Development of a technique for molecular typing of Bacillus anthracis strains using new VNTR and INDEL markers
- Authors: Pechkovskii G.A.1, Eremenko E.I.1, Ryazanova A.G.1, Pisarenko S.V.1, Shapakov N.A.1, Aksenova L.Y.1, Semenova O.V.1, Timchenko L.D.2, Kulichenko A.N.1
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Affiliations:
- Stavropol Plague Control Research Institute
- North-Caucasus Federal University
- Issue: Vol 101, No 3 (2024)
- Pages: 362-371
- Section: ORIGINAL RESEARCHES
- Submitted: 12.01.2024
- Accepted: 01.07.2024
- Published: 16.07.2024
- URL: https://microbiol.crie.ru/jour/article/view/18520
- DOI: https://doi.org/10.36233/0372-9311-487
- EDN: https://elibrary.ru/kjnhyg
- ID: 18520
Cite item
Abstract
Introduction. Bacillus anthracis, the pathogen of a particularly dangerous zoonotic disease known as anthrax, requires strict epidemiological control and is characterized by high genetic homogeneity, which necessitates the development of genotyping methods.
The aim of the study were to to find and characterize the VNTR and INDEL loci of B. anthracis and to develop on their basis a genotyping technique by PCR with electrophoretic detection of the results.
Materials and methods. Marker search and phylogenetic analysis were performed on a sample of 388 genomes of B. anthracis strains, 322 from the GenBank collection (RefSeq) and 66 from the collection of the Stavropol Anti-Plague Institute of Rospotrebnadzor. Phylogenetic analysis was performed on the basis of SNP crustal alignment using the Parsnp program. The search for markers was carried out using the Mauve program and author's scripts in Python. PCR was performed using a ScreenMix-HS kit (CJSC "Eurogen", Russia).
Results. Genomic variations of B. anthracis strains (SNP — 25,664, SNR — 14,387, VNTR — 693, INDEL — 14,667) were found, bioinformatic analysis of which revealed nine new VNTR and six INDEL molecular markers most suitable for genotyping. The genetic (allelic) variants of the markers are described. Primers were selected for the found markers and a PCR protocol with detection by electrophoresis in agarose gel was developed. When typing using VNTR markers was applied, the strains were divided into nine clusters: A.Br.Ames, A.Br.001/002, A.Br.Aust94, A.Br.005/006, A.Br.008/009 (Tsiankovskii), A.Br.008/009 (STI), A.Br.008/009 (A.Br.125), A.Br.008/009 (strain 228/269), B.Br.001/002. When typing using INDEL markers, the strains were divided into six clusters: A.Br.Ames, A.Br.001/002, A.Br.Aust94, A.Br.008/009(Tsiankovskii), B.Br.001/002(B.Br.014), as well as a cluster comprising several genetic lineages: A.Br.008/009 (STI), A.Br.008/009 (A.Br.125), A.Br.005/006 и B.Br.001/002.
Conclusion. The use of the developed methodology for the identification of variable VNTR and INDEL loci makes it possible to reliably determine the phylogenetic position of B. anthracis strains and is promising for use in the epidemiological investigation of anthrax outbreaks.
Full Text
Introduction
Bacillus anthracis is a spore-forming Gram-positive bacillus, the pathogen of anthrax, a particularly dangerous infection with a global distribution area. In early studies, attempts to determine the genetic variability of B. anthracis were unsuccessful, indicating the high genetic monomorphism of this species [1]. The first genetic marker suitable for differentiation of B. anthracis strains was tandem repeats in the chromosomal locus vrrA, which are sequentially repeated identical DNA fragments (variable number tandem repeats, VNTR) [2]. Allelic variants of vrrA with the number of repeats from 2 to 6 allowed all strains to be divided into 5 groups [2, 3]. The marker was included in the first typing scheme by MLVA8 (Multiple loci VNTR analysis, MLVA) consisting of 6 chromosomal and 2 plasmid VNTR loci. VNTR loci in general differ from other variable regions in the fact they have a high frequency of variability and a larger number of variants, as well as the manifestation of the homoplasy effect, i.e. independent or parallel mutations in different genetic lineages [4]. Therefore, genotyping based on the analysis of VNTR loci makes it difficult to study intraspecific evolution, but this method is convenient for epidemiologic investigation of anthrax outbreaks. Active searches for B. anthracis loci with tandem repeats led to the discovery of 32 VNTR markers in 6 MLVA genotyping schemes [5–10].
