB incidence and mortality. New approaches are needed to organize the system of epidemiological surveillance and control of TB infection

Diagnostics of endowments of students of higher education institutionin the field of art and creative activityby means of the Internet resource

The relevance of the problem considered in article is caused by need of tool ensuring identification, development, diagnostics and escort of the gifted youth studying in higher education institution, in various areas of creative activity at different educational steps and stages of personal development.Актуальность проблемы, рассматриваемой в статье, обусловлена необходимостью инструментального обеспечения выявления, развития, диагностики и сопровождения одаренной молодежи, обучающейся в вузе, в различных областях творческой деятельности, на разных образовательных ступенях и этапах личностного развития

Genetic variation of Mycobacterium tuberculosis circulating in Kharkiv Oblast, Ukraine

<p>Abstract</p> <p>Background</p> <p>A persistent increase of tuberculosis cases has recently been noted in the Ukraine. The reported incidence of drug-resistant isolates of <it>M. tuberculosis </it>is growing steadily; however, data on the genetic variation of isolates of <it>M. tuberculosis </it>circulating in northern Ukraine and on the spectrum and frequency of occurrence of mutations determining resistance to the principal anti-tuberculosis drugs isoniazid and rifampicin have not yet been reported.</p> <p>Methods</p> <p>Isolates of <it>M. tuberculosis </it>from 98 tuberculosis patients living in Kharkiv Oblast (Ukraine) were analyzed using VNTR- and RFLP-IS6110-typing methods. Mutations associated with resistance to rifampicin and isoniazid were detected by RFLP-PCR methods, and also confirmed by sequencing.</p> <p>Results</p> <p>We identified 75 different genetic profiles. Thirty four (34%) isolates belonged to the Beijing genotype and 23 (23%) isolates belonged to the LAM family. A cluster of isolates belonging to the LAM family had significant genetic heterogeneity, indicating that this family had an ancient distribution and circulation in this geographical region. Moreover, we found a significant percentage of the isolates (36%) belonged to as yet unidentified families of <it>M. tuberculosis </it>or had individual non-clustering genotypes. Mutations conferring rifampicin and isoniazid resistance were detected in 49% and 54% isolates, respectively. Mutations in codon 531 of the <it>rpoB </it>gene and codon 315 of the <it>katG </it>gene were predominant among drug-resistant isolates. An association was found for belonging to the LAM strain family and having multiple drug resistance (R = 0.27, p = 0.0059) and also for the presence of a mutation in codon 531 of the <it>rpoB </it>gene and belonging to the Beijing strain family (R = 0.2, p = 0.04).</p> <p>Conclusions</p> <p>Transmission of drug-resistant isolates seems to contribute to the spread of resistant TB in this oblast. The Beijing genotype and LAM genotype should be seen as a major cause of drug resistant TB in this region.</p

Water Ozonation with Copper Catalyst for Organic Pollutants Removal

This work presents high-porous honeycomb copper catalyst for organic pollutants removal from water during the ozonation process. This catalyst demonstrates high efficiency in removing target compounds (oxalic and benzoic acids and methylene blue), appropriate stability and resistance to abrasion. Copper catalyst behavior in the ozonation process was investigated. It was found that under ozonation conditions reversible В  oxidation/reduction of the copper surface layer takes place. In contact with ozone, copper surface can easily be oxidized resulting in formation of copper oxides. As expected, it leads to decomposition of organic substances during ozonation and reduction of copper catalyst surface layer. Copper (II) oxide was also found to be an active catalyst in oxidation of organic pollutants with ozone, but it is not appropriate to use bulk CuO because of its low abrasion resistance. Copper (II) ions that form due to dissolution of catalyst surface layer with participation of the acidic medium in the ozonation process were detected. Pollutants removal efficiency at different pH values was also studied. It was found that catalytic removal of organic pollutants takes place at low pH, as compared to low efficiency of hydroxyl-radical formation at the acidic pH. A possible scheme for organic pollutants removal during ozonation with copper catalyst was proposed

