Analysis of the Diversity and Functional Potential of Bacterial Communities in Tuberculomas.

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.

Online Service with Automated Interpretation of Sequencing Data and Prediction of Pyrazinamide Resistance in Mycobacterium tuberculosis.

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.

A Method to Determine Xenobiotic Acetylation Rate by Taq SNP rs1495741.

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.

A Method for Evaluation of the Level of Circulating Mitochondrial DNA by ND1 and ND2 Genes.

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.

SNP rs657152 Is Not Associated with the Level of Viral Load in COVID-19 or the Probability of Disease in the Population of Caucasians in Eastern Siberia.

Cross-replicating associations with rs657152 at the 9q34.2c locus and rs11385942 at the 3p21.31 locus found in patients with severe COVID-19 in the Caucasian population require the study of the discovered phenomenon in various populations, including as an independent biological marker. Primers and TaqMan probes for PCR discrimination of the A and C alleles in single nucleotide polymorphism (SNP) rs657152 have been developed. The polymorphism of the rs657152 A/C locus was determined in 129 patients with COVID-19 and in a control group of 466 healthy individuals. There were no significant differences in the frequency of distribution of the A and C alleles, 0.47/0.53 and 0.45/0.55, between patients and healthy subjects, respectively. Also, no differences were found in the distribution of alleles in patients with a high viral load in the smear (Ct in the range of 16-25) in comparison with an average and low viral load (Ct in the range of 26-40).

[Assessment of external risk factors of hepatocellular cancer development and markers of genetic predisposition to its development in the ethnic group of yakut - men].

AIM: To establish the main external and genetically determined risk factors for the development of hepatocellular cancer in the ethnic group of male Yakuts living in the Republic of Sakha (Yakutia) [RS (Y)] in the epidemiologically unfavorable conditions of the incidence of viral hepatitis. MATERIALS AND METHODS: A total of 97 male Yakuts were examined, including 44 people diagnosed with hepatocellular cancer and 53 people diagnosed with chronic viral hepatitis. HCC risk factors were identified by analyzing medical records and questioning patients. In the experimental and control groups, genetic studies of single nucleotide polymorphisms of genes mapped on the X-chromosome and involved in the activation of antiviral immunity along the TLR7 signaling pathway were performed. RESULTS AND DISCUSSION: In 100% of patients with hepatocellular cancer, infection with hepatitis B, C, D viruses or co - infection with these agents was detected. Every fourth patient with HCC in the RS (Y) was infected with hepatitis D. The course of hepatocellular cancer associated with HDV was characterized by rapid progression of liver cirrhosis, development of portal hypertension, bleeding from varicose veins of the stomach and esophagus (36.4%) and edematous ascitic syndrome (63.6%). In addition to viral agents, additional risk factors for liver cancer were identified, such as alcohol abuse, overweight, diabetes mellitus, and smoking. Among the studied variation sites of genes localized on the X-chromosome and encoding the reaction of innate antiviral immunity, no genetic marker was found with a sufficient degree of confidence determining the likelihood of hepatocellular cancer developing. CONCLUSIONS: The high incidence of hepatocellular carcinoma of the male population in the RS (Y) is due to the widespread prevalence of parenteral viral hepatitis, especially viral hepatitis D. Due to the introduction of mass vaccination of the population against hepatitis B in the Russian Federation in the foreseeable future in the RS (Y) we should see a decrease in the proportion of hepatocellular cancer associated with hepatitis B and D viruses, and therefore the focus should be on the treatment and prevention of hepatitis C virus and non - infectious risk factors.

[The detection of highly-transmissible genotypes of agent in clinical samples for prognosis of unfavorable course of tuberculosis.]

