What Our Sewage Can Teach Us By Joshua A. Krisch November 10, 2014 Via NYtimes Beneath Visionaire, a breathtaking high-rise overlooking the southern tip of Manhattan, sewage gushes through a network of pipes and then drools into a stone tank, which is draped in quivering cockroaches. They scatter as Dennis Keefe, a contractor for Natural Systems Utilities, dips a metal ladle into the putrid stew and gently stirs. Jane M. Carlton, a geneticist and director of New York University’s Center for Genomics and Systems Biology, hovers near as her graduate students snap on latex gloves and draw samples from Mr. Keefe’s grimy ladle. Each vial of sewage that they collect is teeming with microscopic life and saturated with dangerous viruses and essential bacteria — exactly what Dr. Carlton is looking for. By analyzing wastewater samples from each of the five boroughs, Dr. Carlton hopes to uncover trends in infectious disease — to detect flu viruses before the next outbreak, for instance, and keep tabs on antibiotic-resistant bacteria. But her ultimate goal is far more ambitious: Dr. Carlton wants to sequence the microbiome of New York City. More than 1.3 billion gallons of wastewater courses through 6,000 miles of the New York City sewage system every day. The city combines residential and commercial sewage with animal waste and groundwater runoff, so even a single sample of sludge can speak volumes about the local environment. “We want to take an environmental sample, like sewage, and extract all of the DNA from all of the microbes in that sample,” Dr. Carlton said. If her team could sample sewage from every neighborhood in the metro area, Dr. Carlton reasoned, the resulting genetic map would highlight the city’s microbial diversity across different districts. Once public health officials knew what normal bacteria and viruses to expect in each sector of the city, she hopes, they will be better able to identify dangerous outliers — a new strain of the flu, for instance, or an outbreak of food-borne illness. “It’s a preventative public health question,” Dr. Carlton said. “We need to know the baseline to know how the baseline changes over time.” Dr. Carlton started off by tackling smaller pilot experiments. Last April, her team presented the results of the Dirty Money Project, which involved sequencing all of the DNA found on a wad of dollar bills. Dr. Carlton had assumed whatever bacteria she found would be dead. Instead, she found that thousands of bacteria — most of them harmless — thrive on paper money. In a separate study, the Microbikeome Project, Dr. Carlton and her team examined the microbial life on public bicycles in Manhattan and London in an effort to see how bacteria migrate about a city. Both efforts, Dr. Carlton said, helped her team develop laboratory standards and refine sequencing techniques. But she and other scientists believe the wealth of information hidden in sewage is far greater. Eric Alm, a professor at the Massachusetts Institute of Technology, envisions a future in which policy makers and health care providers alike monitor sewage for real-time information about the state of public health, a sort of real-time epidemiology. Dr. Alm recently received a grant to develop a smart sewage device that will analyze public refuse and relay broad public health data back to experts and officials. The so-called Underworld platform will scour sewage for the biomarkers of health and disease, and even detect trace chemicals used in bomb manufacturing. “We are interested in genomics, but we’re also looking for different chemicals that might not be within the DNA,” he said. If city officials were to start a public health campaign to reduce intake of sugary drinks, the device might track the presence of sugar in sewage to help policy makers determine whether the campaign was having an effect. “This whole field has enormous potential,” Dr. Alm said. “It’s hard to imagine that in 20 years, every city won’t be monitoring sewage as an information platform.” While Dr. Carlton awaited approval for access to public sewage, which she received in mid-September, she found creative ways to get her hands on New York City sewage. Green apartment complexes occasionally maintain their own sewage systems, and the Visionaire, along with its sister building, the Solaire, agreed to accommodate the N.Y.U. researchers. With wastewater obtained from private apartment complexes, Dr. Carlton’s students are already beginning to conduct genomics research. Julia Maritz, a doctoral student in Dr. Carlton’s lab, is focused on developing the best methods for extracting DNA from sewage samples. In the coming months, she will be studying how diseases move among humans and animals by tracking small changes in the genetic makeup of sewage-borne parasites. Susan Joseph, a postdoctoral researcher, will be keeping tabs on antibiotic-resistant bacteria such as MRSA and Clostridium difficile in the sewage system. As studies continue to show that most of the bacteria in our bodies are healthy and even necessary, Dr. Carlton hopes that her work will not only improve public health, but also educate the public about the “good” bacteria that surround us. “People need to understand that knowing about the microbes in our environment is a positive thing,” she said. “People shouldn’t be afraid to find out what’s out there.”
Posted on: Tue, 11 Nov 2014 13:42:01 +0000
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