The death toll in Flint, Michigan, from contaminated water may be much higher than state health officials have acknowledged, an ongoing FRONTLINE investigation has found. The likely killer: Legionnaires’ disease, a severe form of pneumonia caused by the legionella bacteria.

Officially, 90 people were sickened and 12 died from exposure to waterborne legionella bacteria during the 18 months that the city of Flint drew its water from the Flint River in 2014 and 2015. But FRONTLINE’s investigation has found 115 deaths from pneumonia during that time, some of which scientists say could actually have been caused by legionella. The tally is based on an extensive review of death records and interviews with epidemiologists and other scientists who are experts in the field of infectious diseases.

If the death toll is higher, as the records and interviews suggest, a 15-month delay by state officials in notifying the community about the legionella outbreak may have cost even more lives than the deaths state prosecutors have cited in an ongoing criminal case. More than a dozen state and city officials, including from the Michigan state departments of health, and environmental quality, are facing criminal charges associated with failing to alert the public about the risks of legionella until well after the outbreak had subsided.

“The worst case scenario is when [doctors] don’t realize a bacterial infection is present in the water,” said Dr. Victor Yu, a former professor of medicine at the University of Pittsburgh who helped prove in 1982 that legionella outbreaks can stem from bacteria in drinking water. “Whenever drinking water is involved” you should treat patients assuming that they have Legionnaires’ without waiting for definitive results, he said, “because it takes so long to run tests.

“People can die waiting.”

The idea that there were more legionella deaths than previously reported has also been raised in court by Todd Flood, the state-appointed special prosecutor overseeing the criminal investigation. Flood recently introduced a stack of death certificates showing that deaths from pneumonia in Flint skyrocketed in the months after the city switched its water source. He also argued in court that some of those deaths could be misdiagnosed cases of Legionnaires’ disease connected to the outbreak.

On July 25, a judge was expected to determine whether to allow Flood to bring involuntary manslaughter charges against Nick Lyon, director of the Michigan Department of Health and Human Services, for his role in the crisis. At the hearing, Judge David Goggins delayed his ruling to August 20, saying he needed more time to review materials. The case centers around two Legionnaires’ patients who died after contracting the disease during the Flint outbreak: Robert Skidmore and John Snyder.

Flood declined to comment, but said in court earlier this month that the high number of pneumonia deaths underscored the severity of the case: “There was a clear, willful and wanton disregard… knowing that someone was going to get sick, someone was going to die,” he said. “And they sat on the information, and that being specifically Director Nick Lyon.”

Lyon’s attorney, John Bursch, told FRONTLINE there’s no merit to the charges against his client. “The prosecutor’s theory is that Director Lyon caused two individuals to contract Legionnaires’ and die because of his failure to make a public announcement regarding the Legionnaires’ outbreak,” he said. “There’s no evidence that anybody would have done anything different.”

FRONTLINE’s analysis examined six years of death records in Flint and the surrounding Genesee County, and included door-to-door interviews with victims’ families. It showed an unusual uptick in pneumonia deaths in the city at the same time as the legionella outbreak. During the period when the city was using Flint River water — May 2014 through October 2015 — pneumonia killed 115 people in the city of Flint, up more than 43 percent from that same time period a year earlier, according to the data. The extent of any possible overlap between the 12 reported legionella deaths and these pneumonia deaths is unclear. The state has released little information about the Legionnaires’ victims.

Five epidemiologists and infectious disease specialists who reviewed the data say the timing, coupled with the fact that the deaths rose in the summer when legionella flourishes, shows that at least some of those 115 deaths are likely attributed to Legionnaires’ disease.

“What you have is something that’s biologically plausible,” said Dr. Janet Stout, a microbiologist and leading legionella expert who runs the Special Pathogen Lab in Pittsburgh. “And what remains to be done perhaps is the statistical analysis. And certainly, people will point to other potential causes for an increase. But when you take the picture in its totality, it’s not an unreasonable association to make that some of those deaths could have been due to legionella.”

In 2015, Stout was hired to advise a local hospital, McLaren Flint, on best practices for handling legionella cases there, and was later retained to provide expert testimony in an ongoing lawsuit against the hospital by legionella victims.

