Genetic variation of Mycobacterium tuberculosis circulating in Kharkiv Oblast, Ukraine

<p>Abstract</p> <p>Background</p> <p>A persistent increase of tuberculosis cases has recently been noted in the Ukraine. The reported incidence of drug-resistant isolates of <it>M. tuberculosis </it>is growing steadily; however, data on the genetic variation of isolates of <it>M. tuberculosis </it>circulating in northern Ukraine and on the spectrum and frequency of occurrence of mutations determining resistance to the principal anti-tuberculosis drugs isoniazid and rifampicin have not yet been reported.</p> <p>Methods</p> <p>Isolates of <it>M. tuberculosis </it>from 98 tuberculosis patients living in Kharkiv Oblast (Ukraine) were analyzed using VNTR- and RFLP-IS6110-typing methods. Mutations associated with resistance to rifampicin and isoniazid were detected by RFLP-PCR methods, and also confirmed by sequencing.</p> <p>Results</p> <p>We identified 75 different genetic profiles. Thirty four (34%) isolates belonged to the Beijing genotype and 23 (23%) isolates belonged to the LAM family. A cluster of isolates belonging to the LAM family had significant genetic heterogeneity, indicating that this family had an ancient distribution and circulation in this geographical region. Moreover, we found a significant percentage of the isolates (36%) belonged to as yet unidentified families of <it>M. tuberculosis </it>or had individual non-clustering genotypes. Mutations conferring rifampicin and isoniazid resistance were detected in 49% and 54% isolates, respectively. Mutations in codon 531 of the <it>rpoB </it>gene and codon 315 of the <it>katG </it>gene were predominant among drug-resistant isolates. An association was found for belonging to the LAM strain family and having multiple drug resistance (R = 0.27, p = 0.0059) and also for the presence of a mutation in codon 531 of the <it>rpoB </it>gene and belonging to the Beijing strain family (R = 0.2, p = 0.04).</p> <p>Conclusions</p> <p>Transmission of drug-resistant isolates seems to contribute to the spread of resistant TB in this oblast. The Beijing genotype and LAM genotype should be seen as a major cause of drug resistant TB in this region.</p

Investigation on Mycobacterium tuberculosis Diversity in China and the Origin of the Beijing Clade

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Hydrogen and chlorine abundances in the Kimberley formation of Gale crater measured by the DAN instrument on board the Mars Science Laboratory Curiosity rover

The Dynamic Albedo of Neutron (DAN) instrument on board the Mars Science Laboratory Curiosity rover acquired a series of measurements as part of an observational campaign of the Kimberley area in Gale crater. These observations were planned to assess the variability of bulk hydrogen and neutron‐absorbing elements, characterized as chlorine‐equivalent concentration, in the geologic members of the Kimberley formation and in surface materials exposed throughout the area. During the traverse of the Kimberley area, Curiosity drove primarily over the “Smooth Hummocky” unit, a unit composed primarily of sand and loose rocks, with occasional stops at bedrock of the Kimberley formation. During the Kimberley campaign, DAN detected ranges of water equivalent hydrogen (WEH) and chlorine‐equivalent concentrations of 1.5–2.5 wt % and 0.6–2 wt %, respectively. Results show that as the traverse progressed, DAN observed an overall decrease in both WEH and chlorine‐equivalent concentration measured over the sand and loose rocks of the Smooth Hummocky unit. DAN measurements of WEH and chlorine‐equivalent concentrations in the well‐exposed sedimentary bedrock of the Kimberley formation show fluctuations with stratigraphic position. The Kimberley campaign also provided an opportunity to compare measurements from DAN with those from the Sample Analysis at Mars (SAM) and the Alpha‐Particle X‐ray Spectrometer (APXS) instruments. DAN measurements obtained near the Windjana drill location show a WEH concentration of ~1.5 wt %, consistent with the concentration of low‐temperature absorbed water measured by SAM for the Windjana drill sample. A comparison between DAN chlorine‐equivalent concentrations measured throughout the Kimberley area and APXS observations of corresponding local surface targets and drill fines shows general agreement between the two instruments

Hydrogen and chlorine abundances in the Kimberley formation of Gale crater measured by the DAN instrument on board the Mars Science Laboratory Curiosity rover

