NYC Pathomap

NDSU Microbiology
by NDSU Microbiology

Guest Blogger, Liza Stremick, VMS Undergrad

While recently scrolling across the Internet, a certain headline jumped out at me: “Researchers find Bubonic Plague Fragments on the NYC Subway.” If this doesn’t grab your attention, I’m not sure what will. But, I wondered, if this story is true, how has half of NYC not already been infected?

Researchers from Cornell University are working to produce a Pathomap – a map of pathogens – of the NYC subway that will give riders, as well as scientists, an idea of what really is going on in the popular transportation system. The map will be used to track diseases, monitor bioterrorism threat migration, and help with health management.

The first step in mapping is to collect a variety of samples. Researchers swabbed many different surfaces – from benches to kiosks, hand railings to trashcans – in the subway during all four seasons. After collecting and sequencing over 1,400 samples, researchers started piecing the information together. The results were truly astonishing.

In one particular part of the subway, the findings resembled that of a marine ecosystem. However odd this might sound, it is actually an impressive representation of this particular station’s past. This is the Ferry South station located in lower Manhattan. In 2012, this station was flooded with water from Hurricane Sandy. Now, almost three years later, the station has been fixed up and reopened, but the resilient bacteria still remain.

The marine microbes were unexpected, but perhaps even more eye-opening were the samples that mapped to pathogens. Twelve percent of the samples linked to disease-causing bacteria, including the microbes that cause anthrax and bubonic plague – which sounds like an outbreak waiting to happen…or maybe not. These particular samples showed that the strains were no longer living and posed no threat to the subway users. Researchers don’t think this is anything we should be concerned about.In fact, they believe the findings and lack of medical cases are a testament to the human immune system.

In addition to bacteria, 0.2 percent of the findings mapped uniquely to the human genome. The scientists used software to investigate the alleles that were found in the human genome samples. With this data, they created a census of particular areas of the subway. By piecing together this information, they were able to accurately show the background of the humans that most frequently used that portion of the subway. For instance, when they sampled a Hispanic region in Manhattan located near Chinatown, they uncovered a mix of largely Asian and Hispanic human genes.

Now that the NYC subway Pathomap is complete, the researchers aim to continue similar mapping throughout the US – in airports, taxis, public parks and other locations. They will use the findings to track pathogens and to develop the Pathomap as a public health surveillance tool.

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This entry is part of the MICR 354 (Scientific Writing) student-blog series.


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