The state has consistently maintained since the outbreak that the legionella deaths could not be definitively linked to the water because the necessary water samples and patient laboratory tests weren’t collected during the outbreak. “Whether or not we can definitively say it’s tied to the water, or not tied to the water, the samples just don’t exist,” said Angela Minicuci, a spokesperson for the Michigan Department of Health and Human Services (MDHHS). “It is certainly an issue in terms of being able to definitively rule out something from the environmental perspective.”

However, several independent scientists who have studied the problem, including in published peer-reviewed papers, have concluded that the water was almost certainly the source of the outbreak. In Feb. 2017, the U.S. Centers for Disease Control and Prevention found a genetic match between legionella bacteria in Flint water and a sample taken from confirmed Legionnaires’ patients.

When asked about the increase in pneumonia deaths found by FRONTLINE, Minicuci said the state had also noted a similar increase in the summer of 2014 in the data it examined. Because the deaths declined the following year, she said the state concluded they were likely linked to influenza, which is a common cause of pneumonia in Michigan during the winter. Minicuci said that the state also analyzed a subset of cases of pneumonia patients — those who had already tested negative for legionella — and concluded there were no additional legionella cases.

“The level of data that we have access to, it’s going to be much more in-depth,“ she said. “We feel very confident that this data is very thorough.”

When compiling its mortality statistics, Michigan’s state health department follows federal reporting standards, and assigns just one underlying cause of death. But experts told FRONTLINE that it’s important to consider all causes of death — what’s known as all-cause mortality — when investigating a public health problem such as the outbreak in Flint.

“When we write papers that are peer reviewed and look at pneumonia death, we do all-cause mortality because you can’t separate the pneumonia and underlying disease as cause of death,” said Dr. Marcus Zervos, the head of the infectious disease department at Henry Ford Hospital in Detroit.

“Even if somebody does have cancer…you still want to know about the pneumonia because you want to sort out what’s going on. Why is there an increase in pneumonia? Is there Legionnaires,’ or is there some other bacteria?”

The death certificates FRONTLINE reviewed don’t reveal what caused the pneumonia that claimed these residents’ lives — whether they were sickened by legionella or another waterborne bacteria, or something else entirely. And a full account may never be known, since it’s not possible to test posthumously for the bacteria, and the city is no longer using the river as a water source.

But epidemiologists who reviewed the data for FRONTLINE said there are multiple reasons why some of these deaths were likely caused by legionella. One of the main reasons is that Legionnaires’ disease is misdiagnosed as pneumonia in about 40 percent of cases because the symptoms are so similar, said Stout, who helped develop the first US guidelines for legionella prevention in 1993 with Yu. Those guidelines have since become an international model.

“The tracking of the outbreak really is very dependent on the physicians making the diagnosis so the initial cases are identified,” she said, and added: “So it wouldn’t be surprising, if you ask any experts in Legionnaires’ disease, that some of those pneumonia deaths would be due to legionella, and that they wouldn’t know it was legionella pneumonia.”

Since doctors in Flint were unaware of the legionella threat, scientists familiar with outbreaks say, they would not have been routinely testing pneumonia patients for the bacteria, or giving them the life-saving antibiotic they needed. If improperly treated, the bacteria can quickly turn fatal, particularly for vulnerable populations such as the infants and the elderly, cancer patients or those with compromised immune systems.

So when the patients succumbed, pneumonia would be listed on their death certificates — and the legionella bacteria would continue to spread.

Just weeks after the city switched its water to the Flint River in April 2014, Flint residents began contacting local, state and federal government agencies with complaints. The water was brown, they said, and had a foul odor. Some people had developed rashes and their hair was falling out. The concerned residents blamed these problems on the river, which had a reputation as a dumping ground for cars and industrial waste, not drinking water.

Later, the city’s nearly 100,000 residents would learn that they and their children had been exposed to toxic levels of lead that had leached into the water from corroded pipes.

In the meantime, residents were coming down with other symptoms. They had chills in the middle of the summer. They were coughing, running high fevers and having difficulty breathing. Then people began dying.