The bio-information search was carried out and the design of primers and TaqMan probes was developed to detect DNA of agent of tuberculosis subtypes CC1 and CC2-W148 of Beijing genotype and also Ural genotype in various clinical material (phlegm, spinal fluid, pleural fluid, etc.) using real-time polymerase chain reaction technique. The 180 clinical samples from 143 patients with tuberculosis of lungs were used to carry out an approval of sensitivity and specificity of the developed tests concerning studies at the genetic analyzer GeneXpert. The sensitivity of tests on CC1, CC2-W148 и Ural relating to polymerase chain reaction of analyzer Gene Expert made up to 91%, 106% and 81% correspondingly. In all cases, the specificity made up to 100%. In parallel studies the samples with DNA of СС2-W148 genotype were more often positive on mutation of resistance to Rifampicin-Rif (+) according the results of GeneXpert (χ² = 27,1; p < 0,01) related to other genotypes. At the same time, detection of СС2-W148 strain in patient was more often accompanied by discrepancy of results: GeneXpert - Rif (+) and resistance to Rifampicin in bacteriological study under ultimate validation of multiple medicinal resistance of tuberculosis (χ² = 5,1; p < 0,05). The analysis was applied to negative effect of combination of allele-336G of CD209 gene of patient with genotype of tuberculosis mycobacterium Beijing detected previously (Ogarkov et al., 2012). The significant prevalence was observed related to widespread medicinal resistance (χ² =4,3; p < 0,05) in patients with allele-336G of CD209 gene in combination with CC2-W148 clone in comparison with other combinations in patients. The obtained results testify a possibility of application of genetic typing of tuberculosis agent and patient for early diagnosis of development of various complications of tuberculosis at the stages of primary examination of primarily detected patients with tuberculosis.

Draft genome sequence of Mycobacterium tuberculosis strain B9741 of Beijing B0/W lineage from HIV positive patient from Siberia.

We report a draft genome sequence of Mycobacterium tuberculosis strain B9741 belonging to Beijing B0/W lineage isolated from a HIV patient from Siberia, Russia. This clinical isolate showed MDR phenotype and resistance to isoniazid, rifampin, streptomycin and pyrazinamide. We analyzed SNPs associated with virulence and resistance. The draft genome sequence and annotation have been deposited at GenBank under the accession NZ_LVJJ00000000.

Population Polymorphism of IFNL3 and IFNL4 Genes of Type 3 Interferon Associated with Spontaneous Clearance of Hepatitis C Virus in Representatives of Caucasian and Mongoloid Races.

The frequency of single nucleotide polymorphisms of IFNL3 gene (rsl12979860 and rs8099917) and dinucleotide polymorphism of IFNL4 gene (ss469415590) were estimated in healthy inhabitants of Mongolia and Irkutsk regions taking into account their races. Population and genetic studies were performed in 1520 conventionally healthy volunteers (blood donors), representatives of Caucasian and Mongoloid races. Significant race-related differences in the incidence of IFNL3 and IFNL4 gene polymorphisms associated with spontaneous clearance of hepatitis C virus were found in healthy volunteers.

Undertreated HIV and drug-resistant tuberculosis at a referral hospital in Irkutsk, Siberia.

SETTING: A referral hospital for tuberculosis (TB) in Irkutsk, the Russian Federation. OBJECTIVE: To describe disease characteristics, treatment and hospital outcomes of TB-HIV (human immunodeficiency virus). DESIGN: Observational cohort of HIV-infected patients admitted for anti-tuberculosis treatment over 6 months. RESULTS: A total of 98 patients were enrolled with a median CD4 count of 147 cells/mm(3) and viral load of 205 943 copies/ml. Among patients with drug susceptibility testing (DST) results, 29 (64%) were multidrug-resistant (MDR), including 12 without previous anti-tuberculosis treatment. Nineteen patients were on antiretroviral therapy (ART) at admission, and 10 (13% ART-naïve) were started during hospitalization. Barriers to timely ART initiation included death, in-patient treatment interruption, and patient refusal. Of 96 evaluable patients, 21 (22%) died, 14 (15%) interrupted treatment, and 10 (10%) showed no microbiological or radiographic improvement. Patients with a cavitary chest X-ray (aOR 7.4, 95%CI 2.3-23.7, P = 0.001) or central nervous system disease (aOR 6.5, 95%CI 1.2-36.1, P = 0.03) were more likely to have one of these poor outcomes. CONCLUSION: High rates of MDR-TB, treatment interruption and death were found in an HIV-infected population hospitalized in Irkutsk. There are opportunities for integration of HIV and TB services to overcome barriers to timely ART initiation, increase the use of anti-tuberculosis regimens informed by second-line DST, and strengthen out-patient diagnosis and treatment networks.

