Research Institute of Phthisiopulmonology

Saint Petersburg, Russia

Research Institute of Phthisiopulmonology

Saint Petersburg, Russia
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Malashchenko V.,Research Institute of Phthisiopulmonology | Zyubin A.,Research Institute of Phthisiopulmonology | Babak S.,Immanuel Kant Baltic Federal University | Lavrova A.,Immanuel Kant Baltic Federal University
Proceedings of SPIE - The International Society for Optical Engineering | Year: 2017

We consider the method of confocal microscopy as a convenient instrument for determination of chemical compounds in biological tissues and cells. In particular, we study the dynamics of adenosine triphosphate (ATP) concentration that could be used as a bio-marker of energy metabolism pathologies at the treatment of acute lymphoblastic leukaemia (ALL). On the basis of data obtained by the confocal microscopy, the values of ATP concentration have been calculated for each case. Possible correlations with other characteristics of pathology processes obtained from plasma of leukemia patients show that ATP value could be a prognostic factor of the treatment success. The role of ATP in the drug metabolism switching is also discussed within the context of kinetic modelling of metabolism processes leading to the production of 6-Thioguanosine monophosphate, which is a principal acting agent in chemotherapy. © 2016 SPIE.


PubMed | University of Latvia, St Petersburg Pasteur Institute, Ural Research Institute of Phthisiopulmonology, Aitkhozhin Institute of Molecular Biology and Biochemistry and 5 more.
Type: | Journal: Molecular phylogenetics and evolution | Year: 2016

Currently, Mycobacterium tuberculosis isolates of Latin-American Mediterranean (LAM) family may be detected far beyond the geographic areas that coined its name 15years ago. Here, we established the framework phylogeny of this geographically intriguing and pathobiologically important mycobacterial lineage and hypothesized how human demographics and migration influenced its phylogeography. Phylogenetic analysis of LAM isolates from all continents based on 24 variable number of tandem repeats (VNTR) loci and other markers identified three global sublineages with certain geographic affinities and defined by large deletions RD115, RD174, and by spoligotype SIT33. One minor sublineage (spoligotype SIT388) appears endemic in Japan. One-locus VNTR signatures were established for sublineages and served for their search in published literature and geographic mapping. We suggest that the LAM family originated in the Western Mediterranean region. The most widespread RD115 sublineage seems the most ancient and encompasses genetically and geographically distant branches, including extremely drug resistant KZN in South Africa and LAM-RUS recently widespread across Northern Eurasia. The RD174 sublineage likely started its active spread in Brazil; its earlier branch is relatively dominated by isolates from South America and the derived one is dominated by Portuguese and South/Southeastern African isolates. The relatively most recent SIT33-sublineage is marked with enigmatic gaps and peaks across the Americas and includes South African clade F11/RD761, which likely emerged within the SIT33 subpopulation after its arrival to Africa. In addition to SIT388-sublineage, other deeply rooted, endemic LAM sublineages may exist that remain to be discovered. As a general conclusion, human mass migration appears to be the major factor that shaped the M. tuberculosis phylogeography over large time-spans.


Vyazovaya A.A.,St Petersburg Pasteur Institute | Vetrov V.V.,St Petersburg Pasteur Institute | Lyalina L.V.,St Petersburg Pasteur Institute | Mokrousov I.V.,St Petersburg Pasteur Institute | And 4 more authors.
Russian Journal of Infection and Immunity | Year: 2017

