Anthrax and Bubonic Plague Found in the New York Subway

On the morning of February 5, 2015, researchers at Weill Cornell Medical College published a study in the journal Cell Systems that generated headlines across the world within hours. Bubonic plague found in NYC subway, wrote The Daily Beast. Your subway seat mate: Bubonic plague, anthrax and mysterious DNA, reported Yahoo News. NY subway has bubonic plague, declared Newser. The story had everything that a viral news piece requires: a familiar setting, a terrifying historical disease, and the implication that every New York commuter was sharing their morning journey with the bacterium that killed one third of medieval Europe. The truth, as is almost invariably the case with viral science stories, was considerably more interesting and considerably more reassuring than the headlines suggested. This is what they actually found, what it actually means, and why the New York subway is not, in fact, trying to kill you.

1. The PathoMap Study: What Scientists Actually Did

The study that generated the plague headlines was called the PathoMap, and its stated purpose had nothing to do with terrifying commuters. It was, in the words of its senior investigator, Dr. Christopher Mason, an assistant professor in the Department of Physiology and Biophysics at Weill Cornell Medical College, a baseline assessment of the urban microbiome: a systematic, scientific survey of the microbial life present throughout the New York City subway system, designed to establish what is normally present and to create a framework that could be used for long-term disease surveillance, bioterrorism threat detection and large-scale public health management.

The scale of the project was considerable. Over a period from June 2013 to the time of publication, the research team collected 1,457 DNA samples from all 466 open stations on all 24 lines of the New York City subway. The sampling was systematic and comprehensive: swabs were taken from benches, turnstiles, stairway railings, train seats, poles, trash cans, kiosks and MetroCard vending machines. The samples were then subjected to metagenomic DNA sequencing, a technique that allows researchers to identify the genetic material of every organism present in a sample rather than culturing specific organisms in the laboratory, which would only reveal organisms capable of growing in controlled conditions.

The resulting dataset was, by any measure, extraordinary. The team identified the DNA of more than 1,688 types of bacteria, of which the vast majority, the researchers were careful to emphasise, were entirely harmless to healthy humans: the normal, expected inhabitants of any shared urban environment, the commensal bacteria that live on human skin, in the human gut and on the surfaces of every object handled by millions of people every day. These are not threatening organisms. They are the microbial background radiation of human civilisation, and their presence in the subway was neither surprising nor alarming.

In addition to the bacterial findings, the team identified fungi, viruses and fragments of human DNA. They found DNA from two insects, the Mediterranean fruit fly and the mountain pine beetle. They found DNA from food plants: bacteria associated with the production of mozzarella cheese at 151 stations, chickpea DNA on many platforms and benches. They found, at one station, evidence of what they described as a marine ecosystem. And they found that nearly 48 percent of the DNA profiles they identified belonged to organisms so poorly characterised by science that they could not be matched to any known species in the existing databases. The subway, in other words, is a genuinely novel ecological environment.

2. The Anthrax and Plague DNA: What It Means and What It Does Not Mean

Among the 1,688 bacterial types identified in the subway, the team found two findings that generated the alarming headlines. The first was the detection of DNA fragments of Bacillus anthracis, the bacterium responsible for anthrax, in two samples: one from a railing at a subway station and one from a handhold in a subway car. The second was the detection of a plasmid associated with Yersinia pestis, the bacterium responsible for bubonic plague, in three samples, collected from a garbage can, a MetroCard vending machine and a stairway railing at three separate stations.

Before discussing what these findings mean, it is worth being precise about what they represent scientifically. A DNA fragment is not a living organism. A plasmid is a small circular piece of DNA that can exist independently of a bacterium. The presence of DNA associated with a pathogenic organism in an environmental sample does not indicate that the organism is present, alive, infectious or in any way capable of causing disease. It indicates only that at some point, under some circumstances, genetic material derived from or related to that organism ended up on the surface in question. The DNA could come from dead bacteria, from bacterial remnants, from organisms that share genetic sequences with the target pathogen without being pathogenic themselves, or from environmental contamination of any number of kinds.

The PathoMap researchers were clear about this distinction from the beginning. They emphasised that the DNA fragments they detected showed no evidence of being alive in culture experiments: when they attempted to grow bacteria from the positive samples under laboratory conditions, nothing grew. They stated explicitly that there was no evidence that the DNA fragments were linked to any instance of disease. They noted that no case of bubonic plague had been reported in New York City since the study began. And they concluded that the findings were "generally reassuring, indicating no need to avoid the subway system or use protective gloves."

