Mercy Hospital said in a statement patients are safe, and it welcomes an investigation by both the city and state health departments.
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Officials said the public is not at risk.
Thursday city and state inspectors were at Mercy Hospital collecting samples for testing.
Illinois officials said a report showed water at Mercy did positive for Legionella. Precautions are in place as of Friday night.
The hospital has flushed its water system. It is replacing water fixtures and also adding filters to sinks.
People can contract Legionnaires' by inhaling droplets of water with Legionella bacteria. Most healthy people don't get the disease, but people over 50 are at a higher risk.
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The Illinois Department of Health is taking this seriously after more than a dozen people died following an outbreak of Legionnaires here at a Quincy veterans' home.
A recent Inspector General report showed the veterans' home mishandled the severity of the outbreak and failed to notify health officials in a timely fashion.
It's still unclear if the two reported cases of Legionnaires' disease were a result of patients being exposed to Legionella at Mercy Hospital.
A hospital spokeswoman said one of the patients had been previously treated at two other healthcare facilities.