In the late 90-ies of XX century in Russia there was an exacerbation of the epidemic situation of tuberculosis (TB) and "explosive" increase in pathogen drug resistances. Regardless of lower incidence of pulmonary TB in recent years, the number of cases caused by multidrug-resistant (MDR) mycobacteria was increasing due to a reduction in the effectiveness of treatment. Among the 11 subjects of the North-West Federal District the Leningrad Region is leading in the number of ineffective chemotherapy outcomes in newly diagnosed bacteriologically confirmed TB cases. A specific feature of the current epidemic situation in the Leningrad Region is the prevalence (74.1% in 2014) of MDR strains among previously treated patients with pulmonary TB. The aim of the research was a comparative genotypic characterization of Mycobacterium tuberculosis strains, isolated from patients with chronic pulmonary tuberculosis in the Leningrad Region in 1999-2004 and 2010-2014. As defined by spoligotyping, the Beijing family genotype was prevailing among M. tuberculosis strains of previously treated patients from Leningrad region (76.5% in 2010-2014 versus 56.3% in 1999-2004). The proportion of other genotypes strains -LAM and T decreased from 16.7 and 12.5% to 10.3 and 2.9%, respectively. The proportion of multi-drug resistance in the studied subpopulations of the Beijing genotype strains remained virtually constant (86.5 and 88.9%). The extensive drug resistance was not observed among MDR Beijing strains in 1999-2004, whereas in 2010-2014 it reached 33.3%. MIRU-VNTR-typing (12 loci) of 68 M. tuberculosis strains revealed 20 profiles; of these, five were presented by clusters MIT1, MIT46, MIT16, MIT17, MIT571, comprising two or more strains. The largest clusters MIT16 (223325153533) and MIT17 (223325173533) included 25 (48.1%) and 21 (40.4%) apparently highly transmissible Beijing genotype strains. Previously, clinical significance and mainly epidemic pathways for MDR M. tuberculosis Beijing strains belonging to these MIRU-VNTR-types were proved in a number of Russian regions. These findings require in-depth analysis of the situation in the region studied.


News Article | August 22, 2016
Site: www.rdmag.com

Researchers from the Federal Research and Clinical Centre of Physical-Chemical Medicine, and staff from MIPT's Systems Biology Laboratory, the Research Institute of Phthisiopulmonology and the St. Petersburg Pasteur Institute, conducted a large-scale analysis of the proteins and genomes of mycobacterium tuberculosis strains that are common in Russia and countries of the former Soviet Union and found features that provide a possible explanation for their epidemiological success. A paper detailing the results has been published in the prestigious journal Scientific Reports, part of Nature Publishing Group. Up until the 20th century, tuberculosis was considered an incurable disease and, despite newly developed methods of curing it at its early stages, the death rate is still high. There are 22 countries, including Russia, in which the infection rate is four times greater than in the rest of the world. It is important to note that the term "tuberculosis" covers a wide range of bacteria strains that cause the disease. Strains of the Beijing family (this genotype was first discovered in Beijing) are prevalent in Russia - every year about 150,000 people are infected with it. To understand the reason behind the "success" of this strain, scientists compared proteins produced by Beijing B0/W148 with a control strain. In order to do this, separated bacterial proteins were enzymatically cleaved into smaller fragments - peptides and their mass and relative abundance were measured precisely using mass spectrometry. After analysing the data collected, the scientists knew which and how many proteins there were in each strain. It was found that in Beijing B0/W148 strains, 266 proteins were differentially abundant compared with the control strain. 57 of them were entirely absent in the study group and 17, on the contrary, were unique to it, others differed quantitatively. Analysis of the functions associated with differing proteins revealed that in Beijing B0/W148 strains there are more proteins producing long-chain fatty acids and less proteins destroying them. Bacteria use these acids to produce mycolic acids, which integrate themselves in the bacterial cell membrane and make it waxy, which is why mycobacteria can survive and even reproduce in macrophages (special human cells that destroy foreign substances). Normally, if a bacterium is "eaten" by a macrophage it dies. However, mycobacterium tuberculosis strains have evolved to reproduce in macrophages and in doing so they hide from the immune system. Mycolic acids not only protect bacteria, but also play a crucial role in synthesizing substances that inhibit macrophages so they stop fighting disease. The features of lipid metabolism that have been discovered could explain the success of Beijing B0/W148 strains in relation to other tuberculosis mycobacteria.


Mokrousov I.,St Petersburg Pasteur Institute | Narvskaya O.,St Petersburg Pasteur Institute | Vyazovaya A.,St Petersburg Pasteur Institute | Otten T.,Research Institute of Phthisiopulmonology | And 5 more authors.
Journal of Clinical Microbiology | Year: 2012

We describe a multiplex PCR assay to detect the Mycobacterium tuberculosis Beijing genotype variant B0/W148, which is considered a "successful" clone of M. tuberculosis, widespread in Russia. Specificity and sensitivity of the assay were 100% based on the analysis of a collection of 516 M. tuberculosis isolates of different genotypes and origins. This assay may be used for accurate and simple detection and surveillance of this clinically and epidemiologically important variant of M. tuberculosis. Copyright © 2012, American Society for Microbiology. All Rights Reserved.


