High resolution genotyping of Bacillus anthracis outbreak strains using four highly mutable single nucleotide repeat markers

Abstract

Aims: Bacillus anthracis is a genetically monomorphic bacterium with little diversity to be expected during an outbreak. This study used more rapidly evolving genetic markers on outbreak samples to ascertain genetic diversity. Methods and Results: Forty‐seven isolates from a B. anthracis outbreak during the summer of 2005 in South Dakota were analysed using single nucleotide polymorphisms (SNP) and multi‐locus VNTR analysis (MLVA). Results indicated that all of the outbreak strains belonged to a single clonal lineage. However, analysis of four single nucleotide repeat (SNR) markers resolved these isolates into six distinct genotypes providing insights into disease transmission. Conclusions: Strain determination of unknown B. anthracis samples can be ascertained by SNP and MLVA markers. However, comparison of many samples obtained during an outbreak will require markers with higher rates of mutation to ascertain genetic diversity. Significance and Impact of the Study: SNR4 analysis allowed discrimination of closely related B. anthracis isolates and epidemiological tracking of the outbreak. When used in conjunction with other genotyping schemes that allow broad genetic relationships to be determined, SNR markers are powerful tools for detailed tracking of natural B. anthracis outbreaks and could also prove useful in forensic investigations.

Ecology of Speciation in the Genus Bacillus

“…This is consistent with the existence of multiple temperature-distinguished ecotypes within the ES-identified ecotypes. This hypothesis could be tested through analysis of a more rapidly evolving molecular marker (10), such as variable-number tandem repeat (VNTR) loci (27), or by a genomewide single-nucleotide polymorphism (SNP) analysis (18). Here we would expect to find two or more molecular clusters within a given ES-identified ecotype, one with a significantly higher mean heat adaptation index and greater SFS association than the other.…”

Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

“…Studies of genetic diversity of B. anthracis have relied on multiple-locus variable-number tandem repeat analysis (MLVA) (10,14,17), single-nucleotide polymorphisms (SNP) (15,17) and single-nucleotide repeat analysis (SNRA) (12,13,16). Keim et al described a hierarchical approach called PHRANA (progressive hierarchical resolving assays using nucleic acids) that uses markers that are progressively less stable but have increasing resolving power for typing B. anthracis (SNP, MLVA, and SNRA) (11).…”

Texas Isolates Closely Related toBacillus anthracisAmes

“…A recent study in Turkey compared 2 neighboring villages with different socioeconomic status. The only factor that was statistically signifi cantly related to pediculosis capitis was size of the household; >6 inhabitants was associated with increased prevalence (9).…”

“…Resolution of nearly identical genotypes might also be accomplished by using additional VNTRs (8) or hypermutable loci (9). However, we doubt that this approach would be better than whole-genome sequencing with interrogation of resultant SNPs because these markers would most likely result in topologic confl icts due to homoplasy (10).…”