Comparative Analysis of Genotyping Methods for Bacillus anthracis

Еременко, Е. И.; Ryazanova, A. G.; Писаренко, С. В.; Aksenova, L. Yu.; Семенова, О. В.; Koteneva, E. A.; Tsygankova, O. I.; Kovalev, Dmitry; Golovinskaya, T. M.; Чмеренко, Д. К.; Куличенко, А. Н.

doi:10.1134/s102279541901006x

Cited by 3 publications

(3 citation statements)

References 39 publications

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“…All 17 strains belong to MVLST pXO1 GT-3 (Table 8 and Table S1)-i.e., they have no other differences among themselves in terms of the sequence of genes described in this work. Thus, our results complement the data of Eremenko and Okinaka [36,37] and indicate that SNP pagA 981A→T is a marker of a rather large subgroup of the A.Br.008/011 group. This subgroup is spread over territory stretching over 6000 km from west to east and about 4000 km from north to south, including Central Asia, the Caucasus, the Black Sea and Caspian steppes, the European part of Russia, and even the eastern Arctic (Yakutia).…”

Section: Discussionsupporting

confidence: 87%

“…This SNP had earlier been proposed as a specific marker for a small subgroup of the canSNP group A.Br.008/009, which was originally isolated in Russia (the so-called Sverdlovsk group) but has also been found in Norway, Hungary, and Slovakia [36]. A little later, Eremenko, during the genotyping of B. anthracis strains from the Stavropol Antiplague Institute collection, found this SNP in all eight strains belonging to the canSNP group A.Br.008/009 in the studied sample [37]. In the present study, we found SNP pagA 981A→T in 17 out of the 27 strains in the A.Br.008/011 group (as we have already indicated, A.Br.008/011 together with group A.Br.011/009 is included in the A.Br.008/009 group) isolated in the territory of the former USSR (Table 1, Table 8 and Table S1).…”

Section: Discussionmentioning

confidence: 78%

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Sequence Variability of pXO1-Located Pathogenicity Genes of Bacillus anthracis Natural Strains of Different Geographic Origin

et al. 2021

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The main pathogenic factor of Bacillus anthracis is a three-component toxin encoded by the pagA, lef, and cya genes, which are located on the pXO1 plasmid. The atxA gene, which encodes the primary regulator of pathogenicity factor expression, is located on the same plasmid. In this work, we evaluated the polymorphism of the pagA, lef, cya, and atxA genes for 85 B. anthracis strains from different evolutionary lineages and canSNP groups. We have found a strong correlation of 19 genotypes with the main evolutionary lineages, but the correlation with the canSNP group of the strain was not as strong. We have detected several genetic markers indicating the geographical origin of the strains, for example, their source from the steppe zone of the former USSR. We also found that strains of the B.Br.001/002 group caused an anthrax epidemic in Russia in 2016 and strains isolated during paleontological excavations in the Russian Arctic have the same genotype as the strains of the B.Br.CNEVA group circulating in Central Europe. This data could testify in favor of the genetic relationship of these two groups of strains and hypothesize the ways of distribution of their ancestral forms between Europe and the Arctic.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 78%

Sequence Variability of pXO1-Located Pathogenicity Genes of Bacillus anthracis Natural Strains of Different Geographic Origin

et al. 2021

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“…методы молекулярного типирования возбудителя сибирской язвы характеризуются различными дискриминирующими возможностями. MLST-типирование изолятов B. anthracis, обладая относительно низкой разрешающей способностью (индекс дискриминации составляет 0,58), позволяет получить общую генетическую характеристику штаммов патогена без корректной их дифференциации [3]. Широко используемое сanSNPгенотипирование применяется при дифференциации штаммов B. anthracis с возможностью установления их расположения в глобальной структуре популяции, представленной тремя главными генетическими линиями (клады) -а, в и с -и насчитывающей 12 «канонических» SNP-групп.…”

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Evaluation of the Analytical Capabilities of MALDI-TOF Mass Spectrometry in the Molecular Typing of <i>Bacillus anthracis</i>