The Dynamic Albedo of Neutron (DAN) instrument on board the Mars Science Laboratory Curiosity rover acquired a series of measurements as part of an observational campaign of the Kimberley area in Gale crater. These observations were planned to assess the variability of bulk hydrogen and neutron‐absorbing elements, characterized as chlorine‐equivalent concentration, in the geologic members of the Kimberley formation and in surface materials exposed throughout the area. During the traverse of the Kimberley area, Curiosity drove primarily over the “Smooth Hummocky” unit, a unit composed primarily of sand and loose rocks, with occasional stops at bedrock of the Kimberley formation. During the Kimberley campaign, DAN detected ranges of water equivalent hydrogen (WEH) and chlorine‐equivalent concentrations of 1.5–2.5 wt % and 0.6–2 wt %, respectively. Results show that as the traverse progressed, DAN observed an overall decrease in both WEH and chlorine‐equivalent concentration measured over the sand and loose rocks of the Smooth Hummocky unit. DAN measurements of WEH and chlorine‐equivalent concentrations in the well‐exposed sedimentary bedrock of the Kimberley formation show fluctuations with stratigraphic position. The Kimberley campaign also provided an opportunity to compare measurements from DAN with those from the Sample Analysis at Mars (SAM) and the Alpha‐Particle X‐ray Spectrometer (APXS) instruments. DAN measurements obtained near the Windjana drill location show a WEH concentration of ~1.5 wt %, consistent with the concentration of low‐temperature absorbed water measured by SAM for the Windjana drill sample. A comparison between DAN chlorine‐equivalent concentrations measured throughout the Kimberley area and APXS observations of corresponding local surface targets and drill fines shows general agreement between the two instruments

Drug Resistant Mycobacterium tuberculosis of the Beijing Genotype Does Not Spread in Sweden

BACKGROUND: Drug resistant (DR) and multi-drug resistant (MDR) tuberculosis (TB) is increasing worldwide. In some parts of the world 10% or more of new TB cases are MDR. The Beijing genotype is a distinct genetic lineage of Mycobacterium tuberculosis, which is distributed worldwide, and has caused large outbreaks of MDR-TB. It has been proposed that certain lineages of M. tuberculosis, such as the Beijing lineage, may have specific adaptive advantages. We have investigated the presence and transmission of DR Beijing strains in the Swedish population. METHODOLOGY/PRINCIPAL FINDINGS: All DR M. tuberculosis complex isolates between 1994 and 2008 were studied. Isolates that were of Beijing genotype were investigated for specific resistance mutations and phylogenetic markers. Seventy (13%) of 536 DR strains were of Beijing genotype. The majority of the patients with Beijing strains were foreign born, and their country of origin reflects the countries where the Beijing genotype is most prevalent. Multidrug-resistance was significantly more common in Beijing strains than in non-Beijing strains. There was a correlation between the Beijing genotype and specific resistance mutations in the katG gene, the mabA-inhA-promotor and the rpoB gene. By a combined use of RD deletions, spoligotyping, IS1547, mutT gene polymorphism and Rv3135 gene analysis the Beijing strains could be divided into 11 genomic sublineages. Of the patients with Beijing strains 28 (41%) were found in altogether 10 clusters (2-5 per cluster), as defined by RFLP IS6110, while 52% of the patients with non-Beijing strains were in clusters. By 24 loci MIRU-VNTR 31 (45%) of the patients with Beijing strains were found in altogether 7 clusters (2-11 per cluster). Contact tracing established possible epidemiological linkage between only two patients with Beijing strains. CONCLUSIONS/SIGNIFICANCE: Although extensive outbreaks with non-Beijing TB strains have occurred in Sweden, Beijing strains have not taken hold, in spite of the proximity to high prevalence countries such as Russia and the Baltic countries. The Beijing sublineages so far introduced in Sweden may not be adapted to spread in the Scandinavian population

Testing Lunar Permanently Shadowed Regions for Water Ice: LEND Results from LRO

We use measurements from the Lunar Exploration Neutron Detector (LEND) collimated sensors during more than one year of the mapping phase of NASA's Lunar Reconnaissance Orbiter (LRO) mission to make estimates of the epithermal neutron flux within known large Permanently Shadowed Regions (PSRs). These are compared with the local neutron background measured outside PSRs in sunlit regions. Individual and collective analyses of PSR properties have been performed. Only three large PSRs, Shoemaker and Cabeus in the south and Rozhdestvensky U in the north, have been found to manifest significant neutron suppression. All other PSRs have much smaller suppression, only a few percent, if at all. Some even display an excess of neutron emission in comparison to the sunlit vicinity around them. Testing PSRs collectively, we have not found any average suppression for them. Only the group of 18 large PSRs, with area >200 square kilometers, show a marginal effect of small average suppression, approx. 2%, with low statistical confidence. An approx. 2% suppression corresponds to approx. 125 ppm of hydrogen taking into account the global neutron suppression near the lunar poles and assuming a homogeneous H distribution in depth in the regolith. This means that all PSRs, except those in Shoemaker, Cabeus and Rozhdestvensky U craters, do not contain any significant amount of hydrogen in comparison with sunlit areas around them at the same latitude

Genotypic and phenotypic characteristics of <i>Mycobacterium tuberculosis</i> drug resistance in TB children

