In 1988, 61 people from five different states contracted hepatitis. Eventually, the source of their illness was traced to a single lot of contaminated oysters grown in the waters off Panama City, Fla.

Some of the shellfish had been harvested in an area called North Bay. Nobody had known the bay was tainted. While the water had not been tested for hepatitis virus specifically, public health officials considered the coastline safe because regular counts for bacteria turned up normal. Unfortunately, for the 61 who became sick, this was flawed reasoning.When sewage floods into ocean waters, or contaminants seep into local drinking water, government agencies traditionally rely on a standard "bacterial indicator" test to check for hazardous levels of contamination. Rather than measuring the levels of every single bacterium and virus present, this test checks only for the designated indicator organism, an organism which, it is assumed, reflects the overall makeup of the water. The theory has always been that if the specific indicator is high, then bacterial and viral levels overall are high and the waters are unsafe. The reverse, of course is also assumed. The case of the Florida shellfish, however, proved how unreliable this assumption can be.

Now, frustrated with the limitations of present testing methods, researchers have turned to DNA technology to develop more accurate approaches. These new tests can identify all the microorganisms in a given sample while providing answers quickly.

"You need the results immediately, so you can make the information public and close the beaches, not two or three days after, when the danger has come and gone," comments Erik Avaniss-Aghajani, a researcher at the University of California, Los Angeles. The culturing methods used with traditional tests take anywhere from 24 hours to several weeks. With DNA-based techniques, scientists can have answers within two to eight hours.

Avaniss-Aghajani is testing the reliability of this new technology in waters off the coast of Los Angeles. In work funded by California Sea Grant, he is assembling a complete profile of all bacteria living in this particular region. The identification process relies on a technique called polymerase chain reaction (PCR), whose developer won a Nobel prize last fall.

With PCR, Avaniss-Aghajani is able to take tiny amounts of DNA (the genetic material contained within every cell) from his bacterial samples and reproduce that material millions of times over. The final DNA soup contains large amounts of genetic material from all the bacterial species found in a given water sample. Using a special apparatus, he is able to sort out this DNA mixture and determine the types and quantities of each bacterial species.

Aside from providing valuable safety information following a sewage spill, DNA technology also allows scientists to develop a complete bacterial map of any coastal environment.

"No one has had this capability ever before to go out and use this technology to find out what's out there," comments Carol Palmer, a molecular microbiologist with the County Sanitation Districts of Orange County, Calif.

With today's monitoring techniques, scientists are confined by their existing knowledge. They can only grow and identify microbes they already know about rather than objectively scanning the lot for anything new. That's because each microorganism requires its own specific conditions for growth.

"Culturing methods basically have a bias," Avaniss-Aghajani says. "If you don't have the correct ingredients in your broth, some of the bacteria don't grow." Those unidentified microbes simply get passed by. With gene-based techniques, public health officials will be able to detect the whole spectrum of living entities in the water.

This includes both bacteria and viruses. Avaniss-Aghajani's team has been looking at bacteria in particular. Viruses, however, represent an equal hazard and often go ignored. If they are suspected, some viruses can be cultured, just like bacteria. But some, such as hepatitis A virus, which was spread through the Florida seafood, cannot be grown in culture. Until the advent of DNA testing, no reliable test for hepatitis A virus existed.

Now, molecular microbiologist Palmer and her colleagues are already using genetic techniques to measure viruses in three different coastal waters: Hawaii, Southern California and North Carolina. With different climates and environmental forces in each area, the makeup of the three marine regions varies considerably.

Like Avaniss-Aghajani, Palmer and her colleagues are developing a map to determine normal microorganism levels in each location.

"What we're doing," Palmer says, "is establishing a baseline, telling people what is out there. If normally there are a hundred organisms per liter of water and we find a million at some point, we know something is off balance, something is wrong."

Scientists don't want to scare the public needlessly by reporting the detection of a single hepatitis virus. Rather, they hope to put measurements in perspective, to give people an idea of what is normal and what is high.

Avaniss-Aghajani and Palmer focus their attention on marine waters. However, contamination of drinking water, hot tubs, cooling towers for air conditioners and any other waters that may spread disease can also threaten public welfare. For example, the bacteria Legionella, which causes Legionnaire's disease, can travel through any type of water source. Now, using one of the first commercially available genetic tests, scientists have detected Legionella in places where culture has failed to detect it. Thus far, the test has been used on a limited basis. Ultimately, however, Ronald Atlas, its developer, plans to use the test to track disease outbreaks back to their source.

While the Legionella test has entered the commercial arena, the vast majority of gene-based technology remains in the research phase. Before regulatory agencies begin sanctioning any changes, many hurdles must be overcome. While gene technology can detect DNA, it can't determine if the microbes are actually living. Large quantities of DNA from a particular bacteria may be present, but that doesn't mean the microbe is alive and thriving.

"In their current state of development, the newer methods are excellent for screening," says Christine Paszko-Kolva, senior microbiologist with the Metropolitan Water District of Southern California. But they aren't yet sophisticated enough to replace culture entirely. With a large sample, it's impossible to culture every possible microorganism. Using PCR, one can hone in on the most prevalent bacteria present in a sample and then rely on traditional methods to grow those particular microbes.

Other roadblocks also hamper the path to commercialization. Cost always remains a significant issue. "Gene-type tests are typically more expensive than conventional plate counts," says Atlas, professor of biology at the University of Louisville. "It becomes a matter of either bringing the costs down or ascertaining what the market will bear."

As with any new technology, the initial capital investments are often costly. David Chapman, who leads Avaniss-Aghajani's team at UCLA, feels confident that costs will eventually come down. "Computers once upon a time were hideously expensive," he remarks. And now they're practically a household item.

Looking at the big picture, the price may actually be small. Scientists estimated the cost of medical expenses and lost productivity during the hepatitis outbreak of 1988 at $200,000. A gene-based test can certainly compete with that expense. If quicker, more accurate information means timely warnings for the public in the event of a sewage spill or disease outbreak, the cost of gene technology may begin to look like the ounce of prevention that outweighs the pound of cure.