Administrative interventions associated with increased initiation on antiretroviral therapy in Irkutsk, Siberia.

A bundle of initiatives to integrate human immunodeficiency virus (HIV) and tuberculosis (TB) services was assessed for the impact on antiretroviral therapy (ART) initiation at a TB referral hospital in Irkutsk, Russian Federation, from February 2014 to December 2015. The ART initiation rates in 166 ART-naïve patients undergoing anti-tuberculosis treatment (34.1% with multidrug or extensively drug-resistant TB) increased significantly from 14 (17%) pre-intervention to 44 (54%) post-intervention (P < 0.001). A survey of TB hospital staff identified administrative prioritisation as the most important initiative for increasing ART initiation.

Un ensemble d'initiatives visant à intégrer les services relatifs au virus de l'immunodéficience humaine (VIH) et à la tuberculose (TB) a été évalué en termes d'impact sur la mise en route du traitement antirétroviral (TAR) dans un hôpital de référence de la TB à Irkoutsk, Fédération de Russie, entre février 2014 et décembre 2015. Les taux de mise en route du TAR chez 166 patients n'en ayant jamais reçu et traités pour TB (34,1% avec une TB multi-résistante ou ultra-résistante) ont significativement augmenté de seulement 14 (17%) avant l'intervention à 44 (54%) après l'intervention (P < 0,001). Une enquête auprès du personnel de la TB a identifié la priorisation administrative comme l'initiative la plus importante dans l'augmentation de l'initiation du TAR.

Se evaluó un conjunto de iniciativas encaminadas a integrar los servicios de atención de la infección por el virus de la inmunodeficiencia humana (VIH) y la tuberculosis (TB), con el objeto de determinar la repercusión de la integración sobre el comienzo del tratamiento antirretrovírico (TAR) en el hospital de referencia de la TB de Irkutsk, en la Federación de Rusia, de febrero del 2014 a diciembre del 2015. La tasa de iniciación del TAR en 166 pacientes que nunca lo habían recibido y que estaban en curso de tratamiento antituberculoso (34,1% con TB multirresistente o extremadamente multirresistente) aumentó de manera significativa de solo 14 pacientes antes de la intervención (17%) a 44 pacientes después de la misma (54%; P < 0,001). Al interrogar al personal encargado de la TB en este hospital de referencia, se puso en evidencia que la priorización administrativa del TAR constituía la iniciativa de más había influido en el incremento de su utilización.

GENETIC DIVERSITY OF THE MYCOBACTERIUM TUBERCULOSIS ISOLATES IN THE REPUBLIC SAKHA (YAKUTIA), RUSSIA.

The population structure of the M. tuberculosis in Yakutia was estimated by the MIRU-VNTR method of 24 loci genotyping. 199 strains from 199 patients with pulmonary tuberculosis were tested. The greatest number of the strains (34.2%, 68/199) belonged to the genotype Beijing. The significant predominance (X² = 15.5; p < 0.001) of the multidrug and extensively drug-resistance (MDR/XDR) among the isolates of Beijing genotype was revealed in subtype CC2/ W148 - 9.5% (19/199). Strains of the genotype S (15.6%, 31/199) were the second most common genotype after Beijing. The majority of S-strains had an identical profile 233325153325141344222372. S genotype strains also significantly more frequently carried the MDR/ XDR (X² = 59.8;p<0.001) among non-Beijing isolates. The genotype strain Ural ranks the third in the prevalence - 10.0% (20/199). The strains belonging to the family LAM (8.5%, 17/199) had considerable genetic heterogeneity. A great genetic diversity was also found in minor genotypes T and Haarlem. A phylogenetic reconstruction of the epidemic spread of the S-genotype and subtype CC2/W148 of the Beijing genotype in Yakutia was performed with estimation of the probable time of origin in the scale proposed by Merker M. et al. (2015). It was shown that the strains of the subtype CC2/W148 had been formed from four distinct phylogenetic sublines in recent historical period (XX century). It was estimated that phylogenetic relationships accounted for 30 MIRU-VNTR profiles of S-strains from Yakutia and 31 reference S-profiles from Europe and Canada. The profiles of the S-genotype from Yakutia form a phylogenetically compact group, indicating that all evolutionary history of these strains happened in the Sakha Republic. The time of the ancestral S-genotype spreading in Yakutia was estimated to be in the range from 300 to 600 years.

