The criminal charges filed Wednesday, which were authorized by a Genesee County district court judge, include more than a dozen separate counts against two officials at the Michigan Department of Environmental Quality, as well as a Flint water quality supervisor.

Stephen Busch and Michael Prysby, the two state environmental quality officials, each face multiple felonies, including misconduct in office and tampering with evidence. Prysby faces an additional felony charge for authorizing a permit for the Flint treatment plant “knowing it would fail to provide clean and safe drinking water to families,” Schuette said.

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Several of the felony charges carry maximum penalties of up to five years in prison. The two men also are charged with misdemeanor violations of the state’s drinking water regulations.

Michael Glasgow, a Flint water official, faces a felony charge of tampering with evidence for allegedly altering and falsifying reports to state and federal regulators that made it appear lead levels in the city’s water supply were lower than they actually were. He also faces a misdemeanor charge of willful neglect of duty.

An attorney for Busch said he pleaded not guilty to all counts at an arraignment Wednesday afternoon. An attorney for Prysby did not immediately respond to a request for comment. Neither Glasgow nor an attorney representing him could immediately be reached for comment; however, Glasgow recently told The Flint Journal he was following “marching orders” from supervisors who were racing to switch the city’s water supply to the Flint River in 2014.

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The charges come barely three months after Schuette announced that he would investigate the circumstances that led to Flint’s crisis to see if laws were broken during what he called “a human tragedy.” They are the first charges to stem from the catastrophe in Flint — which potentially exposed nearly 100,000 residents to water tainted with lead — but Schuette and other investigators on Wednesday vowed that they mark only the beginning of a broadening investigation.

“We have a long way to go. We have a lot of people to interview, a lot of evidence to get,” said former Wayne County prosecutor Todd Flood, who is helping lead the probe. “We’re not targeting any person or people. But nobody is off limits, either.”

Local resident William Chatman, 61, was at Bible study in a Flint church where he has helped distribute water when the charges were announced Wednesday.

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“It’s a victory,” Chatman said. “Those people that … allowed it to happen, you have to pay the consequences for your actions. This sends a signal out to others. You need to take your job seriously and do the right thing.”

He said he hopes investigators don’t stop until they’ve dug even deeper into any potential misconduct. “If they have to go to the top, that’s what they should do,” Chatman said.

In fact, authorities were asked repeatedly Wednesday whether they were investigating Michigan Gov. Rick Snyder (R) or other top state officials. They repeated only that they would follow the facts of the case wherever they lead, no matter the outcome.

Snyder said Wednesday afternoon that he has not been questioned or interviewed as part of Schuette’s investigation, though he said his office has been cooperating with the probe. Asked if he felt he did anything criminally wrong, Snyder answered: “I don’t even want to get into that kind of speculation. I don’t believe so.”

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The debacle in Flint began to unfold two years ago. For decades, the once-thriving industrial city bought its water from Detroit. It was piped from Lake Huron, with anti-corrosion chemicals added along the way.

But in early 2014, with the city under the control of an emergency manager appointed by Snyder, officials switched to Flint River water as part of a money-saving measure. But the state’s environmental quality agency failed to ensure that corrosion-control additives were part of the new water supply.

Flint’s water was contaminated with toxic lead soon after the city switched to the Flint River as its source in April 2014 and a Michigan state department failed to ensure that anti-corrosive chemicals were added to the supply. That allowed lead rust, iron and, most dangerous, lead to leach from aging pipes into the city’s tap water.

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Most residents are still living on bottled water, even after the city switched back to its previous water source last fall.

Officials also are investigating possible links between the tainted water and a dozen deaths from Legionnaires’ disease.

A task force appointed by Snyder to investigate the water-contamination crisis in Flint issued a report last month that largely blamed state officials in what it called “a story of government failure, intransigence, unpreparedness, delay, inaction and environmental injustice.”

It detailed a widespread lack of responsibility and leadership behind the catastrophe. The report found that the state Department of Environmental Quality “failed in its fundamental responsibility” to enforce drinking-water regulations and assured the governor’s office that Flint’s water was safe when it wasn’t. It said Snyder and his administration failed to act even after “suggestions to do so by senior staff members in the Governor’s office.” It said the Flint Water Department “rushed unprepared” into switching to a new water source without proper use of corrosion controls. It blamed the federal Environmental Protection Agency’s delayed enforcement of federal drinking-water standards for “prolonging the calamity.”

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Flint’s water system is in much better shape six months after the city switched its water source and began adding chemicals to control corrosion of aging pipes, researchers from Virginia Tech University reported last week. During a round of tests last month, a lower percentage of homes showed high lead levels, and even in those where levels still exceed federal standards, the amount of lead appears to be falling, the researchers said.

But the researchers found that too many homes still had lead levels above the federal “action level” of 15 parts per billion. In addition, they said, lead levels throughout Flint’s water system are “highly variable.”

“Thus, virtually all homes in Flint must be considered at risk, at the present time, for elevated lead in water,” researchers wrote in a summary of their findings, “unless the homeowner is certain that there is no lead plumbing . . . in the home.”

This story has been updated.