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Background This study included tuberculosis (TB) patients from high-burden Russian regions of Siberia and Far East. We aimed to assess the impact of the COVID-19 pandemic on the genotypic structure of Mycobacterium tuberculosis population and on epidemiology and clinical course of tuberculosis in TB and TB/COVID-19 coinfected patients. Methods A total of 456 M . tuberculosis isolates were studied and submitted to drug susceptibility testing and genotyping. The modern Beijing genotype and its main Russian epidemic and endemic clusters (B0/W148 and Central Asian/Russian), and ancient Beijing sublineage were detected by PCR assays targeting specific molecular markers. Non-Beijing isolates were spoligotyped and compared to SITVIT2 database. Results More than 80% of strains belonged to the Beijing genotype. Among Beijing strains, genetic clusters B0/W148 and Central-Asian/Russian (94–32) accounted for 94.2% in the pre-pandemic period and 96.6% during the pandemic in the TB group, and 81.5% of TB/COVID-19 group. Moreover, in the pre-pandemic TB group, the ratio of B0/W148 and 94–32 was almost 1:1 (49.7:44.4%), during the pandemic—1.5:1.0 (57.9:38.8%), while in the TB/COVID-19 group, the ratio shifted in favor of the 94–32 cluster and became 1:2 (31.8:65.9%). In TB/COVID patients, the structure of clinical forms shifted from chronic forms (fibrous cavernous TB, tuberculoma) to forms with more active inflammatory and destructive-inflammatory reactions (infiltration, dissemination, cavernous TB). In TB (without COVID-19-coinfection) group, the effectiveness of TB treatment during the pandemic decreased by 20.6% ( p  = 0.002). In the TB/COVID-19 group, the effectiveness of treatment increased, likely due to the predominance of the less frequently MDR Beijing 94–32 cluster in this group. A statistically significant positive correlation was shown between the detection of the 94–32-cluster and the effectiveness of treatment of patients with TB/COVID-19 (Q = 0.56, p  = 0.006). Conclusions Our results are consistent with the reportedly higher ability of Beijing B0/W148 strains (compared to Beijing 94–32) to acquire resistance to anti-TB drugs, their increased virulence and transmissibility. Thus, the seemingly paradoxical, milder clinical course of TB in patients who further developed COVID-19 is explained by a shift in the ratio of M. tuberculosis subtypes due to syndemic interaction between the two epidemics.

Bedaquiline is a cornerstone drug for treating drug-resistant tuberculosis. We analyzed 11 isolates from 9 patients who were treated with a bedaquiline-based regimen and remained culture-positive long after treatment start. In 4 of 8 resistant isolates, we found substitutions in AtpE, which encodes subunit c of the Mycobacterium tuberculosis ATP synthase and is rarely identified in clinical isolates. We found Ile66Met and Glu61Asp substitutions in 2 cases each. Additional mutations in mmpL5, mmpL4, and atpB genes could affect the susceptibility to bedaquiline. MmpL5(Asn772Thr) emerged during bedaquiline treatment, whereas AtpB(Val165Leu) was found in 1 case simultaneously with the loss-of-function mmpR5 mutation in a susceptible strain. The loss-of-function mutation in the mmpL4 efflux gene was identified in the mixed state, pointing to ongoing selection in a bedaquiline-resistant isolate. Another case of the emergence of the mmpL4 mutation, accompanied by a proportional increase in bedaquiline MIC, was identified by retrospective analysis of genomes from bedaquiline-resistant isolates.

The Haarlem genotype is a significant yet understudied part of the Euro-American lineage of Mycobacterium tuberculosis , characterized by unique pathogenetic features. Spoligotyping is a primary method for its detection, but it is not suitable for isolates with long blocks of deleted spacers. We have developed a simple and robust method to detect the Haarlem genotype. The real-time PCR (RT-PCR) assay with LNA probes was designed to detect the Rv0282 211 C > T mutation that was shown to be specific for the Haarlem genotype. The developed RT-PCR assay was optimized with 68 isolates with known whole-genome sequencing (WGS) data and applied to the geographically and genetically diverse collection of 428 isolates. As a result, 396 isolates were concordantly assigned to either Haarlem or non-Haarlem genotypes by both methods, whereas 32 isolates were discrepant cases. Twenty-two isolates of “unknown genotype” (Russia, Belarus, and Poland) were assigned to Haarlem by SNP-based assay. WGS of these isolates confirmed the results of the RT-PCR assay. To conclude, the developed RT-PCR method provides a reliable detection of the Haarlem genotype in retrospective collections and under prospective epidemiological surveillance. Its actual proportion in M. tuberculosis populations in certain world regions is higher than previously thought. Abridged spoligoprofiles with large deleted blocks of spacers require caution in interpretation.

