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Medical officer of health Dr Marion Poore said there had been 80 cases in Otago and Southland in the past two months.
It was more than twice the number usually reported at this time of year.
Twenty-five of the cases had been in children aged under 5.
''We usually see more cases this time of year, as lambing and calving can increase people's exposure to this protozoa and other bacteria which can cause gastroenteritis-type illnesses.''
The best way to avoid illness was good hand hygiene practices, Dr Poore said.
''Anyone working with livestock should change out of their work clothes before going about routine family or non-farm-related activities,'' Dr Poore said.