In order to study genetic diversity, a genotyping method based on the analysis of canonical SNPs (canSNP typing) with the identification of 12 major genetic lineages was developed and tested on a large selection of strains [8]. The canonical lineages most accurately reflect the evolutionary groups of B. anthracis; therefore, they are best suited to describe the distribution of anthrax strains in the world. Subsequently, large-scale phylogenetic studies were performed with detailed descriptions, creation of a nomenclature of names and relationships of genetic clusters. Subclusters of canonical lineages were assigned numbers or trivial names [11, 12]. In particular, the canonical lineage A.Br.008/009 includes the Tsiankovskii and STI subclusters, which are widely represented in the Commonwealth of Independent States.
In 2019, an anthrax outbreak occurred in the Republic of Dagestan with isolates that clustered into a separate phylogenetic group A.Br.125 belonging to the STI subcluster.
The canonical lineage B.Br.001/002 contains the Siberia and Europe clusters, making up B.Br.014, as well as the Asia and B.Br.018 clusters.
Taking into account the established and newly identified designations of genetic lineages and groups, we used the following order in the subsequent description. The canonical lineage is indicated first, followed by a new subgroup or cluster within it with an established designation, if identified. For example, most strains of the main lineage A, isolated in Russia, are designated as A.Br.008/009 (Tsiankovskii) or A.Br.008/009 (STI).
Molecular markers also include INDELs (insertion/deletion), which are non-repeat variable regions that exist predominantly as two genetic variants: with deletion or with insertion.
For Francisella tularensis, an INDEL typing scheme was developed, including 38 INDEL loci. The study showed that the use of such markers increases the accuracy of typing [13]. Genotyping methods based on INDEL-locus analysis have also been developed for Helicobacter pylori, Burkholderia pseudomallei, Vibrio cholerae, Yersinia pseudotuberculosis and proved to be of high resolution and reliable in determining the phylogenetic position of strains [14-17]. Currently, the INDEL genotyping system for B. anthracis has not been developed.
The objectives of the study were to find and characterize VNTR and INDEL loci of B. anthracis and to develop on their basis a genotyping technique by PCR with electrophoretic detection of the results.
Materials and methods
Marker search and phylogenetic analysis were performed on a sample of 388 genomes of B. anthracis strains: 322 from the GenBank collection (RefSeq), 66 from the collection of pathogenic microorganism genomes of the Stavropol Anti-Plague Institute, described earlier [12]. Genome numbers are given in Appendix 1 on the journal website (https://doi.org/10.36233/0372-9311-487-s1). Genomic sequences of B. anthracis strains from the collection of the Stavropol Anti-Plague Institute have been deposited in the “National Interactive Catalog of Pathogenic Microorganisms and Biotoxins” (State Scientific Center for Applied Microbiology and Biotechnology).
Markers were searched with the help of an algorithm (Pipeline) consisting of pairwise alignment of complete genomes to a reference sequence using the Mauve program and subsequently, with the help of the author’s scripts in the Python language, extraction of genetic variants from the alignments, merging and their analysis.
Marker verification and determination of marker lengths were performed in the BLASTn program using flanking sequences or specific primers.
In order to compare phylogenetic groups with genetic markers, a phylogenetic tree was constructed on the basis of core SNP alignment using the Parsnp program from the Harvest suit package with the reference genome of B. anthracis Ames Ancestor (GCF_000008445.1). Positions with the unknown N nucleotide were removed from the core SNPs. The SNPs from the VCF file were then converted to a FASTA file. The phylogenetic tree was constructed in the MEGA XI program using the maximum likelihood method with the Tamura-Nei substitution model [18].
