Abstract
In this study we evaluate the capacity of Virtual Hybridization to identify between highly related bacterial strains. Eight genomic fingerprints were obtained by virtual hybridization for the Bacillus anthracis genome set, and a set of 15,264 13-nucleotide short probes designed to produce genomic fingerprints unique for each organism. The data obtained from each genomic fingerprint were used to obtain hybridization patterns simulating a DNA microarray. Two virtual hybridization methods were used: the Direct and the Extended method to identify the number of potential hybridization sites and thus determine the minimum sensitivity value to discriminate between genomes with 99.9% similarity. Genomic fingerprints were compared using both methods and phylogenomic trees were constructed to verify that the minimum detection value is 0.000017. Results obtained from the genomic fingerprints suggest that the distribution in the trees is correct, as compared to other taxonomic methods. Specific virtual hybridization sites for each of the genomes studied were also identified.
Highlights
Anthrax affects mostly cattle and sometimes humans, causing respiratory distress and bleeding.This disease can be potentially transferred from warm-blooded animals to man, acting as vectors for human infection
Information produced by the Virtual Hybridization software is stored in an output file in text format; this includes: file name, total number of genomes hybridized, number of experimental probes, name of the file where the probes set is stored, name of the genome hybridized, number of times that the same probe hybridized across the genome, probe number, probe sequence, position in the genome where the probe hybridized, complementary sequence, and Δ°G between the probe and the target sequence
The two virtual hybridization methods used in this study are useful to discriminate between organisms with highly similar genomes
Summary
Anthrax affects mostly cattle and sometimes humans, causing respiratory distress and bleeding. This disease can be potentially transferred from warm-blooded animals to man, acting as vectors for human infection. Anthrax is caused by the bacterium Bacillus anthracis, an aerobic spore-forming bacillus. Bacteria are released into the bloodstream once the infected macrophage lyses, whereupon they rapidly multiply, spreading throughout the circulatory and lymphatic systems, a process that results in septic shock, respiratory distress and organ failure. The spores of this pathogen have been used as a terror weapon. Virulence factors that set Bacillus anthracis apart from Bacillus cereus are encoded in two plasmids, pXO1 (anthrax toxin) and pXO2 (capsule genes) [2]
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