An Alexandria teen who died last month after swimming in Lake Minnewaska was not infected with a deadly lake amoeba after all, according to confirmatory tests by the U.S. Centers for Disease Control and Prevention.

Hunter Boutain died from bacterial meningitis, not from contact with the rare but deadly Naegleria fowleri amoeba, the Minnesota Department of Health reported Monday.

The state Health Department initially had reported the amoeba as the likely cause of the infection, which raised alarm over lake swimming across Minnesota because Naegleria fowleri is usually found in warmer, southern waters in the U.S. But CDC testing did not corroborate that finding.

State health officials decided at the time not to wait six weeks for the final CDC lab results before warning swimmers about the potential risk, said Health Department spokesman Doug Schultz. Boutain’s death, symptoms and swimming activity shortly before he became ill all pointed to Naegleria fowleri as the cause, and the teen’s doctors along with state and federal health officials agreed with the decision to alert the public.

“You always worry about being the boy who cried wolf,” Schultz said, “but you also don’t want to say nothing.”

Boutain did not die from Primary Amebic Meningoencephalitis, or PAM, the condition that results from inhaling the amoeba through the nose, Schultz said, but that doesn’t lessen the tragedy.

Boutain played bass in the middle school orchestra and jazz band, enjoyed baseball and sports, and had memorized 368 Bible verses in preparation for a national Bible Quizzing competition in Oklahoma, according to a YouCaring fundraising page for his parents.

Nor does it eliminate the low-level risk of infection from the amoeba. Minnesota reported two other deaths, in 2010 and 2012, of children who came in contact with the amoeba while swimming in Lily Lake in Stillwater.

Cases remain rare nationally. There have been fewer than 130 confirmed cases in the past 50 years, though almost all of them were fatal.

The suspicion of another case was high enough that the CDC dispatched an experimental medication, which had been used to successfully keep an Arkansas girl alive after she had been infected by the amoeba in 2013. Doctors also treated Boutain with antibiotics in the event of a bacterial infection, said Dr. Ed Ehlinger, state health commissioner. The Boutain family gave him permission to discuss details of their son’s case.

Boutain had previously suffered a head injury from a skateboard fall, and the resulting trauma may have torn the protective layer surrounding the brain and left him more susceptible to the infection, Ehlinger said. “Its like an open pipe into the brain.”

The initial state announcement had caused alarm, particularly in the area around Minnewaska. Swimming lessons were moved from the lake to a nearby hotel pool. Planners considered delaying or altering the annual Waterama festival in the lakeside community of Glenwood, but ultimately decided to proceed.

Coincidentally, Ehlinger had scheduled a community meeting in Glenwood on Monday afternoon to discuss the implications of the apparent presence of the amoeba in Minnewaska, a popular recreational lake. Instead, he provided them with the final test information from the CDC.

On his Facebook page, Glenwood Mayor Scott Formo Sr. expressed relief as the earlier state announcement raised fears and hurt lake business.

“A child died and it affected the community as well as the family,” he wrote. “Without forgetting that fact, locally we are relieved to know that the fear of what was suspected as a case of PAM contracted from Lake Minnewaska is not the case.”

Ehlinger appreciated the understanding from community leaders about the need to err on the side of caution. He recalled the outcry in Stillwater when news of one of the infections in Lily Lake had been later than they wanted.

“The people around that lake were really upset when we didn’t get that information out earlier,” he said.

CDC testing of Lily and other lakes in Washington County had found some traces of the amoeba in 2010, but none in 2013 or 2014. Lily remains closed to swimming.