The hunt was on.
An outbreak of Legionnaires’ disease had erupted in Harlem, killing six people and sickening more than 100 others. Officials said the bacteria that cause the illness had been spread through the air starting in late July by mist from infected water towers atop buildings in the neighborhood.
While doctors treated infected patients, public health researchers were in a race to pinpoint which towers were harboring the pathogen.
By late August, bacteria had been found in 12 towers, and the search had moved from the rooftops of Harlem to a hulking building farther south in Manhattan, where scientists needed to match bacterial samples from patients with those taken from water tanks.
That has moved the hunt into a stage that health officials say hinges on the slow growth of bacterial cultures and the exacting process of genomic sequencing, all of which can take weeks to get right.
“We watch science shows or ‘Law & Order,’ and the same day a murder happens, Mariska Hargitay is in the medical examiner’s office and is like ‘OK, what’s the verdict?’ and they already know everything,” Chantal Gomez, a spokeswoman for the New York City health department, said. “But that’s not reality. The reality is public health takes time.”
The juxtaposition between the anxious wait for answers and the slow process of growing and analyzing bacterial samples has been a defining feature of this stage of the outbreak, which was detected through routine public health surveillance.
Roughly two dozen scientists at the New York City public health lab in Kips Bay, Manhattan, are responsible for tracking down the source of the outbreak — just one of several maladies they are tracking, including mosquito-borne illnesses such as West Nile virus and food-borne pathogens such as salmonella.
“I understand that folks might feel antsy,” Dr. Enoma Omoregie, the associate director of environmental sciences at the lab, said. “They see stuff in the news.”
He said it was his job to make sure his staff members “take the time to do the work properly” and do not feel buffeted by the news cycle or pressure from people in their daily lives.
“If I could, I would snap my fingers and be done, but unfortunately it’s not like that,” he added. “Sometimes, things grow slowly.”
Legionnaires’ disease is a form of pneumonia that is caused by a bacterium called Legionella. It thrives in warm, stagnant water, and many outbreaks in New York are caused by vapor from rooftop cooling towers. Researchers say the vapor can carry the pathogen for thousands of feet before it is inhaled and sickens someone.
Most healthy people don’t become sick after being exposed to the bacteria, but it can be perilous for those who are more vulnerable, including older adults, smokers and people with chronic diseases and compromised immune systems.
Between 200 and 500 people are diagnosed with Legionnaires’ disease each year in New York City, and just over a dozen die.
After Legionella was found in 12 cooling towers in Central Harlem during the current outbreak, the owners of those buildings were ordered to immediately disinfect their tanks, which they did, the health department said.
The tests used in those cases could not determine if the bacteria were alive or dead, but once the tanks were disinfected, the rate of new infections began to decline. Health officials said that led them to believe the outbreak’s source has been neutralized, even if it has not been pinpointed.
To do that, scientists must find a match between samples of the bacteria taken from the rooftop water tanks and the sputum or other material from infected patients.
Patient samples are taken by doctors, who pass them along to the health department. Collecting a water sample can be trickier.
Researchers have to gain access to a building, climb onto the roof and retrieve water from the cooling towers. They then test those samples to see if living or dead Legionella is present in the water. If any trace of Legionella is found, the building is ordered to disinfect the tank.
The city tested dozens of towers in Harlem before finding the 12 with traces of Legionella. But the rapid tests used in the initial water analysis cannot discern between living and dead samples, and only living bacteria can cause an infection.
The positive samples were sent to a different team to analyze and to culture them, a process that encourages living bacteria to multiply into bacterial colonies.
That takes up to two weeks, said Dr. Elizabeth Watts, the health department’s chief of environmental sciences. She supervises the department’s Legionella team, which was formed after an outbreak linked to a cooling tower at a Bronx hotel killed 16 people in 2015.
Bacterial samples are placed in a petri dish, and as the cultures grow, they form into competing blooms of different colors, only some of which may be Legionella. Scientists separate the cultured Legionella from other bacteria that may have accompanied them into the petri dish.
“I believe it is like 10 percent of water systems that are tested are positive for Legionella,” said Dr. Watts, although she said only a few of the many species of Legionella bacteria cause sickness in humans. “We don’t exactly know why outbreaks happen from time to time.”
Legionella blooms are purple-gray. Greta Ohanian, a microbiologist on the Legionnaires’ team, said the bacterium is “really pretty” when you look at its violet-hued colonies under a microscope.
“There are a lot of colonies that we see where we might say, ‘OK, this looks gray or sort of green, this might be Legionella,’ but then we analyze it and it is a doppelgänger,” Ohanian said.
Her colleague, Stefan Silver, a fellow microbiologist, added: “It is like finding a needle in a haystack.”
Once Legionella is identified, the bacteria are then sent to a separate team that sequences their genomes — the DNA instructions that are the building blocks of life. The process can take up to two days. The same sequencing lab analyzes the genomes of many different pathogens and is especially busy in the summer when food-borne illnesses are more common, said Aaron Olsen, the lab’s genome sequencing chief.
“A lot of times, we’ll put a whole bunch of samples on the sequencer on a Friday evening, and then on Monday morning, it’ll just be finishing up,” Dr. Olsen said.
Samples from patients are cultured, analyzed and sequenced in a similar way. The genomic sequences from both samples are then sent to a different team, bioinformatics, for analysis.
It is the job of that team to match samples from patients to the water tower whose mist made them sick, which they do by determining if multiple samples belong to the same genomic cluster.
Dr. Faten Taki, the lab’s chief of bioinformatics, said advances in information technology, not to mention in genomic sequencing, had sped up work that in years past might have taken much longer. Because of that, “this work can be just business as usual,” she said, even when the clock is ticking and scientists at the lab have several health crises to address at once.
“It takes a village,” Dr. Taki said. “But what we have done in non-outbreak times, in times of peace, has prepared us well for an outbreak.”
Liam Stack is a Times reporter who covers the culture and politics of the New York City region.
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