Tracing germs through the aisles

Sabrina Tavernise / New York Times News Service /


Twice a month for a year, Lance Price, a microbiologist at George Washington University, sent his researchers out to buy every brand of chicken, turkey and pork on sale in each of the major grocery stores in Flagstaff, Ariz. As scientists pushed carts heaped with meat through the aisles, curious shoppers sometimes asked if they were on the Atkins diet.

In fact, Price and his team are trying to answer worrisome questions about the spread of antibiotic-resistant germs to people from animals raised on industrial farms. Specifically, they are trying to figure out how many people in one American city are getting urinary infections from meat from the grocery store.

Price describes himself as something of a hoarder. His own freezer is packed with a hodgepodge of samples swabbed from people’s sinuses and inner ears, and even water from a hookah pipe. But the thousands of containers of broth from the meat collected in Flagstaff, where his nonprofit research institute is based, are all neatly packed into freezers there, marked with bar codes to identify them.

He is now using the power of genetic sequencing in an ambitious attempt to precisely match germs in the meat with those in women with urinary infections. One recent day, he was down on his hands and knees in his university office in Washington, studying a family tree of germs from some of the meat samples, a printout of more than 25 pages that unfurled like a roll of paper towels. Its lines and numbers offered early clues to Price’s central question: How many women in Flagstaff get urinary infections from grocery store meat? He expects preliminary answers this fall.

Researchers have been warning for years that antibiotics — miracle drugs that changed the course of human health in the 20th century — are losing their power. Some warn that if the trend isn’t halted, there could be a return to the time before antibiotics when people died from ordinary infections and children did not survive strep throat. Currently, drug-resistant bacteria cause about 100,000 deaths a year, but mostly among patients with weakened immune systems, children and the elderly.

There is broad consensus that overuse of antibiotics has caused growing resistance to the medicines. Many scientists say evidence is mounting that heavy use of antibiotics to promote faster growth in farm animals is a major culprit, creating a reservoir of drug-resistant bugs that are finding their way into communities. More than 70 percent of all the antibiotics used in the U.S. are given to animals.

Agribusiness groups disagree and say the main problem is overuse of antibiotic treatments for people. Bugs rarely migrate from animals to people, and even when they do, the risk they pose to human health is negligible, the industry contends.

Scientists say genetic sequencing will bring greater certainty to the debate. They will be able to trace germs in people to their origins, be it from a farm animal or other patients in a hospital. Rep. Louise Slaughter, D-N.Y., who has pushed for legislation to control antibiotic use on farms, said such evidence would be the “smoking gun” that would settle the issue.

Price is seeking to quantify how extensively drug-resistant bugs in animals are infecting people. He is trying to do that by analyzing the full genetic makeup of germs collected from both grocery store meat and people in Flagstaff last year. The plummeting cost of genomic sequencing has made his research possible.

He is comparing the genetic sequences of E. coli germs resistant to multiple antibiotics found in the meat samples to the ones that have caused urinary tract infections in people (mostly women).

Urinary infections were chosen because they are so common. American women get more than 8 million of them a year. In rare cases the infections enter the bloodstream and are fatal.

Resistant bacteria in meat are believed to cause only a fraction of such infections, but even that would account for infections in several hundred thousand people annually. The E. coli germ that Price has chosen can be deadly and is made even more dangerous by its tendency to resist antibiotics.

The infection happens when meat containing the germ is eaten, grows in the gut, and then is introduced into the urethra. Price said the germ could cause infection in other ways, such as through a cut while slicing raw meat. The bugs are promiscuous, so once they get into people they can mutate and travel more easily among people. A new strain of the antibiotic-resistant bug MRSA, for example, was first detected in people in the Netherlands in 2003, and now represents 40 percent of the MRSA infections in humans in that country, according to Jan Kluytmans, a Dutch researcher. That same strain was common in pigs on farms before it was found in people, scientists say.

Sounding the alarm

Price, 44, began his career testing anthrax for resistance to the Cipro antibiotic for biodefense research in the 1990s. His interest in public health led him to antibiotic resistance in the early 2000s. It seemed like a less theoretical threat.

First-line antibiotics were no longer curing basic infections, and doctors were concerned. “I thought, ‘Wow this is so obviously crazy, I have to do something about this,’” he said. He has done his research on antibiotics at a nonprofit founded in 2002, the Translational Genomics Research Institute, in Phoenix. His lab in Flagstaff, an affiliate, is financed mostly by federal sources, including the National Institutes of Health and the Defense Department.

Price, trained in epidemiology and microbiology, has been sounding the alarm about antibiotic resistance for a number of years. He recently told a congressional committee that evidence of the ill effects of antibiotics in farming was overwhelming.

He thinks the Food and Drug Administration’s efforts to limit antibiotic use on farms have been weak. In 1977, the FDA said it would begin to ban some agricultural uses of antibiotics. But the House and Senate appropriations committees — dominated by agricultural interests — passed resolutions against the ban, and the agency retreated. More recently, the agency has limited the use of two important classes of antibiotics in animals. But advocates say it needs to go further and ban use of all antibiotics for growth promotion. Sweden and Denmark have already done so.

Slaughter said aggressive lobbying by agribusiness interests has played a major role in blocking passage of legislation. According to her staff, of the 225 lobbying disclosure reports filed during the last Congress on a bill she wrote on antibiotic use, nearly 9 out of 10 were filed by organizations opposed to the legislation.

But the economics of food presents perhaps the biggest obstacle. On large industrial farms, animals are raised in close contact with one another and with big concentrations of bacteria-laden feces and urine. Antibiotics keep infections at bay but also create drug resistance. Those same farms raise large volumes of cheap meat that Americans have become accustomed to.

Governments have begun to acknowledge the danger. The U.S. recently promised $40 million to a major drug company, GlaxoSmithKline, to help it develop medications to combat antibiotic resistance. But Price says that new drugs are only a partial solution.

“A lot of people say, ‘let’s innovate our way out of this,’” he said. “But if we don’t get a handle on the way we abuse antibiotics, we are just delaying the inevitable.”