BackgroundTuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome.DescriptionHere we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes.ConclusionsImplementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains.

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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 IS 6110 -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.

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 ( Extrapulmonary tuberculosis (EPTB) remains a major health problem due to a significantly high rate of morbidity and mortality in both developing and developed countries and constitutes a significant part of the total TB incidence (1, 2). In Russia, the rate of EPTB decreased from 9.4% in 1992 to 3.4% in 2011, and the EPTB incidence constituted 2.4/100,000 in 2011 (3, 4). At the same time, the rate of tuberculous spondylitis (TBS) among all new EPTB cases increased in Russia from 23% in 2006 to 33% in 2010, which is higher than TB rate for of all other sites of the disease (3, 5).Tuberculous spondylitis constitutes about half of bone and joint TB cases and thus represents the most severe orthopedic disease, frequently leading to irreversible neurological disorders and disability and constituting a serious social and economic problem (6-8). TBS is developed as a result of blood-born dissemination of Mycobacterium tuberculosis. Bacteriological diagnosis of bone and joint TB is a most challenging task, and findings of drug resistance in these isolates may be crucial for adequate management of such cases. Delayed initial diagnosis and confirmation (from 3 months to 10 years after onset of the disease) and the increasing incidence of the multidrug-resistant TBS with spondyloarthropathy in adults require improvement of the etiological diagnostics, taking into account biological and molecular properties of the pathogen (4, 6, 7).M. tuberculosis has a clonal population structure, and it has been demonstrated that not only its large genetic families but also their variants or subgenotypes may play a special role in the disease progression. Russian strain Beijing B0/W148, initially defined by IS6110-restriction fragment length polymorphism (RFLP) analysis (9), presents a remarkable example of a successful clone highly associated with multidrug resistance (MDR) (10). Correlating different typing schemes, 24-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) type 1...

M ycobacterium tuberculosis isolates of the Beijing 94-32 cluster (also named the Central Asian/Russian Beijing strain) constitute an important component of the population structure of the pathogen in the countries of the Former Soviet Union (1-4). A variable-number tandem-repeat (VNTR)-based analysis suggested that this genotype could speculatively trace its origins to the northwestern regions of China (5). Beijing 94-32 is the largest type within the VNTR-defined CC1 group (6) and falls within the East Europe 1 group as defined by whole-genome sequencing (WGS) (7). Our analysis of all CC1 isolates compiled in the work of Merker et al. (6) demonstrated that type 94-32 presents the largest node in the central position in the phylogenetic network (see Fig. S1 in the supplemental material), and we therefore suggest naming this clonal complex the Beijing 94-32 cluster. The 94-32 cluster isolates were associated with multidrug-resistant/extremely drug-resistant tuberculosis in Russia (8) and in Uzbekistan (termed the Central Asia outbreak strain [2]), and in immigrants in Western Europe (9, 10). This justifies the interest in having a simple tool to rapidly detect this clinically and epidemiologically relevant strain. In this study, DNA of 19 Russian M. tuberculosis isolates of the Beijing genotype was subjected to WGS on the MiSeq platform (Illumina). The next-generation sequencing (NGS) data were deposited in the NCBI Sequence Read Archive (project number PRJNA305488). The fastq and vcf files were subjected to comprehensive bioinformatics