Selection of IS6110 conserved regions for the detection of Mycobacterium tuberculosis using qPCR and LAMP.

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.

Variations in tuberculosis prevalence, Russian Federation: a multivariate approach.

OBJECTIVE: 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. METHODS: 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. FINDINGS: 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. CONCLUSION: 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.

Population structure of Mycobacterium tuberculosis from referral clinics in Western Siberia, Russia: Before and during the Covid-19 pandemic.

The dramatic change in global health imposed by the Covid-19 pandemic has also impacted TB control. The TB incidence decreased dramatically not because of the improved situation but due to undertesting, reduced resources, and ultimately, substantially reduced detection rate. We hypothesized that multiple and partly counteracting factors could influence changes in the local Mycobacterium tuberculosis population. To test this hypothesis, we analyzed M. tuberculosis isolates collected in Western Siberia, Russia, before and during the Covid-19 pandemic. A total of 269 M. tuberculosis isolates from patients admitted at referral clinics were studied. The pre-pandemic and pandemic collections included 179 and 90 isolates, respectively. Based on genotyping, both pre-pandemic and pandemic samples are heavily dominated by the Beijing genotype isolates (95% and 88%) that were mostly MDR (80 and 68%). The high proportion of MDR isolates is due to the specific features of the studied collections biased towards patients with severe TB admitted at the National referral center in Novosibirsk. While no dramatic change was observed in the M. tuberculosis population structure in the survey area in Western Siberia during the Covid-19 pandemic in 2020-2021 compared to the pre-pandemic collection, still we note a certain decrease of the Beijing genotype and an increase in the proportion and diversity of the non-Beijing isolates. However, the transmissible and MDR Beijing B0/W148 did not increase its prevalence rate during the pandemic. More generally, the high prevalence rate of the Beijing genotype and its strong association with MDR both before and during the pandemic are alarming features of this region in Western Siberia, Russia.

Studies of the Specific Activity of Aerosolized Isoniazid against Tuberculosis in a Mouse Model.

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.

Modeling of Mycobacterium tuberculosis dormancy in bacterial cultures.

The currently available methods are unable to directly detect dormant forms of Mycobacterium tuberculosis (Mtb) in vivo. The persistence of Mtb in the host body is detectable only in an indirect manner via the immunological response to Mtb-specific antigens. It is commonly recognized that the pathogen prevalently exists in the human body in a latent stage. Additional research efforts focusing on the Mtb dormancy are needed for development of sterilizing drugs, which are necessary to control LTBI and stop TB epidemic. To this end, the in vitro models of Mtb dormancy may be useful. This review briefly describes the phenomenon of Mtb dormancy and its role in the context of tuberculosis as a persistent bacterial infection; then the article characterizes in details the in vitro methods used for modeling the Mtb dormancy in bacterial cultures.

BCG infection in mice is promoted by naïve mesenchymal stromal cells (MSC) and suppressed by poly(A:U)-conditioned MSC.

Mesenchymal stromal cells (MSC) transplantation is an actively studied therapeutic approach used in regenerative medicine and in the field of control of immunoinflammatory response. Conditioning of MSC in culture can form their predominantly pro- or anti-inflammatory phenotypes. We demonstrated that poly(A:U)-conditioning of bone marrow-derived mouse MSC induced predominantly pro-inflammatory phenotype. The effects of administration of naïve MSC (nMSC) or conditioned MSC (cMSC) on the course of mycobacterial infection were studied. BALB/c mice infected i.p. with 5 × 106 M. bovis BCG were successively injected i.v. with 0.75 × 106 of nMSC or cMSC in 11 and 12.5 weeks after infection and sacrificed at the week 14. Histological and bacteriological examination of BCG-infected animals revealed low bacterial loads in liver, lungs and spleen; the bacterial load in spleen was higher than in other organs. Treatment with nMSC induced 3-fold increase of the number of bacteria in spleen granulomas, while cMSC decreased significantly the number of bacteria in BCG-positive granulomas. Analysis of preparations of organ homogenates by luminescent microscopy, MGIT cultures and CFU count on Lowenstein-Jensen medium revealed that nMSC promoted mycobacterial growth whereas cMSC suppressed mycobacterial growth significantly. We concluded that MSC therapy can be effective in mycobacterial infection, but only in a case of appropriate conditioning of the cells.