image: Weill Cornell Medicine is collecting samples in the New York City subway. view more
Credit: Getty/Weill Cornell Medicine
NEW YORK, NY (June 21, 2016) -- Weill Cornell Medicine is kicking off its groundbreaking international study of antimicrobial resistance with an event called Global City Sampling Day. Spanning six continents, 32 countries and 54 cities, this synchronized event brings together more than 400 people, who are expected to collect about 12,000 samples of DNA, RNA and microbes from surfaces in subways, buses, airports and other well-traveled public meeting spaces.
After samples are collected from these transportation hubs, they will be sequenced, analyzed and then used to develop a genetic and epigenetic map detailing the community of microorganisms that inhabit each participating city, known as its microbiome. This data will then help scientists who are part of the Grand Challenges Explorations-winning MetaSub Global Consortium project (for the Metagenomics and Metadesign of Subways and Urban Biomes) better understand antimicrobial resistance in urban centers, and also identify new, naturally occurring drugs made by microbes, known as biosynthetic gene clusters. Investigators will share their findings with local public health officials and city planners, who can use these data to make each city safer and more resilient for the people who live there.
"Global City Sampling Day gives us an opportunity to learn about more than 600 different microbes riding the subway with New Yorkers every day. We are grateful to Weill Cornell Medicine, Dr. Christopher Mason, and hundreds of volunteers who are helping us learn more about our city's health one swab at a time," said Councilman Ben Kallos (5th District), who will help initiate the New York City collection by swabbing a subway station on the Upper East Side with project principal investigator Dr. Mason.
"Every time I look around a room or a subway station, I always wonder -- what's there?" said Dr. Mason, an associate professor of physiology and biophysics and of computational genomics in the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine at Weill Cornell Medicine. "With this work, we'll be able to answer that question, and not just in New York City, but in locations all over the globe. This is truly the fulfillment of a long-sought goal of genetic understanding of the world around us."
That understanding will begin when Global City Sampling Day commences in Auckland, New Zealand at noon New Zealand Standard Time -- 16 hours ahead of Eastern Daylight Time. From there, the sampling day will start at noon local time in each city, moving from Auckland to Melbourne, Australia, and then through Asian cities including Hong Kong and Beijing; Tokyo; and Seoul, South Korea. It will continue to roll out according to time zones around the world -- "kind of like the genetics equivalent of celebrating New Year's as it passes around the Earth," said Dr. Mason, who is also the WorldQuant Foundation Research Scholar at Weill Cornell Medicine. Samples will be collected in every continent but Antarctica, in cities including New Delhi; Moscow; Tehran; Doha; Johannesburg; Rome; Paris; Oslo; Buenos Aires; and Bogota. Many U.S. cities are also participating in this effort, including Boston, Chicago, Los Angeles, San Francisco and Seattle.
Throughout the project, the sample collection protocol stays the same regardless of location. Samples will be collected with nylon swabs, which are then put in a sterile solution to keep each specimen stable during transport. At each collection site, the investigator will log the sample into an app on their mobile device, and include a geotagged location and metadata about where they are; the current temperature and relative humidity; information about the collection surface (whether it's concrete, wood, plastic, etc.); the time of day and other environmental measures. They'll also take a photo at each collection site, and then move onto their next location to continue that process again. Each sample will either be analyzed locally or frozen and sent to a central processing center for sequencing. The extensive data collection and photo documentation will allow lab technicians to "make sure they have the right sample from the right place matching the right picture," Dr. Mason said.
Although the collection process is the same, that's where the similarities end. Because each participating city is unique, each has its own sample collection plan, which can vary depending on population, location, number of participating collectors, and other variables. In Fairbanks, Alaska, for instance, where there is no subway system, collections will be made at bus stops and on bus lines, while in New York City, investigators are looking outside of transportation centers, and also making collections in the 1.8-mile-long Gowanus Canal, a contaminated body of water in Brooklyn named a U.S. Environmental Protection Agency Superfund Site. A number of cities, including Rio de Janeiro and Montevideo, Uruguay are also collecting samples from their beach sands and shallow beach waters, a subset of the project that they're calling MetaBeach, while other cities, like Boston, are making collections from their sewer systems, which they're calling MetaSew.
In addition to making collections from different locations within each of the cities, some local teams will do additional work. Boston will look at how many live cells are on surfaces in addition to dead cells, and about half the participating cities will take live cells back to the lab and try to culture some of the bacteria there.
The team in Rio de Janeiro will not only collect samples on June 21, but will continue to make collections leading up to, during and after the August Olympic Games. They will look at all kinds of life, including human DNA, insect DNA and bacterial DNA to see how these measures change during and after the Olympics. They hypothesize that the changes will be proportional to the number of people that come from different countries, Dr. Mason said.
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