Botulism derives its name from the Latin word, botulus (sausage), based upon observations in the late 1700s and early 1800s by physicians in southern Germany who noted the occurrence of an unusual but frequently fatal disease following ingestion of spoiled sausage. Justinius Kerner, a district health officer in W├╝rttemberg, compiled these reports in official documents, with the result that botulism has at times been called "Kerner's disease." A similar illness seen in nineteenth-century Russia in association with eating smoked or pickled fish was labeled "ichthiosismus."

In 1896, Emile von Ermengem, student of Robert Koch and professor of bacteriology at the University of Ghent, established that the disease was caused by a neurotoxin produced by an anaerobic bacterium. This discovery emerged from his laboratory investigation of the cause of a dramatic outbreak of the disease that occurred at a gathering of musicians in a small Belgian village.

Following initial recognition of the disease in the United States in 1899, the repeated occurrence of botulism outbreaks associated with commercially canned foods led to extensive applied research in the 1920s. Sponsored by the National Canners Association, these studies established the safe food processing practices that are now in widespread use by the industry.

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