Comparison of the lengths of genetic variants of markers with phylogenetic dendrogram and data visualization were performed in R language environment with ggtree and ggplot2 libraries.
Primers were designed using the Primer-BLAST program and synthesized at the Stavropol Plague Institute.
Sample preparation of B. anthracis cultures was carried out according to MG 1.3.2569-09 “Organization of laboratories using nucleic acid amplification methods when working with material containing microorganisms of pathogenicity groups I-IV”. DNA extraction of B. anthracis was performed using the DNA-Sorb-B kit (ILC).
A representative phylogenetic sample of sequenced strains was used for verification of data obtained by PCR with electrophoretic detection. PCR was performed using the ScreenMix-HS kit (Eurogen). The amount of primers in the reaction was equal to 0.3 μM. The following thermocycling mode was used: the first stage (activation) — 95ºС, 5 min — 1 cycle, the second stage — denaturation 95ºС, 20 s, annealing 60ºС, 20 s, elongation 72ºС, 60 s — 40 cycles, the third stage (final elongation) — 72ºС, 5 min — 1 cycle. Electrophoresis was performed in 2% agarose gel using a 100 bp molecular weight marker (SibEnzyme).
Clustering of data obtained from PCR results with electrophoretic detection was performed using the single (Nearest Point Algorithm) method in Python with the scipy library.
Results and discussion
The study included two main stages. The first stage involved the search and description of marker loci, and the second stage involved experimental confirmation and validation of the typing technique using the found markers.
The algorithm resulted in the following genomic variations: SNP — 25,664, SNR — 14,387, VNTR — 693, INDEL — 14,667.
The search for markers among all found variations was performed stepwise with filtering according to a number of criteria. The difference in the size of variants of variable loci should be at least 15 bp. We selected mainly such loci with at least one genetic variant in the set of B. anthracis strains from the collection of pathogenic microorganisms of the Stavropol Anti-Plague Institute that was different from the variants of other strains. Variable loci already described were excluded. Using the criteria, 537 variable regions were found.
Following this, the frequency of allelic variants of loci of strains in certain genetic lineages was investigated by comparing the lengths of genetic variants of markers with the phylogenetic dendrogram based on SNPs of the bovine genome (Fig. 1). Most of the variant loci were found in only 1 strain or a minimal number of strains. A significant group consisted of variants sharing the major genetic lineages A, B, and C, including the previously found INDEL indE1 of 38 bp in length. [19], which is logical since these are the most evolutionarily distant genetic lineages.
Fig. 1. Comparison of the phylogenetic tree and selected markers B. anthracis (some strains with repeated marker patterns were removed).
Fifty-six VNTR and INDEL loci were selected (Table 1). The most phylogenetically significant and optimal for electrophoresis were selected from them. Thus, as a result, 9 VNTR markers and 6 INDEL markers most suitable for genotyping were selected (Fig. 1). The peculiarity of the INDELs found lies in the repeats flanking the INDELs, with one of the repeats being included in the deletion and the other not. For this reason, we can assume the formation of a complex structure between DNA strands during replication, which may cause the polymerase complex to mistakenly double the DNA strand by excising part of the sequence. In this case, reverse INDEL insertion is impossible, which likely reduces the effects of homoplasy.