Mokrousov I.,St Petersburg Pasteur Institute | Vyazovaya A.,St Petersburg Pasteur Institute | Otten T.,Research Institute of Phthisiopulmonology | Zhuravlev V.,Research Institute of Phthisiopulmonology | And 5 more authors.
PLoS ONE | Year: 2012

This study aimed to characterize the population structure of Mycobacterium tuberculosis in Pskov oblast in northwestern Russia, to view it in the geographical context, to compare drug resistance properties across major genetic families. Ninety M. tuberculosis strains from tuberculosis (TB) patients, permanent residents in Pskov oblast were subjected to LAM-specific IS6110-PCR and spoligotyping, followed by comparison with SITVITWEB and MIRU-VNTRplus databases. The Beijing genotype (n = 40) was found the most prevalent followed by LAM (n = 18), T (n = 13), Haarlem (n = 10), Ural (n = 5), and Manu2 (n = 1); the family status remained unknown for 3 isolates. The high rate of Beijing genotype and prevalence of LAM family are similar to those in the other Russian settings. A feature specific for M. tuberculosis population in Pskov is a relatively higher rate of Haarlem and T types. Beijing strains were further typed with 12-MIRU (followed by comparison with proprietary global database) and 3 hypervariable loci QUB-3232, VNTR-3820, VNTR-4120. The 12-MIRU typing differentiated 40 Beijing strains into 14 types (HGI = 0.82) while two largest types were M2 (223325153533) prevalent throughout former USSR and M11 (223325173533) prevalent in Russia and East Asia. The use of 3 hypervariable loci increased a discrimination of the Beijing strains (18 profiles, HGI = 0.89). Both major families Beijing and LAM had similar rate of MDR strains (62.5 and 55.6%, respectively) that was significantly higher than in other strains (21.9%; P = 0.001 and 0.03, respectively). The rpoB531 mutations were more frequently found in Beijing strains while LAM drug resistant strains mainly harbored rpoB516 and inhA -15 mutations. Taken together with a high rate of multidrug resistance among Beijing strains from new TB cases (79.3% versus 44.4% in LAM), these findings suggest the critical impact of the Beijing genotype on the current situation with MDR-TB in the Pskov region in northwestern Russia. © 2012 Mokrousov et al.


Vyazovaya A.,St Petersburg Pasteur Institute | Mokrousov I.,St Petersburg Pasteur Institute | Solovieva N.,Research Institute of Phthisiopulmonology | Mushkin A.,Research Institute of Phthisiopulmonology | And 4 more authors.
Antimicrobial Agents and Chemotherapy | Year: 2015

Extrapulmonary and, in particular, spinal tuberculosis (TB) constitutes a minor but significant part of the total TB incidence. In spite of this, almost no studies on the genetic diversity and drug resistance of Mycobacterium tuberculosis isolates from spinal TB patients have been published to date. Here, we report results of the first Russian and globally largest molecular study of M. tuberculosis isolates recovered from patients with tuberculous spondylitis (TBS). The majority of 107 isolates were assigned to the Beijing genotype (n=80); the other main families were T (n=11), Ural (n=7), and LAM (n=4). Multidrug resistance (MDR) was more frequently found among Beijing (90.5%) and, intriguingly, Ural (71.4%) isolates than other genotypes (5%; P<0.001). The extremely drug-resistant (XDR) phenotype was exclusively found in the Beijing isolates (n=7). A notable prevalence of the rpoB531 and katG315 mutations in Beijing strains that were similarly high in both TBS (this study) and published pulmonary TB (PTB) samples from Russia shows that TBS and PTB Beijing strains follow the same paradigm of acquisition of rifampin (RIF) and isoniazid (INH) resistance. The 24-locus mycobacterial interspersed repetitive unit-variable-number tandemrepeat (MIRU-VNTR) subtyping of 80 Beijing isolates further discriminated them into 24 types (Hunter Gaston index [HGI]=0.83); types 100-32 and 94-32 represented the largest groups. A genotype of Russian successful clone B0/W148 was identified in 30 of 80 Beijing isolates. In conclusion, this study highlighted a crucial impact of the Beijing genotype and the especially prominent role of its MDR-associated successful clone B0/W148 cluster in the development of spinal MDR-TB in Russian patients. Copyright © 2015, American Society for Microbiology. All Rights Reserved.


