• Standard water-quality tests for the beach take too long.
• Rachel Noble created a better one using qPCR.
• Coastal communities are using it to keep beachgoers from getting sick.
“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 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 back 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 twenty-four 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 fifty years. But it’s too slow, Noble says. Too many people could swim in that contaminated water while the lab waits for results. She’s come up with a better method. It’s quicker and just as reliable. And now she’s licensed it to a biotech company, which is working with municipalities to protect beachgoers.
Our 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 fast,” she says. “The landscape can be scoured.” All kinds of contaminants can enter our 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. In contaminated food, E. coli O157:H7 can be deadly. But Noble says that particular E. coli strain isn’t typically found in contaminated waterways. 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 that do make us sick—typically 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 rethought her project. Instead of testing for viruses, she’d test for E. Coli in freshwater and Enterococcus in seawater. But she wouldn’t use the same slow methods. She’d measure bacterial DNA using quantitative polymerase chain reactions. More commonly known as qPCR, this method allows scientists to detect specific kinds of DNA in a given sample and then determine how much of that DNA is present.
To test beach water samples for E. Coli and Enterococcus DNA, Noble and research technician Denene Blackwood had to figure out which enzymes, bits of DNA, and other chemicals they needed to add to the qPCR in order to measure how much bacteria was present in a water sample.
She honed the process, and last year her lab received a patent and licensed it to the biotechnology firm BioGX. Scientists there use Noble’s specifications to guide their production of freeze-dryable reagents for use in qPCR machines anywhere. Users just need to add a sterile water sample to reconstitute the freeze-dried reagents, add a concentrated amount of beach water, put it in the qPCR machine, and press “run.”
According to independent studies, including several conducted by the EPA, water tests based on Noble’s qPCR method have proved to be just as good as the conventional way of measuring bacterial levels and correlating those levels to the prevalence of human illnesses. But Noble’s new method takes less than four hours from start to finish.
The City of Los Angeles, Hampton Roads Sanitation District in Virginia, and the North Carolina Recreational Water Quality Monitoring Section are among the municipalities currently comparing Noble’s procedures to the conventional methods. Orange County, California, has used Noble’s Enterococcus test and posted results at beaches. And this spring, the City of Racine, Wisconsin, became the first community to use Noble’s E. Coli test to make management decisions about water quality at freshwater beaches. Every morning at 7:00, Racine lab technicians collect water samples from Lake Michigan, use Noble’s rapid method, and then public health officials post the results on a beach sign by 10:00 a.m.
Right now, the folks in Racine and elsewhere still have to conduct the test at their labs because that’s where the qPCR machines are. Noble hopes to change that to make the entire procedure even quicker.
“We’re hoping to make it completely portable,” she says. With BioGX’s help she’s confident the entire testing kit will one day soon fit easily inside the trunk of a car.