Table 1. Description of the identified molecular B. anthracis markers
Marker | Coordinates of the locus in the genome according to the Ames Ancestor reference strain (GCF_000008445.1) | Replicon | The number of the allele variant (the length of the genetic variant, bp) |
indS1 | 1276500–1276764 | Chromosome | 1 (265, 266), 2 (241) |
indS2 | 1904893–1905267 | Chromosome | 1 (373–375), 2 (312) |
indS3 | 1944246–1944531 | Chromosome | 1 (286), 2 (253) |
indS4 | 402388–402715 | Chromosome | 1 (328), 2 (423–424) |
indS5 | 655408–655662 | Chromosome | 1 (255), 2 (272, 284–285) |
indS6 | 4691499–4691775 | Chromosome | 1 (277), 2 (388–389) |
vrrS1 | 1721221–1721733 | Chromosome | 1 (513), 2 (425) |
vrrS2 | 4489063–4489484 | Chromosome | 1 (422), 2 (381), 3 (299,307), 4 (217), 5 (258) 6 (338–340) |
vrrS3 | 8316–8860 | pXO2 | 1 (544–546), 2 (301–302), 3 (464), 4 (383) |
vrrS4 | 8916–9269 | pXO2 | 1 (354–355), 2 (263–264), 3 (444), 4 (534), 5 (174) |
vrrS5 | 3155556–3155727 | Chromosome | 1 (172), 2 (142) |
vrrS6 | 1092722–1092959 | Chromosome | 1 (238), 2 (198), 3 (318–319), 4 (398), 5 (278) |
vrrS7 | 5088417–5088723 | Chromosome | 1 (306–307), 2 (190), 3 (229), 4 (385), 5 (346), 6 (268) (385) |
vrrS8 | 5031546–5031803 | Chromosome | 1 (258, 263–265), 2 (354, 359–366) |
vrrS9 | 3742896–3743541 | Chromosome | 1 (646), 2 (450) |
indNS1 | 130607–131099 | pXO1 | 1 (454, 456), 2 (494–495) |
indNS2 | 596340–596832 | Chromosome | 1 (352), 2 (492–493) |
indNS3 | 122138–122690 | pXO1 | 1 (551–555), 2 (485, 487) |
indNS4 | 77192–77540 | pXO1 | 1 (330), 2 (349), 3 (619) |
indNS5 | 482012–482157 | Chromosome | 1 (146,149), 2 (504) |
indNS6 | 385564–385837 | Chromosome | 1 (271–276), 2 (305–308) |
indNS7 | 1372136–1372298 | Chromosome | 1 (163), 2 (181) |
indNS8 | 2559203–2559485 | Chromosome | 1 (282–284), 2 (335–336) |
indNS9 | 3855034–3855252 | Chromosome | 1 (219), 2 (231), 3 (239–241) |
indNS10 | 4303573–4303825 | Chromosome | 1 (253), 2 (310–311) |
indNS11 | 4965875–4966088 | Chromosome | 1 (214), 2 (321) |
indNS12 | 1209302–1209701 | Chromosome | 1 (253), 2 (399–401) |
indNS13 | 2728738–2729257 | Chromosome | 1 (229), 2 (519–520) |
indNS14 | 486258–486638 | Chromosome | 1 (285), 2 (381) |
indNS15 | 1287411–1287701 | Chromosome | 1 (201), 2 (291) |
indNS16 | 910496–910796 | Chromosome | 1 (301), 2 (490,491) |
indNS17 | 2533966–2534193 | Chromosome | 1 (228), 2 (634–636) |
indNS18 | 2593388–2593616 | Chromosome | 1 (228–230), 2 (283) |
indNS19 | 3352013–3354229 | Chromosome | 1 (193,194), 2 (2124), 3 (2207, 2215–2218, 2223) |
indNS20 | 3829833–3830053 | Chromosome | 1 (220–221), 2 (251) |
indNS21 | 4811428–4811664 | Chromosome | 1 (236–237), 2 (600, 602) |
indNS22 | 29253–29436 | pXO1 | 1 (184), 2 (269) |
indNS24 | 1146673–1147101 | Chromosome | 1 (256), 2 (270–272), 3 (427–430) |
indNS25 | 2224848–2225376 | Chromosome | 1 (270), 2 (418), 3 (529–530, 537) |