For the plague finding specifically, Dr. Mason offered a plausible explanation for the DNA's presence: rats. New York City's subway system is home to a substantial rat population, and the rodents of the western United States carry Yersinia pestis as an endemic infection. New York rats, which come into contact with the subway through the garbage and food waste that accumulates on the tracks, could plausibly carry traces of plague-related genetic material even if they are not themselves infected with the clinical disease. The DNA, in this scenario, is simply a residue of the complex ecological web that connects the rodent population of the city to the surfaces that millions of humans touch every day.

3. The Full Picture: 1,688 Types of Bacteria and the Real Story of the Subway Microbiome

The anthrax and plague headlines obscured what is, from a scientific perspective, the genuinely remarkable aspect of the PathoMap study: the sheer richness and diversity of the microbial life that inhabits the New York City subway system, and what that diversity reveals about the city above it. The subway, carrying 1.7 billion passengers per year across 600 miles of track through the seventh most heavily used urban transit system in the world, is a uniquely concentrated reflection of the human population of New York and of everything that population brings with it, eats, touches and leaves behind.

The 1,688 bacterial types identified in the PathoMap include the full expected complement of bacteria associated with human skin, the human respiratory tract and the human gut: the organisms that travel with every commuter who holds a pole or sits on a seat or passes through a turnstile, deposited in quantities too small to matter individually but cumulatively detectable in the extraordinary sensitivity of metagenomic DNA sequencing. They also include environmental bacteria from soil, water and air that enter the subway system through every opening and are distributed through the ventilation of the tunnels. And they include, most fascinatingly, the bacteria associated with the food that New Yorkers eat.

The presence of mozzarella-associated bacteria at 151 stations is a reflection of New York's pizza culture, as direct and undeniable a piece of evidence as a discarded crust. The chickpea DNA on platform benches and turnstiles reflects the extraordinary proliferation of hummus, falafel and Middle Eastern food across the city's cuisine in recent decades. The marine ecosystem found at one station, almost certainly the result of flooding events that brought marine organisms up through the drainage system, is a reminder that New York City sits at the edge of one of the most productive marine environments on the east coast, and that the boundary between the city and the sea is more permeable than the concrete and steel suggest.

Of the 1,688 bacterial types, 12 percent showed some association with disease, and 27 percent of the samples contained live antibiotic-resistant bacteria. The antibiotic resistance finding is the one that concerned public health experts most, not because it represents an immediate risk to subway riders but because it is a reflection of the broader crisis of antibiotic resistance that is one of the most serious threats to public health globally: the overuse of antibiotics in medicine and agriculture has driven the evolution of bacterial strains that are no longer susceptible to the drugs we use to treat infections, and the prevalence of these strains in environmental samples from a major urban transit system is a measure of how thoroughly antibiotic-resistant bacteria have integrated themselves into the urban ecosystem.

4. The Scientific Controversy: How the Study Was Corrected

The PathoMap study did not escape scientific scrutiny, and the process by which the initial findings were challenged, corrected and refined is itself an instructive story about how science actually works, as opposed to how science is reported in the popular press. Within months of publication, researchers at the Centers for Disease Control and Prevention and at the New York City Department of Health and Mental Hygiene published a response in which they disputed the finding that Yersinia pestis and Bacillus anthracis had been correctly identified.

The criticism was technical and precise: the CDC researchers argued that the metagenomic sequencing method used in the study was not sufficiently specific to reliably distinguish between Yersinia pestis and other closely related but entirely harmless bacteria in the Yersinia genus. Similarly, Bacillus anthracis shares significant genetic sequences with other Bacillus species that are entirely innocuous environmental organisms. The presence of short DNA fragments that partially match the target organisms is not, the critics argued, sufficient evidence to conclude that those organisms are actually present, and the authors of the PathoMap study had chosen the "more sensational and less plausible interpretation of their data."

The CDC statement was direct: "The NYC subway system is not a source of plague or anthrax disease, and the bacteria that cause these diseases do not occur naturally in this part of North America."

To their considerable credit, the PathoMap authors responded constructively. In an erratum published in July 2015, they acknowledged the limitations of their analysis and issued a correction to the paper. The Summary, Results and Discussion sections were revised to remove and clarify what the erratum described as "misleading and speculative text about pathogenic organisms." The corrected paper maintained the broader scientific value of the PathoMap as a baseline microbiome assessment while scaling back the claims about plague and anthrax to a level that the available evidence could actually support. This is how science is supposed to work: a finding is published, it is scrutinised, it is corrected, and the scientific community moves forward with a more accurate picture of reality.

