Dr. Rachel Noble of the UNC-Chapel Hill Institute of Marine Sciences takes water samples at a beach near Morehead City.
Noble examines water samples in her lab taken from a beach near Morehead City.
In a lab, testers use a QPCR machine called a thermocycler to run samples through a cycle of temperature changes in which the DNA is copied over and over again. One chemical in the test includes a probe that fluoresces when it interacts with DNA. After each cycle, the machine reads the sample’s fluorescence level to determine the DNA level. All data collected by the machine is output to a computer program that analyzes actual bacteria concentrations.
Off the North Carolina coast, a UNC researcher pulls in a sterile bottle containing a water sample before returning to the lab.
Andy Haines, who works for the N.C. Department of Environment and Natural Resources, mixes the extracted DNA with all of the various reagents necessary to carry out the test.
After placing a tray containing a sample of DNA from collected bacteria into the QPCR machine, Haines set up the computer program to run the analysis.
The rapid test kits are used to test water from two beach areas in Racine, Wisc. Here, a lab worker places a tube containing a water sample in the thermocyler. (Photo by Tamara Anan’eva, US EPA ORISE/City of Racine)
Noble’s rapid water-quality tests will enable beach-goers to know much sooner when it’s not safe to swim.
“When a beach is closed, what we’re really saying is that based on yesterday’s water sample, we’re closing the beach today,” says UNC-Chapel Hill marine microbiologist Rachel Noble. “It’s archaic. You’re just telling people that yesterday they swam in contaminated water.”
That’s because the standard water-quality test used at beaches around the country takes time. Lab technicians collect a water sample, carry it to a lab, put it through a filter, place the filter on a Petri dish to grow the bacteria, and incubate the sample at a specific temperature for 18-24 hours. If too many bacteria of a certain variety show themselves and can be counted, then that means the water is contaminated and the beach should be closed for swimming.
It’s a reliable method that researchers and municipalities have been using for many decades. But it’s too slow, Noble says. Too many people could swim in that contaminated water while the lab waits for results. But in 2012, Noble developed a better method that’s quicker and just as reliable. Noble licensed it to biotech company BioGX, which is working with municipalities to protect beachgoers.
Recent changes may speed up the use of rapid water-quality test kits on America’s beaches.
In a National Public Radio interview this month, Noble said that new guidance release by the Environmental Proctection Agency (EPA) allows for use of new DNA-based testing methods developed in her laboratory.
“We’ve been working on these rapid methods for a long time. Now we can get results in about three hours. There are states across the country, including California and Virginia, and a range of other states, including some inland locations in Wisconsin, Ohio and Illinois, that have been using these rapid methods to allow us to put signs up now within a few hours, rather than waiting a day past the time whenever the person was in the water.
In Racine, Wisc., the DNA-based test produces results by 10 a.m. from water samples collected between 7 a.m. and 8 a.m., which “allows for same-day recreational water management decisions,” said Julie Kinzelman, director of the City of Racine Health Department Laboratory. “Those decisions protect public health and safety. Beach managers need quick and reliable methods for determining water quality conditions. The use of rapid laboratory methods or predictive models is one means of doing that.”
Lakes, rivers, and coastal waters can become contaminated in several different ways, but Noble says the two biggest culprits are storm-water runoff and sewage overflows or spills. “In North Carolina, we have storms that come in fast and drop a lot of rain,” she says. “The landscape can be scoured.” All kinds of contaminants can enter waterways, especially fecal matter from livestock, wild animals, faulty septic systems, and leaky sewage pipes.
In that fecal matter are bacteria such as E. coli and Enterococcus, and also microbes, called pathogens, that can make people sick. The E. coli and Enterococcus found in sullied water don’t make us sick. Rather, if they’re in high numbers in water, then there’s a greater likelihood that the viruses and other bacteria that do make us sick — such as noroviruses, adenoviruses, enteroviruses and rotaviruses—could be present, too.
Early in her career at UNC’s Institute of Marine Sciences, Noble wanted to design a rapid method that would test for those viruses. Her research, though, proved difficult. “Finding human viruses in beach water is like finding a needle in a haystack,” Noble says. They cause illnesses, but even in contaminated water they’re not found in high concentrations. That makes it hard to directly measure virus levels at all, let alone measure them quickly.
Noble says that the benefits of swimming and enjoying yourself somewhat outweigh the risk, especially if the water quality is good. But until the rapid DNA-testing methods are more widely used, Noble, an avid swimmer, has some suggestions for decreasing exposure to any pathogens that might be lurking in the water.
* Avoid ingesting huge amounts of water through your nose or mouth.
* Do not play close to flowing storm drain pipes and in areas where there are pools of water coming from the land.
* Watch for signs placed near storm drains and follow their directives.
Noble shares joint appointments with the UNC Department of Marine Sciences, the UNC Institute for the Environment and the Department of Environmental Sciences and Engineering in the UNC Gillings School of Global Public Health.
Published July 26, 2013.