J Vet Sci.  2013 Dec;14(4):457-465. 10.4142/jvs.2013.14.4.457.

Genetic diversity of Korean Bacillus anthracis isolates from soil evaluated with a single nucleotide repeat analysis

• Kim SH
• Jung KH
• Kim SK
• Kim SJ
• Kim JC
• Cho SY
• Chai JC
• Lee YS
• Kim YK
• Hwang HC
• Ryu SG
• Chai YG

• KMID: 1712313
• DOI: http://doi.org/10.4142/jvs.2013.14.4.457

Abstract

Bacillus (B.) anthracis, the etiological agent of anthrax, is one of the most genetically monomorphic bacteria species in the world. Due to the very limited genetic diversity of this species, classification of isolates of this bacterium requires methods with high discriminatory power. Single nucleotide repeat (SNR) analysis is a type of variable-number tandem repeat assay that evaluates regions with very high mutation rates. To subtype a collection of 21 isolates that were obtained during a B. anthracis outbreak in Korea, we analyzed four SNR marker loci using nucleotide sequencing analysis. These isolates were obtained from soil samples and the Korean Center for Disease Control and Prevention. The SNR analysis was able to detect 13 subgenotypes, which allowed a detailed evaluation of the Korean isolates. Our study demonstrated that the SNR analysis was able to discriminate between strains with the same multiple-locus variable-number tandem repeat analysis genotypes. In summary, we obtained SNR results for four SNR marker loci of newly acquired strains from Korea. Our findings will be helpful for creating marker systems and help identify markers that could be used for future forensic studies.

Keyword

Bacillus anthracis; molecular diversity; single nucleotide repeats; subgenotyping

MeSH Terms

Bacillus anthracis/*classification/*genetics/isolation & purification
*Genetic Variation
*Minisatellite Repeats
Polymerase Chain Reaction/veterinary
Republic of Korea
Sequence Analysis, DNA/*methods/veterinary
*Soil Microbiology

Figure

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  Fig. 1 Genetic relationships among the examined Bacillus (B.) anthracis strains were evaluated by SNP analysis. (A) Four SNP marker loci were used to calculate simple matching coefficients. UPGMA cluster analysis was performed to identify groups with similar genotypes among the strains. (B) These genetic relationships among the B. anthracis strains were previously described based on canSNP results from a study by Jung et al. [6]. In this previous experiment, canSNP marker loci (13 loci) were used to calculate simple matching coefficients. UPGMA cluster analysis was then performed to identify groups with similar genotypes among the analyzed strains.

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  Fig. 2 Genetic relationships among the examined B. anthracis strains were determined by SNR analysis. Four SNR marker loci were used to calculate simple matching coefficients. UPGMA cluster analysis was performed to identify groups with similar genotypes among the evaluated strains. In total, three groups were observed and new isolates were found to possess similar genotypes.

• 

  Fig. 3 Genetic relationships of the 14 CH strains. The lines linking different strains indicate SNR mutations. The numbers of base pairs that were deleted (-) or inserted (+) in SGT1 or SGT7 for each mutation are also shown. Detailed genotypic descriptions are presented in Table 3.

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