The aerosol inhalation delivery of isoniazid in mice was investigated, and the specific activity of the aerosol form of isoniazid was studied with the mouse model of tuberculosis infection, the M. tuberculosis H37Rv strain. Aerosol delivery was performed using a laminar-flow horizontal nucleation chamber. The inhalation dose was measured in real-time mode using a diffusion aerosol spectrometer. The mean particle diameter was 0.6 ± 0.03 μm, and the inhalation dose was 5–9 mg/kg. Pharmacokinetic measurements were carried out in nose-only and whole-body chambers. Isoniazid concentration in blood serum and its mass in the lungs were measured as a function of time using high-performance liquid chromatography. Studies of the specific activity of aerosolized isoniazid reveal that treatment with the aerosol lead to the complete recovery of the experimental tuberculosis infection as early as after 28 days after the start of inhalation treatment, while in the animals from the group receiving isoniazid per-orally, sole revivable tuberculosis mycobacteria were detected. Histologic examinations show that only a few macrophagal (nonspecific) granulomas without mycobacteria were detected in the spleen after per-oral and aerosol treatment, the number of granulomas on the 28th day being three times smaller in the latter case. The results show that the developed technique of isoniazid aerosol inhalation may have clinical potential.

IS6110 insertion sequence is a frequently used target for Mycobacterium tuberculosis detection. However, its sequence variability is studied insufficiently. We aimed to identify the most conservative and variable regions in IS6110 sequences and develop qPCR and LAMP oligonucleotide sets for the conservative regions. Using in-house Python scripts, 3609 M. tuberculosis genome sequences from the NCBI database were aligned; conservative regions were identified to design oligonucleotide sets. IS6110 fragments located within the 31–231 bp region were the most conservative and represented in genomes and were used to design qPCR and LAMP oligonucleotides. The in silico sensitivity of the qPCR oligonucleotides on the whole genome set was 99.1% and 98.4%. For the LAMP primers developed, the sensitivity was 96.9%. For qPCR, the limit of detection with 95% confidence (LoD95%) was four IS6110 copies per reaction, with LoD90% being 200 BCG cells per ml of artificial sputum. For LAMP, LoD95% was 16 copies per reaction, with LoD90% being 400 Mycobacterium bovis Bacille Calmette–Guerin (BCG) cells per ml of artificial sputum. We have demonstrated the IS6110 sequence variability and designed highly sensitive qPCR and LAMP oligonucleotides to detect M. tuberculosis.

Infections caused by nontuberculous mycobacteria (NTM) are rising globally throughout the world. The number of species isolated from clinical samples is steadily growing, which demands the implementation of a robust diagnostic method with wide specificity. This study was carried out in in 2022–2024 in three clinical antituberculosis centers in the biggest cities of Russia: Moscow, Saint Petersburg, and Novosibirsk. We developed the DNA hybridization assay ‘Myco-biochip’ that allows the identification of 79 mycobacterial species and analyzed 3119 samples from 2221 patients. Sixty-eight mycobacterial species were identified in clinics, including the three novel species phylogenetically related to M. duvalii, M. lentiflavum, and M. talmoniae. The identification of a close relative of M. talmoniae adds to the existence of separate clade between M. terrae, M. triviale complexes and other slow-growing Mycobacteria, which supports the thesis against the splitting of Mycobacteria into five separate genera. Adding to the list of potentially pathogenic species, we identified M. adipatum and M. terramassiliense, which were previously described as natural habitats. The diversity of acid-fast bacilli identified in TB-suspected persons was not limited to the Mycobacteria genus and also includes species from genera Nocardia, Gordonia, Corynebacterium, Tsukamurella, and Rhodococcus of the order Mycobacteriales. The revealed bacterial diversity in patients with suspected NTM-diseases requires the implementation of relevant species identification assays as the first step in the laboratory diagnostic pipeline.

