Pyrazinamide plays an important role in the treatment of tuberculosis. However, the microbiological test for pyrazinamide resistance is more complex and less reliable than testing of susceptibility ...to other anti-tuberculosis drugs due to the need to grow the pathogen at pH 5.5. Identification of mutations that cause resistance to anti-tuberculosis drugs can replace microbiological methods. Mutations in the
pncA
gene are responsible for the main mechanism of the resistance to pyrazinamide and are found in more than 90% of resistant strains. However, the genetic method for determining drug susceptibility is very complex, because mutations leading to pyrazinamide resistance are diverse and scattered throughout the gene. We have developed a software package for automatic data interpretation and prediction of the resistance to pyrazinamide based on Sanger sequencing results. The effectiveness of detection of pyrazinamide resistance in 16 clinical samples was compared using the BACTEC MGIT 960 automated system and
pncA
gene Sanger sequencing with automated analysis of the results. A significant advantage of the developed method over a single microbiological study was shown, due to greater reliability of the results irrespective of the purity of isolates.
Drug acetylation plays an important role in the medical practice. Modern methods of acetylation phenotype prediction are based on genotyping of polymorphisms in the second exon of the gene
NAT2
. ...Some disadvantages of these methods limit their application in the clinical practice. We developed a method of human genotyping based on identification of
NAT2
gene polymorphism
rs1495741
by real-time PCR. This method of genotype determination has a number of advantages: high sensitivity, simplicity, possibility of automated interpretation of the results, and feasibility in clinical laboratories.
—
The S genotype (first described in Sicily, hence the name) is a part of the Euro-American lineage of
Mycobacterium tuberculosis
. Here, we report a method for its detection based on PCR-RFLP of the
...Rv0557
gene. The method was optimized on strains with known whole genome sequences and further applied to screening the DNA collections from Russia, Bulgaria, China, Japan, and Vietnam. PCR-RFLP analysis confirmed the S genotype in strains with the spoligotypes SIT34 (ancestral to S) and SIT1253 (Yakutia strains). Strains from Bulgaria with abridged spoligoprofiles SIT4 and SIT125 were also assigned to the S genotype. The developed method provides for rapid detection of the
M. tuberculosis
S genotype and reliably resolves phylogenetic ambiguity of the disputed spoligotypes.
Background. In phthisiology, all recurrent respiratory tract infections are considered risk factors for tuberculosis (TB) in children. A differentiated assessment of the predictive value of recurrent ...upper and lower respiratory tract infections will improve the effectiveness of selective TB screening. The aim . To carry out a differentiated assessment of the predictive value of recurrent upper and lower respiratory tract infections in children with tuberculosis and HIV coinfection. Materials and methods . We conducted a retrospective study (2010–2020) of the anamnestic prevalence of recurrent respiratory tract infections in 249 children divided into 4 groups: 72 healthy children (HC); TB – 65 children with tuberculosis; TB/HIV – 56 children with HIV-associated TB; HIV – 65 children with HIV infection. Results. Recurrent lower respiratory tract infections were detected in the anamnesis of 15 (23 %) children of the TB group and in 3 (4 %) children of the HC group (p < 0.001; odds ratio (OR) – 8.6). Lower respiratory tract infections were most common during the year preceding TB disease (11 out of 15 cases), within 2 years before the inclusion of children in the study – in 4 out of 15 cases (p = 0.027; OR = 11.0). In the TB/HIV group, the prevalence of lower respiratory tract infections compared to the HIV group was established only during the year preceding TB – 24 out of 33 cases (73 %) versus 10 out of 34 cases (29 %) in the HIV group (χ 2 = 10.9; p = 0.001; OR = 6.4). The occurrence of upper respiratory tract infections in pairs of HC group – TB group and HIV group – TB/HIV group had no statistical differences. Conclusion. The predictor of TB in children regardless of their HIV status is the recurrent lower respiratory tract infections, registered during the year preceding the TB disease. The recurrent infections of the upper respiratory tract do not affect the realization of TB in children, regardless of their HIV status.