indNS26 | 2687438–2687847 | Chromosome | 1 (240–241), 2 (410,408–410), 3 (429) 4 (580) |
indNS27 | 3304833–3305473 | pXO1 | 1 (245, 257), 2 (640–641) |
vrrNS1 | 226241–226786 | Chromosome | 1 (545–547), 2 (694, 697–699), 3 (845–847), 4 (997–998), 5 (1146), 6 (1296–1298) |
vrrNS2 | 1333990–1334961 | Chromosome | 1 (343), 2 (554, 552), 3 (700), 4 (758, 762–763), 5 (779), 6 (971–974), 7 (1182–1183), 8 (1393) |
vrrNS3 | 2014690–2015095 | Chromosome | 1 (277), 2 (364), 3 (406, 409), 4 (535) |
vrrNS4 | 4233686–4234066 | Chromosome | 1 (237), 2 (273, 279), 3 (306, 309, 322), 4 (381), 5 (417), 6 (345) |
vrrNS5 | 4351696–4351908 | Chromosome | 1 (213), 2 (231) |
vrrNS6 | 4598742–4598948 | Chromosome | 1 (195, 207), 2 (171, 183) |
vrrNS7 | 811781–812154 | Chromosome | 1 (284), 2 (302), 3 (320), 4 (374), 5 (428), 6 (482) |
vrrNS8 | 1395847–1396186 | Chromosome | 1 (340), 2 (385) |
vrrNS9 | 1238148–1238579 | Chromosome | 1 (361, 366), 2 (398), 3 (430–433), 4 (465), 5 (498) |
vrrNS10 | 2264930–2265251 | Chromosome | 1 (244), 2 (283), 3 (322), 4 (361), 5 (439), 6 (517) |
vrrNS11 | 4352078–4352327 | Chromosome | 1 (220), 2 (235), 3 (250, 251), 4 (264–266), 5 (295), 6 (310) |
vrrNS12 | 4927425–4927645 | Chromosome | 1 (181), 2 (221) |
vrrNS13 | 4769700–4770199 | Chromosome | 1 (499–501), 2 (352–353) |
vrrNS15 | 1151194–1151463 | Chromosome | 1 (148), 2 (269–270), 3 (291), 4 (392–393, 396), 5 (514, 520) |
vrrNS16 | 2006677–2007157 | Chromosome | 1 (481), 2 (433, 435–436), 3 (526), 4 (301), 5 (345–347), 6 (390–391), 7 (255–257) |
The indels indS1 (FAD-binding oxidoreductase gene), indS2 (hypothetical protein gene WP_000829051.1), and indS6 (cell surface protein gene) localized in the protein-coding genes are genomic variations without a shift of reading frame. IndS4 localizes in the region between the GBAA_RS02140 (ABC transporter ATP-binding protein) and GBAA_RS02145 (ABC-F family ATP-binding cassette domain-containing protein) genes. IndS5 localizes in the region between the genes GBAA_RS03470 (hypothetical protein) and GBAA_RS03475 (alanine:cation symporter family protein). Indel indS3 shifts the reading frame of the gene encoding the SPFH/Band 7/PHB domain protein.
The indel indS1 genetic variant with deletion is characteristic of the A.Br.008/009 (Tsiankovskii) cluster. The indel indS2 is unusual in that there are 3 genetic variants of this locus: an insertion and 2 deletion variants. The difference between the two deletions is a shift of 9 nucleotide pairs. One variant is characteristic of the Siberia and Europe canSNP subgroups of the B.Br.001/002 group, the other is characteristic of strains of the B.Br.Kruger group. The indS3 locus variant with deletion is found in strains of the A.Br.Aust94 group, except for strain 9080-G isolated in Georgia and Kanchipuram strain from India. Variants indS4, indS5, indS6 with deletion are found in A.Br.004, A.Br.001 and A.Br.Ames clusters, respectively.