Mokrousov I.,St Petersburg Pasteur Institute | Vyazovaya A.,St Petersburg Pasteur Institute | Zhuravlev V.,Research Institute of Phthisiopulmonology | Otten T.,Research Institute of Phthisiopulmonology | And 6 more authors.
Journal of Clinical Microbiology | Year: 2014

Mycobacterium tuberculosis Beijing genotype strains are rapidly disseminating, frequently hypervirulent, and multidrug resistant. Here, we describe a method for their rapid detection by real-time PCR that targets the specific IS6110 insertion in the dnaA-dnaN genome region. The method was evaluated with a geographically and genetically diverse collection representing areas in East Asia and the former Soviet Union in which the Beijing genotype is endemic and epidemic (i.e., major foci of its global propagation) and with clinical specimens. © 2014, American Society for Microbiology. All Rights Reserved.


Zimenkov D.V.,RAS Engelhardt Institute of Molecular Biology | Kulagina E.V.,RAS Engelhardt Institute of Molecular Biology | Antonova O.V.,RAS Engelhardt Institute of Molecular Biology | Zhuravlev V.Y.,Research Institute of Phthisiopulmonology | Gryadunov D.A.,RAS Engelhardt Institute of Molecular Biology
Journal of Antimicrobial Chemotherapy | Year: 2016

Background: Nucleic acid amplification tests are widely used in TB diagnostics. Priority tasks in their development consist of increasing the specificity and sensitivity of the detection of resistance to a wide spectrum of anti-TB drugs. Methods: We developed a multiplexed assay allowing the detection of 116 drug resistance-determining mutations in the rpoB, katG, inhA, ahpC, gyrA, gyrB, rrs, eis and embB genes in the Mycobacterium tuberculosis complex genome and six SNPs to identify the main lineages circulating in Russia. The assay is based on the amplification of 17 fragments of the genome using the universal primer adapter technique and heat pulses at the elongation step, followed by hybridization on a microarray. Results: The method was evaluated using 264 pairs of clinical samples and corresponding isolates. A significant proportion (25%) of smear-negative samples were correctly analysed by microarray analysis in addition to 96% of smear-positive samples. The sensitivity and specificity of the assay exceeded 90% for rifampicin, isoniazid, ofloxacin and second-line injection drugs. In agreement with previous studies, the specificity of ethambutol resistance was as low as 57%, while the sensitivity was 89.9%. Strong association of the Beijing lineage with a resistant phenotype was observed. Euro-American lineage strains, excluding Ural and LAM, were predominantly associated with the susceptible phenotype. Conclusions: The developed test has a high sensitivity and specificity and can be directly applied to clinical samples. The combination of mutation-based drug resistance profiling and basic genotyping could be useful for clinical microbiology studies and epidemiological surveillance of the M. tuberculosis complex. © The Author 2016.


PubMed | Research Institute of Phthisiopulmonology and RAS Engelhardt Institute of Molecular Biology
Type: Journal Article | Journal: The Journal of antimicrobial chemotherapy | Year: 2016

Nucleic acid amplification tests are widely used in TB diagnostics. Priority tasks in their development consist of increasing the specificity and sensitivity of the detection of resistance to a wide spectrum of anti-TB drugs.We developed a multiplexed assay allowing the detection of 116 drug resistance-determining mutations in the rpoB, katG, inhA, ahpC, gyrA, gyrB, rrs, eis and embB genes in the Mycobacterium tuberculosis complex genome and six SNPs to identify the main lineages circulating in Russia. The assay is based on the amplification of 17 fragments of the genome using the universal primer adapter technique and heat pulses at the elongation step, followed by hybridization on a microarray.The method was evaluated using 264 pairs of clinical samples and corresponding isolates. A significant proportion (25%) of smear-negative samples were correctly analysed by microarray analysis in addition to 96% of smear-positive samples. The sensitivity and specificity of the assay exceeded 90% for rifampicin, isoniazid, ofloxacin and second-line injection drugs. In agreement with previous studies, the specificity of ethambutol resistance was as low as 57%, while the sensitivity was 89.9%. Strong association of the Beijing lineage with a resistant phenotype was observed. Euro-American lineage strains, excluding Ural and LAM, were predominantly associated with the susceptible phenotype.The developed test has a high sensitivity and specificity and can be directly applied to clinical samples. The combination of mutation-based drug resistance profiling and basic genotyping could be useful for clinical microbiology studies and epidemiological surveillance of the M. tuberculosis complex.

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