Tuberculosis outcomes related to the Mycobacterium tuberculosis genotype

Mycobacterium tuberculosis strains of different phylogenetic lineages and genetic families differ in biological properties that determine, to some extent, epidemiological features and clinical manifestation in tuberculosis (TB) patients.The aim of the study was to assess the risk of an adverse outcome of the disease in TB patients caused by various M. tuberculosis genotypes.Materials and methods. A total of 425 patients with respiratory TB were enrolled in this study. They were registered at phthisiatric facilities in the Omsk region from March 2015 to June 2017 period and included: males — 73.1%, mean age 39.9 years, females — 26.9%, mean age 42.0 years. M. tuberculosis culture and drug susceptibility testing and DNA extraction were performed in accordance with standard methods. Strains were assigned to the M. tuberculosis Beijing genotype and its epidemiologically relevant clusters B0/W148 and 94-32 by PCR based detection of specific markers. Non-Beijing strains were subjected to spoligotyping.Results. We found that 66.5% isolates belonged to the Beijing genotype, 12.8% — to LAM, 10.1% — to T, and 4.7% — to the Ural genotype. Multi-drug resistance (MDR) to anti-TB drugs was observed in 195 M. tuberculosis strains (45.9%). Moreover, Beijing genotype was more often isolated from patients with MDR-TB infection (PR = 2.09 (95% CI 1.6–2.74) and TB infection associated with HIV infection (PR = 1.14 (95% CI 1.01–1.31). Lethal outcome was double higher in patients infected with Beijing vs. non-Beijing strains, 28.6% vs. 14.0% (PR = 2.03; 95% CI 1.3–3.17). The risk factors were identified as follows: young age 18–44 years (RR = 1.7; 95% CI 1.18–2.7), co-morbidity with HIV (RR = 5.0; 95% CI 3.39–7.45), multiple (RR = 1.7; 95% CI 1.14–2.55) and extensive drug resistance (RR = 2.57; 95% CI 1.35–4.92), and association with the Beijing genotype (RR = 2.0, 95% CI 1.3–3.17).Conclusion. M. tuberculosis spread in the Omsk region is characterised by significant prevalence of the Beijing genotype, associated with multiple and extensive drug resistance. A significant association of adverse clinical outcomes and various factors, including association with the Beijing genotype, requires development of new approaches in the fight against tuberculosis

Proposal of a consensus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem-repeat loci for subtyping of mycobacterium tuberculosis Beijing isolates

Mycobacterium tuberculosis Beijing strains represent targets of special importance for molecular surveillance of tuberculosis (TB), especially because they are associated with spread of multidrug resistance in some world regions. Standard 24-locus mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing lacks resolution power for accurately discriminating closely related clones that often compose Beijing strain populations. Therefore, we evaluated a set of 7 additional, hypervariable MIRU-VNTR loci for better resolution and tracing of such strains, using a collection of 535 Beijing isolates from six world regions where these strains are known to be prevalent. The typeability and interlaboratory reproducibility of these hypervariable loci were lower than those of the 24 standard loci. Three loci (2163a, 3155, and 3336) were excluded because of their redundant variability and/or more frequent noninterpretable results compared to the 4 other markers. The use of the remaining 4-locus set (1982, 3232, 3820, and 4120) increased the number of types by 52% (from 223 to 340) and reduced the clustering rate from 58.3 to 36.6%, when combined with the use of the standard 24-locus set. Known major clonal complexes/24-locus-based clusters were all subdivided, although the degree of subdivision varied depending on the complex. Only five single-locus variations were detected among the hypervariable loci of an additional panel of 92 isolates, representing 15 years of clonal spread of a single Beijing strain in a geographically restricted setting. On this calibrated basis, we propose this 4-locus set as a consensus for subtyping Beijing clonal complexes and clusters, after standard typing

Molecular epidemiological monitoring of the tuberculosis pathogen in the Arkhangelsk region

Introduction. Against the background of improvement of the main epidemiological indicators (morbidity and mortality) for tuberculosis in the Arkhangelsk region, the proportion of newly diagnosed tuberculosis patients with multidrug-resistant pathogen (MDR-TB) increased from 18.7% in 2002 to 33.8% in 2018. The purpose of this study was the genotypic characterization of Mycobacterium tuberculosis strains obtained from newly diagnosed tuberculosis patients in the Arkhangelsk region in 2018. Materials and methods. 89 M. tuberculosis strains isolated in 2018 from newly diagnosed tuberculosis patients were studied. Beijing genotype, its clusters B0/W148 and Central Asian/Russian were determined by PCR detection of the specific markers: IS6110 insertions in the dnaA-dnaN region, mutations in codons 48 of the mutT4 gene (CGG GGG) and 58 of the mutT2 gene (GGA CGA), IS6110 insertions in the Rv2664 region-Rv2665 and Rv1359-Rv1360, substitutions G A in the sigE gene. Non-Beijing strains were spoligotyped. Results. Drug resistance was detected in 41.6% (37/89), MDR — in 33.7% of strains. In 90% (27/30) of MDR strains, resistance to rifampicin and isoniazid was due to rpoB Ser531Leu and katG Ser315Thr mutations. Following M. tuberculosis genotypes were identified: Beijing (67.4%), T (14.6%), Ural (4.5%), Haarlem (4.5%), LAM (2.3%) and CAS1-Delhi (1.1%). Among the Beijing strains, clusters Central-Asian/Russian (60%; 36/60) and B0/W148 (30%; 18/60) prevailed. The majority of MDR strains belonged to the Beijing family (93.3%; 28/30), of which 64.3% (18/28) and 21.4% (6/28) belonged to clusters B0/W148 and Central-Asian/Russian, respectively. Conclusion. In heterogeneous population of the causative agent of tuberculosis in the Arkhangelsk region, the most common strains were those of the Beijing genotype; in 2018 its share increased to 67.4% (40.4% in 1998–1999). Among MDR strains, the proportion of Beijing reached 93.3%, of which more than half (64.3%) belonged to the epidemiologically and clinically significant in Russia cluster B0/W148