The number of allelic variants of the selected VNTR markers varies from 2 to 6 with repeat lengths ranging from 30 bp to 196 bp (Fig. 1). The vrrS1 locus has a 425-bp variant found in A.Br.008/009 and A.Br.WNA, as well as one unique 337-bp variant specific to strain 228/269. Genetic variants of the vrrS2 locus are found in the A.Br.008/009 and A.Br.Aust94 groups. Two VNTR markers, vrrrS3 and vrrS4, were found on the pXO2 plasmid. Separate genetic variants of vrrS3 are found in A.Br.008/009 (Tsiankovskii), B.Br.KrugerB and main lineage B, respectively. The vrrS4 locus separates the strains into lineages A and B. The 142 bp allelic variant vrrS5 is found simultaneously in strains of lineage B, A.Br.WNA and A.Br.003/004 groups. The vrrS6 variants are characteristic of part of the strains of the A.Br.008/009 group, the A.Br.004 cluster and lineage B. The vrrrS7 307 bp genetic variant is specific for the A.Br.Ames group. The 258 bp vrrS8 variant is specific to the A.Br.Ames and A.Br.001/002 groups. The 646 bp vrrS9 genetic variant is specific for A.Br.Ames strains isolated in North America.
Variable loci can be grouped according to their belonging to certain genetic clusters. For example, variants of indels indS3, indNS27, and VNTR - vrrNS7 have similar belonging to the A.Br.Aust94 group. Indels indS4 and indNS11 are characteristic of A.Br.004, indNS17 and vrrS9 are characteristic of A.Br.Ames strains isolated in North America. Variants indNS5, indNS9, indNS10 are found in strains of the A.Br.Ames and A.Br.001/002 groups.
For the major lineage B, the characteristic loci are indNS1, indNS12, indNS19, indNS2, indNS3, indNS13, indNS14, and vrrNS12. Characteristic loci for both lineages B and C are indNS18, indNS21, indNS4, indNS6, indNS7 and indNS8.
Some of the unselected markers could also be used for typing. For example, vrrNS1 has high variability but a long repeat of 150 bp and a large length difference between the minimum and maximum genetic variant, which is difficult for electrophoretic detection by PCR. The VNTR of vrrrNS15 is variable within the A.Br.008/009 group. The tandem repeats vrrNS16, vrrNS2, vrrNS4 do not have strict specificity.
The primers were selected for the found markers (Table 2) and a PCR protocol with detection of the results by agarose gel electrophoresis was developed (Fig. 2, Fig. 3). The selected markers had a nucleotide sequence length sufficient for reliable determination of genetic variants of loci (Table 3).
Table 2. Primers to VNTR and INDEL loci B. anthracis
Name | Forward primer | Reverse prime |
indS1 | TATTGGGCAGCAGCATTTGG | ATGAGTTGTACGGGACGCAA |
indS2 | TGGAGGGGTTGTTCAAGCG | GCGTAACTCGGAGACCATGTA |
indS3 | AGCAACAGAAAAATGGGGCG | AATCGCTCTTGCTTCCCCTT |
indS4 | AGAAGGAACAAAAGGAAAAGTAGAG | CAACATGCTCGCCCTTCAAT |
indS5 | GGTCTATACGGCACACTCCA | GCTTCCAATATTCCCCCTCC |
indS6 | AGCCCCTTCTTTCGGTGTAT | CGATGAAGATGTAAGACAGCCC |
vrrS1 | TCGTCCTGGAGCATCTTTCA | CCAAATCGCCCCTAGACCAA |
vrrS2 | GTTGTTTCATACGTCTATCCCCTTC | GTCCTTTTGGACAGCCTCTCTT |
vrrS3 | ACTGTAGTTGTCCCTACCCTT | AGAAGTACAGGTGGGACAGGA |
vrrS4 | TTTCCTTGCGATGCTTCAGT | TGCTGGTATAGAGCCATCTGC |
vrrS5 | AGCAATGTTTAATTCACCATCAAGT | GTACGCTTTAGTCGGAGACGG |
vrrS6 | AGGAAGCAGGTTAGCGTTGT | GCGCTATGTGGCGTCTTTTC |
vrrS7 | AGGAACACTGGTTCAGCCTAT | AGCAGGATCGCTTGCTAGAT |
vrrS8 | CTGCAATTGCCTTCGCCTTT | GCGAAAAAGAGAAAGCGCTAC |
vrrS9 | ATGAAGGTGTGACATGCCGT | GTGAAGCTGTAATTGTGGCGT |
Fig. 2. Results of PCR reaction of INDEL loci with detection by electrophoresis.
