Ten of the 12 people who became ill were hospitalized.
Two are Anaheim residents, five were visitors who stayed in Anaheim between 9/12 and 9/27, and one works in Anaheim but lives in another county.
One of the three cases not linked to Disneyland was fatal, the agency said.
Health agency officials say the disease is becoming more common, citing 55 reports of Legionella disease in Orange County through October 2017, compared with 53 for the entire year of 2016 and 33 in 2015.
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"We conducted a review and learned that two cooling towers had elevated levels of Legionella bacteria", said Dr. Hymel in a statement. Disney independently chose to take the towers out of operation the day before, Good said.
According to a LA Times report, Disney reported on November 3 that routine testing had detected elevated levels of Legionella in two cooling towers a month earlier, and the towers had been disinfected. "Since that time, HCA staff have visited Park properties and worked with Disney to identify potential sources of Legionella", said Jessica Good, spokeswoman for the Orange County Health Agency. The towers were chemically treated to combat the problem, and there is no ongoing threat to guests' health, the Register reports. Disney took the towers out of service on November 1, performed more testing and disinfection, and brought them back into service on November 5. "We have proactively shared this information with OCHCA and given our actions, they have indicated there is no longer any known risk associated with our facilities".
The 12 cases range in age from 52 to 94, Good said. The outbreak was traced to the convention hotel's air conditioning system, and Legionnaire's disease has since been sourced to contaminated water or mist.
Nine people have contracted Legionnaire's disease after visiting Disneyland in Anaheim, Calif.