Heatmap of the Pseudomonas genus, the most abundant genus found across the city. Hotspots are found in areas of high station density and traffic. [Ebrahim Afshinnekoo]
Heatmap of the Pseudomonas genus, the most abundant genus found across the city. Hotspots are found in areas of high station density and traffic. [Ebrahim Afshinnekoo]

Microbes have been known to take Manhattan, the Bronx, and Staten Island, too. But they were never part of a citywide microbiome census until scientists based at Weill Cornell Medical College developed PathoMap—a baseline assessment of DNA representing New York City’s microbial community.

PathoMap uses New York City’s crowded and heavily trafficked subway system as a proxy for the city as a whole. Although PathoMap indicates that most of the microscopic organisms inhabiting the subway system are harmless, some microbial transfers would be most unwelcome. PathoMap revealed the presence of disease-causing, drug-resistant bacteria as well as DNA fragments associated with anthrax and bubonic plague.

Unlike ordinary subway maps, which hardly ever need to change, PathoMap would offer its greatest benefits if it were updated frequently. Repeated sampling could be used for long-term, accurate disease surveillance, bioterrorism threat mitigation, and large-scale health management for New York, said PathoMap’s senior investigator, Dr. Christopher E. Mason, an assistant professor in Weill Cornell's Department of Physiology and Biophysics.

PathoMap debuted February 5 in the journal Cell Systems, in an article entitled, “Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.”

“We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks,” the authors wrote. “Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter).”

The PathoMap findings are generally reassuring, indicating no need to avoid the subway system or use protective gloves, Dr. Mason says. Most of the 637 known bacterial, viral, fungal, and animal species he and his co-authors detected are nonpathogenic and represent normal bacteria present on human skin and human body. Culture experiments revealed that all subway sites tested possess live bacteria.

The most commonly found organism (46.9%) was bacteria. Despite some riders' fears of catching cold or flu from fellow straphangers, viruses were rare—they made up .032% of the samples. However, some seasonal viruses are RNA viruses, not DNA viruses, and they would not be identified with the collection methods used in the study.

Of the known bacteria, the majority (57%) found on the surfaces of the subway have never been associated with human disease, whereas about 31% represented opportunistic bacteria that might pose health risks for immune-compromised, injured or disease-susceptible populations, researchers report. The remaining 12% have some evidence of pathogenicity.

They found that dozens of microbial species were unique to each area of the train, and that there is a significant range of microbial diversity across different subway lines. The Bronx was found to be the most diverse with the most number of species found, followed by Brooklyn, Manhattan, and Queens. Staten Island was the least diverse.

“We built maps that detail what organisms are present in each area of the city, creating a molecular portrait of the metropolis,” said co-lead author Cem Meydan, Ph.D., a postdoctoral associate at Weill Cornell Medical College.

Despite sampling surfaces of areas of high human traffic and contact, the researchers found that only an average of 0.2% of reads uniquely mapped to the human genome. Using tools like AncestryMapper and ADMIXTURE, the investigators took human alleles and recreated census data of a particular subway station or neighborhood. Their results showed that the trace levels of human DNA left on the surface of the subway can recapitulate the U.S. Census data.

Projects are already underway that build upon PathoMap's initial data and further the researchers' goal of investigating the microbiome of large, complex cities. Collaborators across the country have collected samples from airports, subways, transit hubs, taxis, and public parks located in 14 states—including New Jersey, Massachusetts, Maryland, Florida, Illinois, Texas, and California. By sequencing the DNA of these samples, Dr. Mason hopes to create the first ever comparison of major cities in the nation that contextualizes urban and rural, high-density and low-density environments.