From May through October 2014, 44 people died from pneumonia in Flint, up 57 percent from the 28 pneumonia deaths recorded during the same period in 2013, and well over the historical average.

It’s unusual to see such a severe increase in pneumonia during the summer in Michigan, which typically sees a rise in the winter related to influenza. Legionella and other waterborne bacteria, however, bloom in warmer weather. That summer, as cases of Legionnaires’ disease surpassed historical averages, so too did the number of pneumonia deaths, according to FRONTLINE’s data.

“A rise in pneumonia cases by themselves is significant, and it does require being investigated,” said Zervos, who has worked on outbreaks with health departments around the world. “If we see a spike of cases of pneumonia in the summer, then that would raise concerns about legionella.”

Staff at the state health department noticed the rise in Legionnaires’ cases in June 2014, according to witness testimony in the Lyon case.

By October of 2014, the county health department had completed a preliminary investigation, and some state officials expressed concerns about a link between the outbreak and the water system, according to internal emails released through a public records request. But state officials waited until January 2016 — nearly 15 months — to tell the public.

State officials have maintained they didn’t have enough information about the outbreak to warn the public earlier. “Certainly our investigation into the outbreak was occurring regardless of whether or not a public notice went out,” Minicuci said.

In May 2018, the health department issued a report linking the legionella outbreak to the McLaren Flint Hospital.

County officials had identified McLaren as a potential source early on in the outbreak, although state epidemiologists ruled it out after reviewing preliminary data.

In October 2014, Shannon Johnson, an infectious disease epidemiologist at the state health department, emailed colleagues to say that county health officials initially thought the uptick in Legionnaires’ cases might be linked to a local hospital. But the data didn’t fit that theory, according to Johnson’s analysis. She wrote: “The current hypothesis is that the source of the outbreak may be the municipal water.”

Minicuci, the state health department’s spokesperson, told FRONTLINE that the county health department was low on resources at the time, and might not have properly analyzed the data.

The state’s May 2018 report said that McLaren was the “one common source” between a majority of the Legionnaires’ cases during the outbreak, with 57 percent of the patients associated having visited the hospital at some point in the two weeks prior to falling ill. The report also said that the municipal water was not the “primary contributor” to the outbreak.

At the time of the outbreak, however, McLaren Flint Hospital was drawing its water from the Flint River.

McLaren spokesperson Rosemary Plorin refuted the notion that the hospital was the common factor for a majority of the Legionnaires’ cases. “Many experts and organizations have sought to understand exactly what happened in Flint and what led to the Legionnaires’ disease outbreak,” Plorin said. “Most have reached very different conclusions than those developed by MDHHS.”

Dr. Sammy Zahran, a statistician at the University of Colorado, who worked with the state data for a study on the outbreak published in Feb. 2018 in the journal Proceedings of the National Academy of Sciences, said that McLaren in this case was simply “a big building sitting on a broken system.”

Of the state’s report, he added: “I don’t think it was a rational adjudication of the facts.”

Earl Woods was one of the Flint residents who fell ill in the summer of 2014. His sinuses were dry, so he sniffed the tap water for relief. Days later, his longtime partner Carroll Kinkaid noticed him growing weaker. Then he had trouble breathing. “It was like he wilted,” she said.

Days later, Woods was in the emergency room. He died of pneumonia in August 2014, one of the 10 in the city that month, according to FRONTLINE’s tally. He was 61.

When FRONTLINE shared its findings with Kinkaid, she said the information validated the suspicions she’d held onto since Woods’ death — that the bacteria that caused his death came from the water.

“As a human being, it’s gratifying to know that my instincts were accurate,” she said. “It doesn’t bring Earl back. It doesn’t bring back the loved ones of the family members that were lost in this.”

This story was developed in collaboration with 100Reporters, a nonprofit news organization.

This story has been updated to reflect the most accurate data on pneumonia deaths in the city of Flint. It was previously updated to include Nick Lyon’s correct title, and additional information about Dr. Janet Stout’s work on the Flint water crisis.