Genotyping and phylogenetic location of one clinical isolate of Bacillus anthracis isolated from a human in Russia

Abstract

Background Anthrax is a zoonotic disease caused by the Gram-positive bacterium Bacillus anthracis . In Russia, there are more than 35 thousand anthrax stationary unfavourable sites. At the same time, there is very little published information about the isolates of B. anthracis from the territory of Russia. In this study, we report the use of whole genome sequencing (WGS) and bioinformatics analysis to characterize B. anthracis 81/1 strain isolated in Russia in 1969 from a person during an outbreak of the disease in the Stavropol region. Results We used 232 B. anthracis genomes, which are currently available in the GenBank database, to determine the place of the Russian isolate in the global phylogeny of B. anthracis . The studied strain was characterized by PCR-based genetic methods, such as Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA), canonical single nucleotide polymorphisms (canSNP), as well as the method of full-genomic analysis of nucleotide polymorphisms (wgSNP). The results indicate that the Russian B. anthracis 81/1 strain belongs to Trans-Eurasion (TEA) group, the most representative in the world. Conclusions In this study, the full genomic sequence of virulent B. anthracis strain from Russia was characterized for the first time. As a result of complex phylogenetic analysis, the place of this isolate was determined in the global phylogenetic structure of the B. anthracis population, expanding our knowledge of anthrax phylogeography in Russia. Electronic supplementary material The online version of this article (10.1186/s12866-019-1542-3) contains supplementary material, which is available to authorized users.

Identification of the molecular characteristics of Bacillus anthracis (1982-2020) isolates in East Indonesia using multilocus variable-number tandem repeat analysis

“…Molecular typing of B. anthracis using the MLVA-8 assay revealed the genetic relationship of B. anthracis isolates through eight loci, consisting of six chromosomal and two plasmid markers [ 7 , 9 , 10 , 18 , 19 ]. This method has been used as a subtyping tool due to its power to distinguish between strains of many bacteria, such as Bacillus cereus , Yersinia pestis , Neisseria gonorrhoeae , and Staphylococcus lugdunensis [ 41 - 44 ].…”

“…This study utilized a concatenated nucleotide of DNA sequencing results with a range of 2141-2318 bp (aligned sequences) to construct a phylogenetic tree ( Table-2 ) rather than amino acid translation. Some mutations and deletions inside the amino acid could not be differentiated particularly due to the very low mutation rate of B. anthracis in the same region or a closely related outbreak [ 10 , 11 , 18 ].…”

“…No other lineage of B. anthracis isolates circulating in East Indonesia was found. Other molecular methods, such as extended MLVA assay (MLVA-15, MLVA-25, or MLVA-31), WGS, and canonical SNP, have been recommended for better comparative analysis and genetic study in relation to B. anthracis [ 14 , 15 , 18 - 22 , 24 , 25 , 51 - 54 ]. Further studies are needed that consider the additional loci for VNTR analysis compared to this study.…”

Phylogenetic Placement of Isolates Within the Trans-Eurasian Clade A.Br.008/009 of Bacillus anthracis

“…Notably, the closest relative of strain BUL 40 (63 SNPs distance) was strain LP50_3Ya, isolated from Yakutia in Russia (Figure 2a), rather than the two other Bulgarian strains (BUL 19 and BUL 39) from our collections that had been genome sequenced previously [12]. An additional genome 81/1 from Russia [26], which was not part of our analysis in Figure 1, also branched of the internal A.Br.105 polytomy. Overall, the A.Br.105 clade exhibits a strong dominance of isolates from eastern European countries (Figure 2a).…”

Whole Genome Sequencing for Studying Bacillus anthracis from an Outbreak in the Abruzzo Region of Italy

“…Aust94 is prevalent in Western and Southern Asia and Western China, the A.Br.001/002 was found in Central and Eastern China, the A.Br.WNA in North America, the A.Br.003/004 in South America, the A.Br.005/006 was found in Australia, Africa, and Europe. Finally the sub-group A.Br.008/009, also known as the Trans-Eurasian (TEA) sub-group, is widespread throughout Europe [14,15] and Russia [16]. It occurs in Southern and Eastern Europe and represents the dominant sub-group in Italy [15].…”