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<p>Abstract</p> <p>Background</p> <p>Proteolytic <it>Clostridium botulinum </it>is the causative agent of botulism, a severe neuroparalytic illness. Given the severity of botulism, surprisingly little is known of the population structure, biology, phylogeny or evolution of <it>C. botulinum</it>. The recent determination of the genome sequence of <it>C. botulinum </it>has allowed comparative genomic indexing using a DNA microarray.</p> <p>Results</p> <p>Whole genome microarray analysis revealed that 63% of the coding sequences (CDSs) present in reference strain ATCC 3502 were common to all 61 widely-representative strains of proteolytic <it>C. botulinum </it>and the closely related <it>C. sporogenes </it>tested. This indicates a relatively stable genome. There was, however, evidence for recombination and genetic exchange, in particular within the neurotoxin gene and cluster (including transfer of neurotoxin genes to <it>C. sporogenes</it>), and the flagellar glycosylation island (FGI). These two loci appear to have evolved independently from each other, and from the remainder of the genetic complement. A number of strains were atypical; for example, while 10 out of 14 strains that formed type A1 toxin gave almost identical profiles in whole genome, neurotoxin cluster and FGI analyses, the other four strains showed divergent properties. Furthermore, a new neurotoxin sub-type (A5) has been discovered in strains from heroin-associated wound botulism cases. For the first time, differences in glycosylation profiles of the flagella could be linked to differences in the gene content of the FGI.</p> <p>Conclusion</p> <p>Proteolytic <it>C. botulinum </it>has a stable genome backbone containing specific regions of genetic heterogeneity. These include the neurotoxin gene cluster and the FGI, each having evolved independently of each other and the remainder of the genetic complement. Analysis of these genetic components provides a high degree of discrimination of strains of proteolytic <it>C. botulinum</it>, and is suitable for clinical and forensic investigations of botulism outbreaks.</p>