To analyse the epidemiological trends of tuberculosis in the Siberian and Far Eastern federal districts, the areas with the highest disease burden in the Russian Federation. We applied principal coordinate analysis to study a total of 68 relevant variables on tuberculosis epidemiology, prevention and control. Data on these variables were collected over 2003-2016 in all 21 regions of the Siberian federal district and Far Eastern federal district (total population: 25.5 million) through the federal and departmental reporting system. We identified the regions with a favourable or unfavourable tuberculosis epidemiological profile and ranked them as low or high priority for specific interventions. The median number of tuberculosis notifications in the regions was 123.3 per 100 000 population (range: 54.5-265.7) in 2003, decreasing to 82.3 per 100 000 (range: 52.9-178.3) in 2016. We found large variations in the tuberculosis epidemiological profile across different regions. The principal coordinate analysis revealed that three aggregated indicators accounted for 55% of the variation. The first coordinate corresponded to tuberculosis prevalence and case notifications in the regions; the second to the severity of the disease among patients; and the third to the percentage of multidrug-resistant tuberculosis among tuberculosis patients. The regions where intervention was most urgently needed were Chukotka Autonomous Okrug, Jewish Autonomous Oblast and Tyva Republic. The variability in tuberculosis epidemiology across regions was likely due to differences in the quality of antituberculosis services. Precision in defining necessary interventions, as determined through the principal coordinate analysis approach, can guide focused tuberculosis control efforts.

Metodos Se aplico el analisis de coordenadas principales para estudiar un total de 68 variables relevantes en epidemiologia, prevencion y control de la tuberculosis. Los datos sobre estas variables se recopilaron entre 2003 y 2016 en las 21 regiones del distrito federal de Siberia y del distrito federal del Extremo Oriente (poblacion total: 25,5 millones) a traves del sistema de presentacion de informes federal y departamental. Se identificaron las regiones con un perfil epidemiologico favorable o desfavorable de la tuberculosis y se clasificaron como de baja o alta prioridad para intervenciones especificas.

To identify coping strategies and socio-demographics impacting satisfaction with life and quality of life in Crohn's disease (CD). 402 patients completed the Patient Harvey-Bradshaw Index, Brief COPE Inventory, Satisfaction with Life Scale (SWLS), Short Inflammatory Bowel Disease Questionnaire (SIBDQ). We performed structural equation modeling (SEM) of mediators of quality of life and satisfaction with life. The cohort comprised: men 39.3%, women 60.1%; P-HBI 4.75 and 5.74 (p = 0.01). In inactive CD (P-HBI≤4), both genders had SWLS score 23.8; men had SIBDQ score 57.4, women 52.6 (p = 0.001); women reported more use of emotion-focused, problem-focused and dysfunctional coping than men. In active CD, SWLS and SIBDQ scores were reduced, without gender differences; men and women used coping strategies equally. A SEM model (all patients) had a very good fit (X2(6) = 6.68, p = 0.351, X2/df = 1.114, SRMR = 0.045, RMSEA = 0.023, CFI = 0.965). In direct paths, economic status impacted SWLS (β = 0.39) and SIBDQ (β = 0.12), number of children impacted SWLS (β = 0.10), emotion-focused coping impacted SWLS (β = 0.11), dysfunctional coping impacted SWLS (β = -0.25). In an indirect path, economic status impacted dysfunctional coping (β = -0.26), dysfunctional coping impacted SIBDQ (β = -0.36). A model split by gender and disease activity showed that in active CD economic status impacted SIBDQ in men (β = 0.43) more than women (β = 0.26); emotional coping impacted SWLS in women (β = 0.36) more than men (β = 0.14). Gender differences in coping and the impacts of economic status and emotion-focused coping vary with activity of CD. Psychological treatment in the clinic setting might improve satisfaction with life and quality of life in CD patients.