Researchers at Weill Cornell Medical College in New York City have published the results of a project in which they mapped the pathogens present in the city's subway system.

Weill Cornell officials say the study, published in Cell Systems, demonstrates that it is possible and useful to develop a "pathogen map" — dubbed a "PathoMap" — of a city, with the heavily traveled subway a proxy for New York's population. It is a baseline assessment, and repeated sampling could be used for long-term, accurate disease surveillance, bioterrorism threat mitigation, and large scale health management for New York, according to the study's senior investigator, Christopher E. Mason.

The PathoMap findings are generally reassuring, indicating no need to avoid the subway system or use protective gloves, Mason said. The majority of the 637 known bacterial, viral, fungal and animal species he and his co-authors detected were non-pathogenic and represent normal bacteria present on human skin and human body. But the researchers also said live, antibiotic-resistant bacteria were present in 27 percent of the samples they collected. And they detected two samples with DNA fragments of Bacillus anthracis (anthrax), and three samples with a plasmid associated with Yersinia pestis (Bubonic plague) — both at very low levels. Notably, the presence of these DNA fragments do not indicate that they are alive, and culture experiments showed no evidence of them being alive.

Yet, these apparently virulent organisms are not linked to widespread sickness or disease,  Mason said. "Despite finding traces of pathogenic microbes, their presence isn't substantial enough to pose a threat to human health," he said. "The presence of these microbes and the lack of reported medical cases is truly a testament to our body's immune system, and our innate ability to continuously adapt to our environment.

"PathoMap also establishes the first baseline data for an entire city, revealing that low-levels of pathogens are typical of this environment. While this is expected in rural environments, we've never seen these levels before in cities. We can now monitor for changes and potential threats to this balanced microbial ecosystem."

In the study, the research team — which included investigators from five other New York City medical centers and others from around the country and internationally — sought to define the microbiome in New York City's subway system, which in 2013 was used by an average of 5.5 million people per day, according to the city's Metropolitan Transportation Authority.

Over 17 months, the team — many of them student volunteers, medical students and graduate students — used nylon swabs to collect, in triplicate, DNA from turnstiles, wooden and metal benches, stairway hand railings, trashcans, and kiosks in all open subway stations in 24 subway lines in five boroughs. The team also collected samples from the inside of trains, including seats, doors, poles and handrails. Investigators are currently analyzing additional samples collected during all four seasons to study the temporal dynamics of the microbiome.

The sample collectors were equipped with a mobile app built by the researchers, which allowed them to time stamp each of the samples, tag it using a global positioning system and log the data in real time. DNA from the microbes was sequenced using the most advanced research technology at the Weill Cornell Epigenomics Facility and the HudsonAlpha Institute for Biotechnology. They sequenced 1,457 samples out of more than 4,200 collected.

Efforts like PathoMap in New York can readily be applied to other cities to provide a new tool for disease and threat surveillance, Mason said. "With the further development of sequencing technologies, I believe having a live model tracking the levels of potential pathogens could be possible," he says. "I envision PathoMap to be the first step in that model."

More information and a link to the study is available here.

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