Students swab rail stations to identify, map microbes across Miami

Neha Godbole, an M.D./M.P.H. student at the Miller School of Medicine, swabs the escalator at the Brickell Metrorail station as part of Global City Sampling Day 2021. Photo: Evan Garcia/University of Miami
By Robert C. Jones Jr.

Neha Godbole, an M.D./M.P.H. student at the Miller School of Medicine, swabs the escalator at the Brickell Metrorail station as part of Global City Sampling Day 2021. Photo: Evan Garcia/University of Miami

Students swab rail stations to identify, map microbes across Miami

By Robert C. Jones Jr.
As part of Global City Sampling Day, teams of University of Miami students fanned out across Miami-Dade County on Monday taking microbial samples on surfaces at each of the 23 Metrorail stops. Their efforts will help create a map of the community of microorganisms that inhabit the city.

Metrorail’s Civic Center station bustled with rush-hour activity. Then, the two University of Miami students showed up with packets of swabs and collection vials.

One of them, Umer Bakali, quickly got to work, dipping a swab into a reagent, then rubbing it vigorously back and forth on the buttons of a ticket kiosk. His teammate, Chitvan Killawala, stood nearby, recording the process on a spreadsheet while holding one of the vials into which the swab would be placed for safekeeping and preservation.

The two then swabbed an escalator handrail and an elevator button before hopping aboard a southbound train for the Culmer and Overtown stations, where they would repeat the entire routine, drawing stares from curious onlookers.

Bakali and Killawala were two of 15 University of Miami students and employees who participated in Global City Sampling Day (gCSD) on June 21.

From Boston to Buenos Aires, Cairo to Copenhagen, Miami to Marseille, and Seattle to Singapore, teams of researchers and citizen scientists fanned out across 54 cities on five continents to collect samples of DNA, RNA, and microbes from surfaces at airports, subways, bus terminals, and other mass transit stations. 

The samples—all 6,000 of them—will be packaged and shipped to Weill Cornell Medicine in New York City. There, researchers who lead the international consortium MetaSUB (short for Metagenomics and Metadesign of Subways and Urban Biomes) will spend several months analyzing them using a technique called shotgun sequencing—which will detect microbes, including bacteria and viruses, that use DNA or RNA as their genetic material.

The data will augment an ongoing microbial census of the community of microorganisms that inhabit each city. That census, which MetaSUB has been compiling since 2015, includes new molecules and enzymes that could potentially be used in diagnostic, industrial, or therapeutic applications, according to Christopher Mason, a professor of physiology and biophysics at Weill Cornell Medicine and the co-founder of MetaSUB.

“For example, the more than 800,000 CRISPR arrays we recently found can be used as new tools to remove disease-causing mutations in patients,” said Mason, referring to regions in the bacterial genome that can help defend against invading viruses.

And in the age of COVID-19, fighting viruses is something that hit close to home for many of the University of Miami students who collected samples at each of the 23 Metrorail stations during gCSD.

“The elephant in the room is definitely the COVID-19 pandemic,” said Bakali, a Ph.D. student in biochemistry at the Miller School of Medicine, who commutes on Metrorail each day. “We know, of course, that COVID-19 is a virus. But that doesn’t make it any less important that we take into account what people interact with every single day as they’re going through their methods of transit.”

For Killawala, gCSD allowed him to visualize what he wants to become in the future, he said. The graduate student in biomedical engineering, whose 74-year-old grandfather in India died from complications of the coronavirus, is developing electronic sensors that will analyze molecules in a patient’s breath to detect diseases. 

“We’ll be able to ‘smell’ physiological problems we can’t see, much like what we’re doing with this sampling of microbes that are naked to the human eye,” Killawala explained.

Photos: Evan Garcia and Robert C. Jones Jr./University of Miami

In a new study, MetaSUB recently reported that more than 12,000 bacteria and viruses detected during sampling at global transit systems and hospitals from 2015 to 2017 have never been identified. But while the source of many of those microbes remains unknown, people shouldn’t be afraid of them, according to MetaSUB. They are just part of the ecosystem in which humans live.

“Many risks are too small to be noticed, or they are contained quickly. But, indeed, efforts like ours help to build a genetic catalog of emerging microbes, new biology, and possible threats, while improving our understanding of the biology all around us,” Mason said.

He is collaborating with University of Miami environmental engineer Helena Solo-Gabriele on a National Institutes of Health-funded study to determine whether analyzing wastewater for the presence of SARS-CoV-2, the virus that causes COVID-19, can help predict future outbreaks as well as discover emerging variants.

“A decade ago, we tried to characterize microbes in marine water and the sand, but at the time the technology was not as advanced,” Solo-Gabriele said. “Ten years later, the technology is just amazing. We can now ‘see’ viruses and bacteria in the environment.”

Bhavarth Shukla, assistant professor of clinical medicine and director of Infection Control, called gCSD an effective sampling strategy. “From an epidemiological perspective, it certainly could be a tool used to predict what’s happening in the environment by virtue of what’s going on in the human host that’s walking around and contributing to their surroundings,” said Shukla, who is looking at wastewater in the hospital environment to see if it correlates with COVID-19 outbreaks in the clinical setting.

For Alexis Carrasquillo, an incoming first-year student who plans to study marine biology and ecology on a premed track, Global City Sampling Day was an opportunity to make an impact on her community. But the day was “much bigger than just the city of Miami in that it’s creating new scientific discoveries that could be used for my generation and future generations,” said Carrasquillo, who collected samples at the Martin Luther King Jr. Metrorail station in Liberty City.

“Being part of this project,” she said, “made me feel small, because I know that people around the world are also gathering data from their cities that may contribute to major discoveries.”

Students from all three University campuses participated in the sampling day, swabbing the exterior surfaces of everything from the benches and ATM machines to the ticket kiosks and handrails at all Metrorail stations. 

“In the past year, our U-TRACE team has been working with human surveillance data from the community and correlating it with environmental sampling to monitor changes in COVID-19 infection rates, helping to inform decisions on public health strategy for the University community,” said Natasha Schaefer Solle, research assistant professor of medicine and public health sciences, who organized the event in Miami. “Global City Sampling Day was an opportunity for our students to see public health in action and to learn how team science can translate into greater scientific impact and innovation,” she added.