5. What the Subway Tells Us About the City Above It

One of the most conceptually interesting aspects of the PathoMap study, the aspect that has generated the most sustained scientific interest since its initial publication, is the idea that the subway microbiome is a proxy for the human population of the city above it. This idea, which Dr. Mason and his team articulated explicitly in the original paper, has profound implications for how we think about urban epidemiology and public health surveillance in the twenty-first century.

The subway, carrying 1.7 billion passengers per year and touching every neighbourhood and every demographic in New York City, is a kind of continuous, involuntary sample of the entire population. Every passenger who holds a pole or sits on a seat leaves behind a tiny quantity of genetic material from their own body and from the microbial community that inhabits it. The cumulative effect of this constant deposition, over billions of individual journeys, is a surface that carries a genuinely representative sample of the microbial life of the city as a whole: its diseases, its food culture, its immigrant communities, its ecological connections to the wider world.

The PathoMap team found evidence of this in the distribution patterns of specific bacteria and DNA types across the subway network. Penn Station, they reported, has a bacterial ecology that shifts dramatically by the hour, reflecting the rhythms of commuter traffic and the different populations that pass through at different times of day. Stations in different neighbourhoods carry different microbial signatures that reflect the populations of those neighbourhoods: the food plants, the environmental bacteria, the specific organisms associated with the demographic and culinary character of each area. The subway, in this reading, is not merely a transport system but a continuously updated biological record of the city it serves.

This perspective has important practical applications. If the subway microbiome can be monitored continuously at sufficient resolution, it could provide an early warning system for infectious disease outbreaks that would be detectable in the subway environment before they became visible in the clinical data: before patients started presenting at hospitals, before the health authorities became aware of an emerging situation. It could detect the spread of antibiotic resistance in real time, tracking which resistant strains are present where and in what concentrations. And it could, as the PathoMap team originally argued, provide a baseline against which a bioterrorism event involving the deliberate release of a pathogenic organism in the subway could be rapidly detected and identified.

The PathoMap demonstrates that it is possible and useful to develop a pathogen map of a city, with the heavily traveled subway a proxy for New York's population. The presence of these microbes and the lack of reported medical cases is truly a testament to our body's immune system, and our innate ability to continuously adapt to our environment.

Dr. Christopher Mason, Weill Cornell Medical College, February 2015

6. Should You Worry? The Honest Answer

The honest answer to the question of whether New York subway riders should be concerned about the microbial life they encounter on their daily commute is: not especially, and not for the reasons the headlines suggested. The bacteria, viruses and fungi that inhabit the surfaces of the subway are, in their overwhelming majority, the normal microbial companions of human life in an urban environment. Your immune system has been dealing with organisms of this kind every day of your life, and it does so with a competence and a thoroughness that makes the subway's microbial diversity a manageable reality rather than a genuine threat.

The antibiotic resistance finding is a more legitimate concern, not because it poses an acute risk to any individual subway rider but because it is a reflection of a systemic global problem that affects public health at a level well beyond the New York City transit system. The appropriate response to antibiotic resistance is not to avoid the subway but to use antibiotics responsibly, to support research into new treatments and to maintain the public health systems that monitor and manage resistant infections when they occur.

The plague and anthrax findings, as the subsequent scientific debate made clear, were almost certainly artefacts of the imprecision of the metagenomic sequencing method rather than genuine detections of those organisms. Even if the original identifications had been accurate, the researchers themselves confirmed that no live bacteria were present and that no disease cases had been linked to the findings. The subway is not a source of plague or anthrax. It never was. And the study that generated those alarming headlines was, at its core, a genuinely valuable scientific contribution to our understanding of the microbial world that we inhabit, invisible, beneath the streets of one of the world's great cities.

Getting to New York: Arriving and Using the Subway

New York City is served by three major airports. John F. Kennedy International Airport (JFK), approximately 24 kilometres southeast of Midtown Manhattan, is the largest and most international, with connections to destinations across the globe. The most comfortable way to reach your hotel is a private airport transfer from JFK to Manhattan, which takes approximately 45 to 60 minutes depending on traffic and delivers you directly to your hotel without any luggage management on public transport.

Newark Liberty International Airport (EWR), in New Jersey approximately 26 kilometres from Midtown, offers an excellent alternative with a slightly shorter drive to many Manhattan destinations. LaGuardia Airport (LGA), approximately 13 kilometres from Midtown, is the smallest of the three and handles predominantly domestic and short-haul international traffic. Once in the city, the subway is by far the most efficient way to move around: despite its microbial inhabitants and its much-discussed state of repair, it remains one of the most effective urban transit systems in the world and the fastest way to travel between most points in Manhattan and the outer boroughs at any hour of the day or night. The PathoMap study, whatever its scientific controversies, is at least unambiguous on one point: the subway is not going to give you plague.