[Identification of ubiquitous and endemic Mycobacterium tuberculosis genotypes in the Republic of Buryatia].

The MIRU-12 and MIRU-24 methods were used for genotyping and estimation of M. tuberculosis population structure in Buryatia. It was studied in 283 strains isolated from individuals from the regional TB dispensary and medical clinics of the penitentiary system of the republic. It was found that the prevalence of pandemic genotypes Beijing MIT17 and MIT16 and also subtype Beijing MIT642 (24.5% - 46/188) in the studied area were dominant. The isolates of the Beijing MIT642 were common among all groups of patients with pulmonary tuberculosis with the tendency to formation of MDR and chronic course of the disease.

[Polymorphism of genes of the renin-angiotensin system ACE, AT1R, and AT2R in patients with pulmonary tuberculosis].

The goal of this work was to verify the hypothesis about the possible role of some genes of the renin-angiotensin system in the innate immunity to tuberculosis. The insertion/deletion polymorphism (I/D) of the gene of the angiotensin-converting enzyme (ACE) is known to have an effect on the concentration of the angiotensin II in human body and also an indirect effect on various branches of metabolism. On the one hand, people with homozygote deletion of the ACE gene (DD genotype) are vulnerable to adiposity, arterial hypertension, hypercholesterolemia, and a number of other pathological conditions. On the other hand, it was shown that hypocholesterolemia is the general phenomenon for the patients with pulmonary tuberculosis (Perez-Guzman C. et al., Chest (2005)). In this work, we studied the I/D polymorphism of the gene ACE (genotypes DD, ID, and II), single nucleotide polymorphism (SNP) of the gene AT1R (1166 A/C), and SNP in 3123 positions of the gene AT2R (3123 A/C) in 200 patients with tuberculosis, 202 patients with essential hypertension, and 208 apparently healthy subjects. A group of patients with essential hypertension was used as a contrast group. According to the hypothesis stated above, the excess in the number of patients with the DD genotype (ACE) should be statistically significant in the group of patients with hypertension as compared to the group of patients with tuberculosis (chi2 = 9.64; chi2 = 0.0019; OR = 2.0; CI 1.2-3.3). There was a trend toward an increase in the rate of the DD genotype in the group of patients with tuberculosis relative to healthy subjects. Similar trend was observed in healthy subjects relative to the group of patients with hypertension. However, this difference was found to be statistically insignificant. The genotypes and allelotypes were compared in the group of patients with tuberculosis versus both the two control groups (healthy subjects and patients with hypertension). The significant difference from control was observed only in male rather than female patients with tuberculosis. It was shown that the greatest contribution to the distinction between groups was due to the genes ACE and AT2R. The combination of the genotypes of genes ACE and AT2R (ID+3123C) was met significantly more frequently in male patients with tuberculosis as compared to control group of healthy subjects (chi2 = 9.70; chi2 = 0.002; OR = 2.3; CI 1.2-4.3). The results obtained in this work are discussed in terms of the hypothesis stated above.

[Study of DC-SIGN gene polymorphism in patients infected with Mycobacterium Tuberculosis strains of different genotypes in the Irkutsk Region].

