NYC subway cultures drug resistant bacteria, DNA from Anthrax, Plague

Click to enlargeHeatmap of the Pseudomonas genus

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, says the study’s senior investigator, Dr. Christopher E. Mason…

The PathoMap findings are generally reassuring, indicating no need to avoid the subway system or use protective gloves, Dr. Mason says. 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. Culture experiments revealed that all subway sites tested possess live bacteria.

Strikingly, about half of the sequences of DNA they collected could not be identified — they did not match any organism known to the National Center for Biotechnology Information or the Centers for Disease Control and Prevention. These represent organisms that New Yorkers touch every day, but were uncharacterized and undiscovered until this study. The findings underscore the vast potential for scientific exploration that is still largely untapped and yet right under scientists’ fingertips.

WTF? They’re under everyone’s fingertips.

“Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract,” Dr. Mason says. “These bacteria may even be helpful, since they can out-compete any dangerous bacteria.”

But the researchers also say that 12 percent of the bacteria species they sampled showed some association with disease. For example, 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.

RTFA to see why the researcher say we shouldn’t worry. Certainly, the diversity of microorganisms is a positive activator for our immune systems.

Interesting how they went about the research – and what this presents as a baseline for future evaluations. And an added plus is the unique – and still closed – station shuttered since Superstorm Sandy. Marine species still alive and stable in what should be an abnormal environment for them.

Thanks, Helen

7 thoughts on “NYC subway cultures drug resistant bacteria, DNA from Anthrax, Plague

  1. Doorman says:

    “You want proof evolution is for real, don’t waste your time with fossils; just check out the New York City rat. They started out as immigrants, stowaways in some ship’s cargo hold. Only the survivors got to breed, and they’ve been improving with every new
    litter. Smarter, faster, stronger. Getting ready to rule. Manhattan wouldn’t be the first island they took over.”
    Andrew Vachss, “Another Life” (2008)

  2. Straphanger says:

    News item, Monday, February 10, 2014, NYC: “As subway homeless population grows, new $6M outreach effort by city and MTA to launch in July”. Article reports “There were 968 men and women identified as homeless in the subway in 2009, and 1,841 last year, a 90% increase.” See also “The Mole People: Life in the Tunnels Beneath New York City” (1993) and “Off The Beaten Track : Subway shanytown in NYC” (!/page29 ), which describes
    Marc Singer’s 2000 documentary, “Dark Days”, the subject of which is a group of individuals who lived in the Freedom Tunnel, a 50 block-long stretch of defunct train tunnels beneath Riverside Park before their eviction in 1996. Video clip @ – followed by the entire hour long doc @

  3. Origin of Species says:

    “Junk Food Is Making NYC Ants More Like Humans”
    For humans and ants alike, a diet heavy in grasses such as corn and sugarcane will leave a chemical signature in the body in the form of carbon-13, a carbon isotope. So researchers looked at the levels of carbon-13 present in 21 ant species collected from dozens of sites on New York City’s sidewalks, traffic islands and parks. They found that the species that lived in areas with a greater human presence, like the medians of the city’s broad avenues, generally had higher levels of carbon-13 than the species that stuck to parks. The pavement ant, or Tetramorium Sp. E. — the most common on sidewalks and medians — had the highest levels of carbon-13 of any species, the study determined. According to Clint Penick, a postdoctoral researcher at North Carolina State University, “In the case of pavement ants, the degree to which they’re shifting their diets to human foods is actually changing the chemical makeup of their bodies to look more and more like humans.” Not all ant species living close to people were so keen on eating garbage. One species, Lasius cf. emarginatus, which has only been found in New York in the past five years, was abundant in traffic medians but didn’t seem to have a taste for human foods, the researchers found. “Anecdotally, they’re also one of the only ants you find on the sidewalk, but whenever we found them on the sidewalk, they were always going up the trees and always foraging up there, and not on the ground,” Penick said.

  4. Doc says:

    At any given moment, your body hosts a number of different potential pathogens that could infect you, like viruses and bacteria. Your immune system acts like the bouncer at a bar that keeps the riffraff out. Anything that starts replicating too much in a way that could make us sick gets the boot.
    But how do these cells know when to react, and to what degree?
    Our DNA codes for everything, including the chemicals we need to survive, how much of these substances to produce, and when. University of Utah geneticists have found that some of the code that govern our immune responses come from the genomes of old viral infections from thousands of years ago. Their work was published today (March 3) in Science.

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