The font colors of the strains correspond to the canonical lineages according to Fig. 1.
Fig. 3. Results of PCR reaction of VNTR loci with detection by electrophoresis.
The font colors of the strains correspond to the canonical lineages according to Fig. 1.
Table 3. Lengths of INDEL and VNTR loci according to phylogenetic groups
Markers | Phylogenetic groups | |||||||||
A.Br. Ames | A.Br. 001/002 | A.Br. Aust94 | A.Br. 005/006 | A.Br. 008/00 (STI) | A.Br. 008/00 (A.Br.125) | A.Br. 008/00 Tsiankovskii | A.Br. 008/009 (228-269) | B.Br. 001/002 | B.Br. 001/002 (B.Br.014) | |
indS1 | 265 | 265 | 265 | 265 | 265 | 241 | 241 | 265 | 265 | 265 |
indS2 | 375 | 375 | 375 | 375 | 375 | 375 | 375 | 375 | 375 | 312 |
indS3 | 286 | 286 | 253 | 286 | 286 | 286 | 286 | 286 | 286 | 286 |
indS4 | 328 | 328 | 328 | 424 | 424 | 424 | 424 | 424 | 424 | 424 |
indS5 | 255 | 255 | 285 | 285 | 285 | 285 | 285 | 285 | 285 | 285 |
indS6 | 277 | 388 | 388 | 388 | 388 | 388 | 388 | 388 | 388 | 388 |
vrrS1 | 513 | 513 | 513 | 513 | 425 | 425 | 425 | 337 | 513 | 513 |
vrrS2 | 422 | 422 | 340 | 422 | 422 | 422 | 422 | 422 | 299 | 299 |
vrrS3 | 545 | 545 | 545 | 545 | 545 | 545 | 464 | 464 | 383 | 383 |
vrrS4 | 354 | 354 | 354 | 354 | 354 | 354 | 354 | 354 | 444 | 444 |
vrrS5 | 172 | 172 | 172 | 172 | 172 | 172 | 172 | 172 | 142 | 142 |
vrrS6 | 238 | 238 | 238 | 318 | 318 | 318 | 318 | 318 | 278 | 278 |
vrrS7 | 307 | 346 | 346 | 346 | 346 | 346 | 346 | 346 | 346 | 346 |
vrrS8 | 258 | 258 | 360 | 360 | 360 | 264 | 360 | 360 | 360 | 360 |
vrrS9 | 450 | 450 | 450 | 450 | 450 | 450 | 450 | 450 | 450 | 450 |
Some strains lack the pXO2 plasmid, and accordingly, they also lack the vrrS3 and vrrS4 loci.
As a result of clustering based on the INDEL typing, strains were divided into 6 clusters: A.Br.Ames, A.Br.001/002, A.Br.Aust94, A.Br.008/009 (Tsiankovskii), B.Br.001/002 (B.Br.014), as well as a cluster including representatives of several genetic groups: A.Br.008/009 (STI), A.Br.008/009 (A.Br.125), A.Br.005/006 and B.Br.001/002. The cluster is singled out as a separate group because no specific INDEL markers have been identified for the strains of these lineages (Fig. 4).
Fig. 4. Clustering of B. anthracis strains based on VNTR and INDEL typing.
