Exactly 50 years ago, as the nation celebrated its bicentennial, a mysterious pneumonia began sickening and killing military veterans in Pennsylvania. The victims had gathered at Philadelphia’s largest hotel to attend an American Legion convention.

“The mysterious Legionnaires’ disease,” as the newspapers branded it, had seemingly come out of nowhere. For months, disease detectives searched for the cause, eventually landing on a previously unknown bacteria, which a federal microbiologist named Legionella.

Now, half a century later, amid celebrations of the nation’s 250th birthday, New York City has emerged as a major — and repeated — epicenter of Legionnaires’ disease. This summer, the bacteria have been implicated in the deaths of five people and sickened more than 85 across Manhattan’s Upper East Side.

It is the third major outbreak of Legionnaires’ in a dozen years in the city, following last year’s cluster of cases in Harlem, which killed seven people, and an outbreak in the South Bronx in 2015 that was one of the nation’s worst, after Philadelphia in 1976.

“There are not many other cities on earth that would have that,” said Greg Rankin, the chief executive of a company that sells a Legionella test.

When Legionella was discovered, public health authorities characterized it as a picky and selective bacteria. It had eluded discovery because it was tough to grow using laboratory techniques under which other bacteria thrived. Though it was found naturally in water and soil, it needed certain conditions to multiply in the numbers required to spread disease. It liked warm water, above 90 degrees. And iron or corrosion.

Federal scientists half a century ago saw evidence that the bacteria thrived in old plumbing systems and in the warm, stagnant water that was a byproduct of large air-conditioning systems. In short, the bacteria liked cities.

New York has everything Legionella needs to thrive and infect people: aging and corroded water pipes and a concentration of large apartment buildings with complicated plumbing systems and central air-conditioning systems.

During the past decade, city officials responded with stringent testing and disinfection requirements for the cooling systems of large buildings, which are often implicated as the cause of outbreaks. But there is growing concern that the approach is not working. Some experts and doctors suggest that the battle against Legionnaires’ must go beyond air-conditioning systems that can spew bacteria-laden mist from rooftops and onto passers-by below. The focus, they say, should extend to plumbing systems.

While New York City has among the highest incidence of Legionnaires’, the disease has been rising steadily across the United States. During the past 25 years, the rate of cases rose more than fivefold. The vast majority are not linked to major outbreaks but involve single cases or just a few at a time. These sporadic infections can occur when Legionella has colonized building plumbing systems or shower heads and other fixtures.

Legionella can thrive in biofilm — a slimy layer of microorganisms, including bacteria, that coat the insides of water pipes and plumbing fixtures. When water pressure changes rapidly, the biofilm can dislodge a torrent of Legionella, which causes a severe form of pneumonia.

Lot of things can cause such a change in water pressure, including uncapping fire hydrants during a heat wave so that children can play, said Robert W. Bowcock, a former water utility manager in California who is associated with the Alliance to Prevent Legionnaires’ Disease, an advocacy group that draws support from manufacturers of cooling towers and other equipment manufacturers. In large apartment buildings, changes in water-use patterns can disturb biofilm, he said.

In New York City, sporadic cases of Legionnaires’ disease are linked to building water systems. Those can occur when residents inhale bacteria-rich water droplets, including while showering. From time to time, the city’s Health Department will urge residents of a building to stop using the shower. While healthy people rarely fall ill, those who are older or have underlying health conditions are susceptible.

Still, the large-scale infection events tend to involve mist coming off rooftops.

In large buildings, central air-conditioning systems produce warm water, which is piped to boxy rooftop fixtures known as cooling towers. Fans blow across the water to cool it through evaporation. But these cooling towers, with their warm water, corroding metal and slime, can incubate bacteria. The mist generated by the towers’ fans can infect people blocks away.

“If you want to feed and breed Legionella, the No. 1 food source is algae, and the second source is corrosion,” said Micah Curtis, the sales director at a company that makes cooling towers.

Cooling towers have been implicated previously, including in the 2015 outbreak in the Bronx and last year’s in Harlem.

New York City has about 5,000 cooling tower systems. The Health Department has logged their locations so that they can be tested during outbreaks. The city also began requiring property owners to test them for Legionella, initially every 90 days. After last year’s outbreak, that was shortened to 30 days.

But Dr. Michelle Morse, who was then the acting city health commissioner, cautioned last year that even frequent testing will not stymie all outbreaks, given how fast the bacteria multiply.

Another Outbreak in the Air

Earlier this month, Christine Roussel, 87, collapsed in her apartment on East 82nd Street. An archivist and art conservator, she had once played a role in a blockbuster exhibit at the Metropolitan Museum of Art and the restoration of the Statue of Liberty. She had just wrapped up a book tour.

Now, she could not get up from the floor. A doorman found her there the following day, July 2, and summoned an ambulance, according to her son.

That same day, a half mile away, an 88-year-old Air Force veteran and retired businessman, Robert Goldstein, developed a fever of 104 degrees. His wife insisted he go to the hospital.

Ms. Roussel and Mr. Goldstein became among the first victims of this summer’s outbreak, succumbing after more than two weeks in the hospital.

“It’s something you don’t see, an invisible monster, a vapor that just went into his lungs and just took him away from me,” Mr. Goldstein’s widow, Ida Goldstein, said at a news conference last week.

The Health Department responded by testing more than 180 cooling towers from Central Park to the East River.

More than 70 tested positive upon initial screening, indicating the presence of Legionella DNA, regardless of whether the bacteria were dead or alive. The towers sat atop apartment complexes, schools and leading cultural institutions, including the Guggenheim Museum and the Metropolitan Museum of Art.

“These results are all indicative of just how common Legionella is in our built environment,” Dr. Alister Martin, the city’s health commissioner, said.

He ordered cooling towers that tested positive in the initial screening to be drained and disinfected, rather than wait for confirmatory testing as in past outbreaks.

The city’s response appears to have been effective. Most patients were diagnosed between July 2 and July 9, and a new case has not been reported since July 15.

For the health authorities, the lesson is clear: Cooling towers are teeming with the bacteria.

They have yet to identify the outbreak’s source. They will search for a match between the genetic code of Legionella taken from patients and the samples taken from cooling towers.

But this kind of rapid response will not prevent all of the 200 to 700 cases of Legionnaires’ in New York City each year. When Centers for Disease Control and Prevention researchers in 2016 reviewed dozens of past outbreaks across North America, they concluded that cooling towers were responsible for about a quarter. Potable water caused more than half.

Dr. Michael Skelly, an infectious-disease doctor who treated Legionnaires’ patients during the 2015 Bronx outbreak, said he believed that the greater risk was from the water that came out of taps and showers.

In recent years, it had not been unusual for the Health Department to identify seven or eight buildings where several residents had come down with Legionnaires’, with the bacteria found in worrisome quantities in the plumbing system.

“They keep focusing on the cooling towers,” Dr. Skelly said. “They keep cleaning them, and yet it keeps occurring.”