Ul’shina,

Kovalev,

Eremenko

et al. 2023

Problemy Osobo Opasnykh Infektsii

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The aim of the work was to compare the discriminating capacity of the canSNP13 genotyping and MALDI‑TOF mass spectrometry methods based on the results of the study of anthrax pathogen strains belonging to the two main genetic lines A and B.Materials and methods. 73 Bacillus anthracis strains from the collection of microorganisms of the Stavropol Research Anti-Plague Institute of the Rospotrebnadzor were investigated. Protein profiling was carried out using a Microflex mass spectrometer, data processing – in the environment of the statistical programming language “R”.Results and discussion. It has been experimentally confirmed that the proposed approach for differentiating proteotypes of B. anthracis strains with a discrimination index of 0.952 exceeds the one for the canSNP typing method and is comparable to the discrimination index for the MLVA31 method. The correlation of the results of strain clustering during typing by MALDI-TOF mass spectrometry and canSNP genotyping reaches 95 % as regards the division into the main genetic lines A and B. The studied strains of anthrax microbe, which mostly fall under phylogenetic groups of lineage A, represent more than a dozen protein profiles, which may be due to differences in the level of protein expression in strains of each canSNP genotype. MALDI-TOF mass spectrometry makes it possible to obtain the results comparable with genetic tests, has a better discriminating capacity compared to canSNP typing, and is easier to perform.

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<i>In silico</i> analysis of genomes of Bacillus anthracis strains belonging to major genetic lineages

Еременко

Pechkovskii

Ryazanova

et al. 2023

Journal of microbiology, epidemiology and immunobiology

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Introduction. The global phylogenetic population structure of Bacillus anthracis is represented by major genetic lineages (A, B and C) with nonuniform distribution of isolates, which still cannot be explained. Identification of characteristics of genomes of strains from three lineages, which can affect their spread, is of high importance. The aim of the study is to explore genomic characteristics of different genetic lineages, which may have an effect on their distribution, by using the in silico analysis of a representative subset of B. anthracis strains. Materials and methods. The whole-genome sequences of 49 B. anthracis strains and Bacillus cereus biovar anthracis CI strain were studied. The in silico analysis was performed to identify polymorphisms using BLASTn, MEGA X, Tandem Repeat Finder, Parsnp the Harvest Suite software. Results. The genome variability depended on single nucleotide polymorphisms, single-nucleotide repeats, number of tandem repeats, substitutions and indels. In strains from lineages B and C, they outnumbered 1.613.4 times and in the B. cereus biovar anthracis strain 5150 times those in B. anthracis strains from lineage A. Significant substitutions in housekeeping genes and pathogenicity factor genes caused changes in amino acid sequences in proteins significantly more frequently in B. anthracis strains from major lineages B and C. Based on the molecular typing and a multi-virulence-locus sequence typing analysis (MVLST) with a discrimination index of 0.9633, strains were classified into three major genetic lineages including groups different from the canonical group. Conclusion. The distinctive feature of B. anthracis genomes is that they have a larger number of significant nucleotide substitutions in pathogenicity factor genes and housekeeping genes of strains belonging to major lineages B and C compared to lineage A. Changes in proteins encoded by them can cause differences in ecological adaptation and in prevalence, which are higher in strains of lineage A. MVLST having a high discriminating capacity can be used as an additional method to B. anthracis molecular typing.

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Comparative Analysis of Genotyping Methods for Bacillus anthracis

Cited by 3 publications

References 39 publications

Sequence Variability of pXO1-Located Pathogenicity Genes of Bacillus anthracis Natural Strains of Different Geographic Origin

Sequence Variability of pXO1-Located Pathogenicity Genes of Bacillus anthracis Natural Strains of Different Geographic Origin

Evaluation of the Analytical Capabilities of MALDI-TOF Mass Spectrometry in the Molecular Typing of <i>Bacillus anthracis</i>

<i>In silico</i> analysis of genomes of Bacillus anthracis strains belonging to major genetic lineages

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