Polymorphism of the promoter of DC-SIGN gene in Caucasians was studied at positions -336A/G and -871/G in 134 patients with pulmonary tuberculosis and 112 healthy individuals, who lived in the Irkutsk Region, Eastern Siberia. In 90 patients from the patient cohort M. tuberculosis DNA was isolated and investigated using the MIRU-VNTR typing test by 12 loci. Comparison of DC-SIGN gene polymorphism in patients with tuberculosis and healthy controls revealed no significant differences in loci -336A/ G and -871A/G. Analysis of MIRU-VNTR patterns identified 50 unique profiles, among which there were genotypes of the families Beijing, T. LAM, Haarlem, "Ural" (Haarlem 4) and X. Among 90 MIRU-VNTR genotypes, 42 profiles belonged to the Beijing family. Moreover, the minimum spanning tree (MST) test revealed a number of Beijing-like strains. The genotypes of the subjects affected with Beijing and Beijing-like strains and those affected with the strains of other families (non-Beijing) were compared. A significance reduction was found in the incidence of the -336G genotype among the subjects affected with Beijing strains versus those infected with non-Beijing strains at a frequency of 0.09 and 0.24, respectively (chi2 = 7.64; p = 0.006; OR = 2.7; 95% CI 1.1-6.1).

[MIRU-VNTR genotyping of Mycobacterium tuberculosis strains from East Siberian: Beijing family versus Kilimanjaro family]. / MIRU-VNTR-genotipirovanie shtammov Mycobacterium tuberculosis v Vostochnoi Sibiri: semeistvo Beijing protiv Kilimanjaro.

Seventy-two M. tuberculosis strains isolated from patients in different regions of East Siberia were studied by MIRU-VNTR repeats. Phylogenetic trees of relationship between the studied strains and of those from other world regions were investigated by phylogenetic analysis, i.e. NJ, UPGMA and ML. Phylogenetic evidence is provided for the prevalence of Beijing and Beijing-like strains (71%) in the above region. Besides, there was found a group of strains (115%) with the robust genotype which was given the name of ASU (African-Siberian-Ural). A linkage between MIRU10 (5-10 repeat) and MIRU26 (single repeat) was established as a predominant ASU sign. According to preliminary results, apart from Siberia, ASU strains can be encountered in the Urals and Africa (Tanzania, Kilimanjaro genotype). MIRU-VNTR consensus of ASU for East Siberia is 22( > 6)225113233.

[Estimation of the efficiency of ERIC-PCR typing of Mycobacterium tuberculosis for evaluation of the prevalence of antibiotic-resistant strains]. / Otsenka éffektivnosti ERIC-PCR-tipirovaniia Mycobacterium tuberculosis pri izuchenii rasprostraneniia ustoichivykh k antibiotikam shtammov.

Twenty-four antibiotic-resistant and sensitive strains of M. tuberculosis isolated from different territories of the Irkutsk region (East Siberia) were studied using PCR genotyping by enterobacterial repetitive intergeneric consensus (ERIC). Evolution relationships are illustrated by phylogenetic trees as a result of analysis by UPGMA and ML approaches. It was found that the studied samples belonged to two genetically different groups, both of which included sensitive and resistant strains. The sensitivity of the method was calculated by the Hunter-Gaston index. Based on these data, a probable pattern of emergence and propagation of antibiotic-resistant forms of tuberculosis in the studied region is discussed.

Patterns of evolutionary change in Baikalian gammarids inferred from DNA sequences (Crustacea, Amphipoda).

The Baikalian gammarids (Crustacea, Amphipoda) are the most widely known and most spectacular example of an adaptive radiation among contemporary freshwater invertebrates. To study the phylogeny of the Baikalian gammarids we sequenced a 622-bp-long fragment of the nuclear gene coding for 18S rRNA from species of 18 endemic Baikalian genera and Gammarus pulex-a non-Baikalian taxon. Some important morphological characters appear independently in both lineages and suggest parallelism in the development of gigantism and body armament. The first lineage comprises benthic, mostly unarmed taxa. The second lineage contains predominantly armed taxa, most of which are detrivorous or carnivorous.