As a result of clustering based on VNTR-typing, strains were divided into 9 clusters: A.Br.Ames, A.Br.001 /002, A.Br.Aust94, A.Br.005/006, A.Br.008/009 (Tsiankovskii), A.Br.008/009 (STI), A.Br.008/009 (A.Br.125), A.Br.008/009 (strain 228/269), B.Br.001/002 (Fig. 4). Strain 228/269 is a member of the A.Br.008/009 (Tsiankovskii) group.
The discriminatory power determined using the Hanter–Gaston diversity index [20] was 0.7 for canSNP typing, and 0.79 and 0.84 for typing based on the analysis of new VNTR and INDEL markers, respectively.
Conclusion
Thus, as a result of genome analysis of 388 B. anthracis strains, variable regions were identified and characterized. New VNTR- and INDEL-markers were found and their binding to clusters of global phylogeny was studied. The developed protocol for marker identification by PCR with electrophoretic visualization of the results allows reliable determination of allelic variants of markers. The found 9 VNTR markers and 6 INDEL markers allow to divide B. anthracis strains into 6 and 9 genetic groups when typing with separate analysis of these markers and into 10 groups when analyzing them together. The genotyping technique based on the analysis of new VNTR- and INDEL-markers is recommended to be used jointly or separately as an addition to the existing genotyping schemes. The use of the developed methodology for the identification of variable VNTR- and INDEL-loci allows reliable determination of the phylogenetic position of B. anthracis strains and is promising for use in the epidemiologic investigation of anthrax outbreaks.
About the authors
Grigorii A. Pechkovskii
Stavropol Plague Control Research Institute
Author for correspondence.
Email: grigorii.pechkovskii@gmail.com
ORCID iD: 0000-0001-7033-9972
SPIN-code: 8878-3299
Scopus Author ID: 57223328514
ResearcherId: Q-7273-2016
junior researcher, Anthrax laboratory
Россия, StavropolEvgeny I. Eremenko
Stavropol Plague Control Research Institute
Email: grigorii.pechkovskii@gmail.com
ORCID iD: 0000-0002-8163-1300
D. Sci. (Med.), Professor, principal researcher, Anthrax laboratory
Россия, StavropolAlla G. Ryazanova
Stavropol Plague Control Research Institute
Email: grigorii.pechkovskii@gmail.com
ORCID iD: 0000-0002-5196-784X
Cand. Sci. (Med.), Head, Anthrax laboratory
Россия, StavropolSergey V. Pisarenko
Stavropol Plague Control Research Institute
Email: grigorii.pechkovskii@gmail.com
ORCID iD: 0000-0001-6458-6790
Cand. Sci. (Chem.), leading researcher, Laboratory of biochemistry
Россия, StavropolNikolay A. Shapakov
Stavropol Plague Control Research Institute
Email: grigorii.pechkovskii@gmail.com
ORCID iD: 0000-0001-9152-4026
junior researcher, Laboratory of biochemistry
Россия, StavropolLyudmila Yu. Aksenova
Stavropol Plague Control Research Institute
Email: grigorii.pechkovskii@gmail.com
ORCID iD: 0000-0002-7744-3112
Cand. Sci. (Med.), senior researcher, Anthrax laboratory
Россия, StavropolOlga V. Semenova
Stavropol Plague Control Research Institute
Email: grigorii.pechkovskii@gmail.com
ORCID iD: 0000-0003-0274-898X
Cand. Sci. (Biol.), researcher, Anthrax laboratory
Россия, StavropolLyudmila D. Timchenko
North-Caucasus Federal University
Email: grigorii.pechkovskii@gmail.com
ORCID iD: 0000-0003-2011-880X
D. Sci. (Vet.), Professor, principal researcher, Interdepartmental scientific and educational laboratory of experimental immunomorphology, immunopathology and immunobiotechnology
Россия, StavropolAlexander N. Kulichenko
Stavropol Plague Control Research Institute
Email: grigorii.pechkovskii@gmail.com
ORCID iD: 0000-0002-9362-3949
D. Sci. (Med.), Professor, Academician of RAS, Director
Россия, StavropolReferences
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