Background. Russian Federation is included in the list of 30 countries with the highest burden of tuberculosis, including MDR tuberculosis. The most important part of this problem is the primary MDR/XDR TB in children.The aim: a comparative analysis of the phenotypic and genotypic profile of drug resistance to anti-tuberculosis drugs (ATP) according to whole genome sequencing of M. tuberculosis strains from children.Materials and methods. Whole genome sequencing (WGS) results of 61 M. tuberculosis isolates from children with tuberculosis in 2006–2020 in the Russian Federation were analyzed for anti-TB drug resistance mutations, according to the WHO catalog and were compared with the results of phenotypic drug sensitivity.Results. The M. tuberculosis belonged to two genetic groups: Beijing genotype – 82 % (50/61) dominant Central Asian Russian (31/50) and B0/W148 (16/50) subtypes, and non-Beijing (Ural, S, LAM) – 18 % (11/61). Three isolates belonged to Asian Ancestral subtype (3/50). Of the 61 isolates, only 14.7 % (9/61) were sensitive to antiTB drugs, 49.2 % (30/61) were MDR and 14.7 % (9/61) were pre-XDR. Comparison of the resistance profile (MDR/pre-XDR) with genotype revealed an upward shift for Beijing isolates, in particular Beijing B0/W148 (15/16) subline compared to other Beijing (19/34) (Chi-square with Yates correction = 5.535; p &lt; 0.05) and nonBeijing (5/12) (Chi-square with Yates correction = 6.741; p &lt; 0.05) subtypes. Discrepancies between genotypic and phenotypic drug resistance profiles were found in 11.5 % (7/61) of cases.Conclusions. Based on the analysis of WGS data, the genotypic characteristics of M. tuberculosis and the most complete set of drug resistance mutations were obtained, indicating a significant prevalence in MDR and pre-XDR TB of cases caused by epidemic subtypes of Beijing (B0/W148 and Central Asian Russian). The molecular mechanisms of adaptation of M. tuberculosis to the treatment of anti-TB drugs are not unique for the child population but reflect the general processes of the spread of MDR/XDR in Russia

Insight into Microevolution of Yersinia pestis by Clustered Regularly Interspaced Short Palindromic Repeats

BACKGROUND: Yersinia pestis, the pathogen of plague, has greatly influenced human history on a global scale. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), an element participating in immunity against phages' invasion, is composed of short repeated sequences separated by unique spacers and provides the basis of the spoligotyping technology. In the present research, three CRISPR loci were analyzed in 125 strains of Y. pestis from 26 natural plague foci of China, the former Soviet Union and Mongolia were analyzed, for validating CRISPR-based genotyping method and better understanding adaptive microevolution of Y. pestis. METHODOLOGY/PRINCIPAL FINDINGS: Using PCR amplification, sequencing and online data processing, a high degree of genetic diversity was revealed in all three CRISPR elements. The distribution of spacers and their arrays in Y. pestis strains is strongly region and focus-specific, allowing the construction of a hypothetic evolutionary model of Y. pestis. This model suggests transmission route of microtus strains that encircled Takla Makan Desert and ZhunGer Basin. Starting from Tadjikistan, one branch passed through the Kunlun Mountains, and moved to the Qinghai-Tibet Plateau. Another branch went north via the Pamirs Plateau, the Tianshan Mountains, the Altai Mountains and the Inner Mongolian Plateau. Other Y. pestis lineages might be originated from certain areas along those routes. CONCLUSIONS/SIGNIFICANCE: CRISPR can provide important information for genotyping and evolutionary research of bacteria, which will help to trace the source of outbreaks. The resulting data will make possible the development of very low cost and high-resolution assays for the systematic typing of any new isolate

The Beijing genotype and drug resistant tuberculosis in the Aral Sea region of Central Asia

BACKGROUND: After the collapse of the Soviet Union, dramatically increasing rates of tuberculosis and multidrug-resistant tuberculosis (MDR-TB) have been reported from several countries. This development has been mainly attributed to the widespread breakdown of TB control systems and declining socio-economic status. However, recent studies have raised concern that the Beijing genotype of Mycobacterium tuberculosis might be contributing to the epidemic through its widespread presence and potentially enhanced ability to acquire resistance. METHODS: A total of 397 M. tuberculosis strains from a cross sectional survey performed in the Aral Sea region in Uzbekistan and Turkmenistan have been analysed by drug susceptibility testing, IS6110 fingerprinting, and spoligotyping. RESULTS: Fifteen isolates showed mixed banding patterns indicating simultaneous infection with 2 strains. Among the remaining 382 strains, 152 (40%) were grouped in 42 clusters with identical fingerprint and spoligotype patterns. Overall, 50% of all isolates were Beijing genotype, with 55% of these strains appearing in clusters compared to 25% of non-Beijing strains. The percentage of Beijing strains increased with increasing drug resistance among both new and previously treated patients; 38% of fully-susceptible isolates were Beijing genotype, while 75% of MDR-TB strains were of the Beijing type. CONCLUSION: The Beijing genotype is a major cause of tuberculosis in this region, it is strongly associated with drug resistance, independent of previous tuberculosis treatment and may be strongly contributing to the transmission of MDR-TB. Further investigation around the consequences of Beijing genotype infection for both tuberculosis transmission and outcomes of standard short course chemotherapy are urgently needed