The lead-poisoned water that flowed into Flint homes at the peak of the crisis three years ago carried another deadly threat: Legionella bacteria that triggered an outbreak, sickening 90 people and killing at least 12 over two years.

In the months after Flint’s noxious water drew national attention, Michigan public health officials said that it would be impossible to know if the bacterial outbreak — which happened during the same months the city switched its water supply to the Flint River — had been caused by the water itself.

But a new study published in the Proceedings of the National Academy of Sciences makes the strongest case yet that Flint River water was the source of at least 80% of the Legionnaires’ cases that occurred in 2014 and 2015.

“There was a suspicion that the outbreak was governed by the failure of the water system, but it wasn’t properly quantified,” study leader Sammy Zahran, associate professor of demography at Colorado State University, told BuzzFeed News.

The team found that, for the months that Flint River water ran through their taps, Flint residents were seven times more likely to get Legionnaires’ than were people in other counties.

“This is a big deal,” Janet Stout, research associate professor of civil and environmental engineering at the University of Pittsburgh, who was not involved with the PNAS study, told BuzzFeed News. “The link to the impact of the water quality on the outbreak has been something that has never been seen before or explored in the level of depth as this investigation.”

In a release published Monday, the Michigan Department of Health and Human Services said the work had "numerous flaws" and announced that the state’s relationship with the research group would be terminated.

MDHHS had asked a Dutch research group, KWR Watercycle Research Institute, to review the study ahead of publication. Among its criticisms, MDHHS said that the study did not take into account the correct timeframe of cases, and focused on the wrong strain of bacteria.

The state health agency offered to continue the relationship with the US academics if they would agree to oversight by KWR, according to the release. But the US scientists did not agree to these terms.

“By publishing these inaccurate, incomplete studies at this point, FACHEP has done nothing to help the citizens of Flint and has only added to the public confusion on this issue,” the release stated.

The Flint Legionnaires’ cases made up the second-largest outbreak in recent history, just behind a 2015 outbreak in the Bronx, in which at least 10 people died and more than 100 fell ill, Stout told BuzzFeed News.

Legionnaires’ disease is a form of pneumonia and can be fatal in 10% of cases. The Legionella bacteria find a comfy home in the cooling towers of air-conditioning units, and poorly cleaned pipes, showers, or faucets. If inhaled, the bacteria infect the lungs.

Chlorine, used by water utilities as a disinfectant, typically keeps bacteria like Legionella at bay. Zahran and his team show that the switch in water supply to the Flint river was followed by major fluctuations in chlorine levels across neighborhoods.

But because authorities failed to add necessary anti-corrosion chemicals after switching to Flint River water, it ate through the pipes, releasing lead and flakes of iron. This brew laid waste to the city’s water infrastructure, but it also reacted with and reduced the chlorine, creating an environment in which Legionella bugs are known to thrive.