The dynamics of lung microbiota in tuberculosis remains poorly understood. Sequencing of variable regions of the 16S rRNA gene from surgically excised tuberculosis foci and biopsy specimens of normal ...lung tissue allowed characterization of the diversity and predictive potential of bacterial communities. Taxonomic diversity indices attested to differences in the structure of microbial communities between "healthy" lungs and tuberculomas. The microbial composition of "healthy" lungs varied in taxonomic diversity and was presented by both gram-positive and gram-negative bacteria with sufficiently similar metabolic potential. The microbiota of the examined tuberculomas consisted of Mycobacterium tuberculosis in 99.9% of cases. A significant part of the metabolic pathways predicted by PICRUSt2 included cholesterol catabolism, sulfate assimilation, and various pathways for the biosynthesis of cell wall components.The dynamics of lung microbiota in tuberculosis remains poorly understood. Sequencing of variable regions of the 16S rRNA gene from surgically excised tuberculosis foci and biopsy specimens of normal lung tissue allowed characterization of the diversity and predictive potential of bacterial communities. Taxonomic diversity indices attested to differences in the structure of microbial communities between "healthy" lungs and tuberculomas. The microbial composition of "healthy" lungs varied in taxonomic diversity and was presented by both gram-positive and gram-negative bacteria with sufficiently similar metabolic potential. The microbiota of the examined tuberculomas consisted of Mycobacterium tuberculosis in 99.9% of cases. A significant part of the metabolic pathways predicted by PICRUSt2 included cholesterol catabolism, sulfate assimilation, and various pathways for the biosynthesis of cell wall components.
The aim of this article was to show the labor valour during the Great Patriotic War of the employees of the first research institute in Irkutsk, which began its history in 1912, as well as their ...success of the present time. The oldest scientific institution in the Irkutsk region was originally created on the initiative of the Siberian Medical Society as a laboratory and was transformed into the Chemical and Bacteriological Institute in 1918, and in 1930 it became the Institute of Epidemiology and Microbiology of the People’s Commissariat of Public Health of Russia. By the beginning of the Great Patriotic War, the institute had an epidemiological department and a microbiological laboratory that carried out epidemiological surveillance and diagnosis of a wide range of infections in Siberia. During the war years, the manufacturing sector with the production of vaccines and serums acquired particular importance. By the end of the war, 285 employees worked at the institute, 32 of them had higher education. During the war years, the production of vaccines against typhoid, paratyphoid, dysentery, diphtheria, tuberculosis, and smallpox was significantly increased. Serums against tetanus and measles, and a dysentery bacteriophage were produced. At the same time, research projects and thesis works were carried out. The employees of the institute received national and departmental awards, commendations, honorary distinctions, and rewards for their scientific work and production excellence. Currently, the institute continues the glorious traditions of the past and demonstrates truly heroic efforts in the development of virology and microbiology, working in priority areas of medical and biological science. Of course, the works of scientists of the present time will be appreciated only by descendants, as is now happening with the assessment of the work of the Institute of Epidemiology and Microbiology during the Great Patriotic War.
One of the delayed consequences of SARS-CoV-2 infection is post-acute COVID-19 – polymorphic disorders of various organ systems that affect COVID-19 convalescents and persist for more than four ...weeks after an acute infection. Due to the infectious nature of the COVID-19, we would like to pay special attention to complications from the immune system, especially concomitant and new-onset autoimmune pathology. This review analyzes the current state of the issue of post-acute COVID-19 complications, discusses the molecular features of the SARS-CoV-2 virus and the mechanisms underlying the impaired immune response during acute COVID-19 infection and the occurrence of autoimmune and autoinflammatory conditions during convalescence. Particular attention is paid to the molecular mimicry of antigenic determinants of the SARS-CoV-2 virus, which are structurally similar to the epitopes of human autoantigens. The current data on post-acute COVID-19 autoimmune complications from humoral immunity and the endocrine system, as well as reproductive disorders faced by male patients are presented. For the first time, we hypothesize a role of the structural homology of the human SOX13 autoantigen (HMG box factor SOX13) associated with diabetes mellitus and SARS-CoV-2 envelope (E) protein in the development of the post-acute COVID-19 autoimmune pathologies. Due to the structural similarity of the two proteins and the overlap of their immunogenic regions, we suggest that the increased risk of developing diabetes mellitus and reproductive disorders in men after suffering from COVID-19 may be associated with immunological cross-reactivity.
