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<p>Abstract</p> <p>Background</p> <p><it>Clostridium botulinum </it>is a taxonomic designation for at least four diverse species that are defined by the expression of one (monovalent) or two (bivalent) of seven different <it>C. botulinum neurotoxins </it>(BoNTs, A-G). The four species have been classified as <it>C. botulinum </it>Groups I-IV. The presence of <it>bont </it>genes in strains representing the different Groups is probably the result of horizontal transfer of the toxin operons between the species.</p> <p>Results</p> <p>Chromosome and plasmid sequences of several <it>C. botulinum </it>strains representing A, B, E and F serotypes and a <it>C. butyricum </it>type E strain were compared to examine their genomic organization, or synteny, and the location of the botulinum toxin complex genes. These comparisons identified synteny among proteolytic (Group I) strains or nonproteolytic (Group II) strains but not between the two Groups. The <it>bont </it>complex genes within the strains examined were not randomly located but found within three regions of the chromosome or in two specific sites within plasmids. A comparison of sequences from a Bf strain revealed homology to the plasmid pCLJ with similar locations for the <it>bont/bv b </it>genes but with the <it>bont/a4 </it>gene replaced by the <it>bont/f </it>gene. An analysis of the toxin cluster genes showed that many recombination events have occurred, including several events within the <it>ntnh </it>gene. One such recombination event resulted in the integration of the <it>bont/a1 </it>gene into the serotype toxin B <it>ha </it>cluster, resulting in a successful lineage commonly associated with food borne botulism outbreaks. In <it>C. botulinum </it>type E and <it>C. butyricum </it>type E strains the location of the <it>bont/e </it>gene cluster appears to be the result of insertion events that split a <it>rarA</it>, recombination-associated gene, independently at the same location in both species.</p> <p>Conclusion</p> <p>The analysis of the genomic sequences representing different strains reveals the presence of insertion sequence (IS) elements and other transposon-associated proteins such as recombinases that could facilitate the horizontal transfer of the <it>bonts</it>; these events, in addition to recombination among the toxin complex genes, have led to the lineages observed today within the neurotoxin-producing clostridia.</p>