The measurement of the level of mitochondrial DNA (mtDNA) in the blood is a difficult problem due to high variability of mitochondrial genes, deletions in the mitochondrial genome in some ...pathological conditions, different sources of mtDNA into the bloodstream (mtDNA from tissues, from blood cells,
etc
.). We designed primers and TaqMan probes for highly conserved regions of the
ND1
and
ND2
genes outside the mitochondrial deletions “hot zones”. For standardizing the technique, the true concentration of low-molecular-weight mtDNA was determined by real-time PCR for two targets: a fragment of the
ND2
gene (122 bp) and the
ND1
and
ND2
genes (1198 bp). The sensitivity and specificity of the developed approach were verified on a DNA pool isolated from the blood plasma of healthy donors of various nationalities. The concentration of low-molecular-weight mtDNA in the blood plasma of two patients with COVID-19 was monitored over two weeks of inpatient treatment. A significant increase in the content of low-molecular-weight mtDNA was observed during the first 5 days after hospitalization, followed by a drop to the level of healthy donors. The developed technique makes it possible to assess the blood level of low-molecular-weight mtDNA regardless of the quality of sampling and makes it possible to standardize this biological marker in a wide range of infectious and non-infectious pathologies.
Relevance.
The Irkutsk region belongs to the territories of Russia unfavorable for tuberculosis. The situation in the region is exacerbated by the existence of active tourism and trade and transport ...contacts with Mongolia, which is a country with a higher burden of TB.
Aims.
To assess the applicability of using subtype-specific PCR tests on clinical samples of TB patients to crossborder transmission analysis of the M. tuberculosis.
Materials and methods.
we investigated the cohort of 161 sputum and surgical specimens from newly diagnosed TB patients with a positive molecular genetic test (GeneXpert). The epidemic subtypes of the Beijing genotype (subtypes B0/W148, Central Asian, Asian-African 2) were identified by the method PCR with real-time detection (RT-PCR) with primers and probes of our own design.
Results.
The use of respiratory and surgical specimens with positive results of a molecular genetic test and microscopy makes it possible to differentiate epidemic subtypes of the Beijing genotype in 92.9% of cases. The frequency of detection of the Russian epidemic subtypes Central Asian (45.1%) and B0/W148 (20.3%) in clinical samples does not differ from data strains from the Irkutsk region. The «Mongolian» subtype Asian-African 2 of the Beijing genotype was not identified in the clinical samples in any case.
Conclusions.
The results indicate the applicability of the used tests for rapid monitoring as a stage in the complex of transboundary surveillance of tuberculosis.
Background
. Bedaquiline is a new and promising anti-tuberculosis drug, but longterm use requires resistance. This is due to mutations in the atpE and mmpR genes in M. tuberculosis (MBT).
The aim of ...the research
was to test a system for automated interpretation of results for predicting resistance to bedaquiline by the molecular data.
Materials and methods
. DNA was isolated from strains of M. tuberculosis in the Irkutsk region and Yakutia. The total quantity of DNA samples was 27 strains from Yakutia and 21 strains from the Irkutsk region. The study of MBT genomes was carried out on the DNA previously obtained by the authors in the territories of the Irkutsk region (n = 5), Yakutia (n = 4), Buryatia (n = 3), Zabaykalskiy kray (n = 4) and the Far East (n = 8). We used the BSATool program to detect bedaquiline resistance based on Sanger and genomic data. Sanger sequencing analyzed the atpE and mmpR genes, and whole genome sequencing examined mutations in the same sequences, as well as additionally in mmpL5, mmpS5, Rv0678, Rv1979c, and pepQ.
Results
. Complete agreement between the phenotypic and genotypic analysis of resistance to bedaquiline was found for three strains from Yakutia. One genome with significant mutations to bedaquiline was identified. A conclusion was made about the importance of molecular analysis of target genes with subsequent detection of resistance to bedaquiline in silico.
PDF
