One beautiful spring day last year, Chuck Hofacre was building a barn on his Watkinsville, Ga., homestead when he did something anyone with a hammer does sooner or later: missed the nail and bashed his thumb squarely. Ouch. A few days later, still working on the barn, he did it again — same thumb, same spot. He broke the skin, blackened the nail, but no blood flowed.

That, it turned out, would be critical.

Without blood to rinse the wound in helpful bacteria, a bit of harmful staph bacteria sneaked into the pulpy remains of Hofacre’s thumb. Within days, he would be flat on his back in a local hospital, hitched to IV lines and clinging to life. Doctors began pumping antibiotics through the lines, telling Hofacre matter-of-factly that he could die if the antibiotics didn’t take — and, even if he lived, his thumb might well have to be amputated.

“As I was lying there,” recalled Hofacre, an associate professor of avian medicine in the University of Georgia College of Veterinary Medicine, “I began to think very hard about all the work on antibiotic resistance I had done. And I was hoping, really hoping, that I hadn’t become resistant to whatever bug had gotten me.”

Thankfully, the medicine worked. Within a few days, Hofacre was out of critical condition; his thumb wouldn’t need to be amputated after all.

A year later, sufficiently recovered and back at work, Hofacre was teaching veterinary college students and fielding questions from Northeast Georgia’s poultry farmers — a major part of his job is to service these producers — when a call came: an infection outbreak on a farm near Elberton.

A poultry producer had phoned about what looked like an outbreak of chicken disease in one of his four broiler chicken houses, a diagnosis a veterinarian soon confirmed. After three days of antibiotics, the chickens were recovering, but the university still dispatched a team of researchers. Something much greater was at stake than a single flock of chickens.

Two-pronged attack
Part of that team was Margie Lee, an associate professor of medical microbiology who leads one-half of UGA’s two-pronged approach to research on antibiotic resistance. Her group wants to know whether bacteria acquire this resistance — and, if so, exactly how — or whether it has long been built into the bacteria’s genes.

More importantly, they want to know whether highly resistant bacteria can be passed — through mishandled foods such as poultry and eggs — to humans, where they might be a potentially life-threatening problem.

To date, the team has focused mostly on two bacteria that cause most of the significant food-borne illnesses in humans. While Lee examines Campylobacter, her husband, John Maurer, a UGA associate professor of avian medicine, studies similar questions relating to Salmonella. Both have attracted enough attention to win major grant support: $600,000 for Lee from the U.S. Food and Drug Administration and $900,000 for Maurer from the U.S. Department of Agriculture. It’s appropriate that these researchers are pooling their talents on the issue: UGA’s avian medicine department is, very likely, the largest research group in the world that investigates questions of poultry disease and their implications for human health.

On the infected poultry farm near Elberton, Lee eventually would take more than 50 cotton-swab samples of chicken stool. Standard procedure calls for her to: isolate and culture (grow) the bacteria in those samples; test the bacteria against a class of commonly used antibiotics called fluoroquinolones; then compare any resistance she finds with older bacteria samples taken from the same chickens before the outbreak — and before any antibiotics were administered.

Like Hofacre’s thumb wound, an epidemic in chickens starts simply. Chicken houses hold up to 20,000 birds, making them highly susceptible to disease. Once a bird falls ill — for example, with a respiratory infection such as colibacillosis, air sacculitis (both caused by E. coli bacteria) or fowl cholera — the close quarters virtually guarantee that many others will soon follow suit. So it’s important to move quickly; avian diseases spread not only to neighboring birds but also to neighboring chicken houses. And in a state like Georgia, where poultry is the single largest agricultural product — contributing more than $3 billion annually to the state’s economy — that’s a very big deal.

To control poultry infections, avian veterinarians treat them in much the same way doctors treat human ones: with different kinds of antibiotics, depending on the kind of infection revealed in the lab cultures.

“It’s analogous to a human influenza outbreak,” Hofacre said. “When an outbreak happens, you want to keep it from spreading from, say, Watkinsville beyond to places like Winder and Athens. You’re thinking about containing the infection to just that [infected] population.”

For poultry, that means treating an entire infected population of birds simultaneously, usually by either adding antibiotics to the feed or — most commonly — adding them to the drinking water supply. But that’s not cheap.

“If a producer has to use them, he does it so that he won’t lose money already invested in the birds,” Hofacre said. “But once he’s spent that much money on antibiotics, he won’t make a profit off that batch, either.”

Therefore, antibiotics tend to be a last resort. In fact, industry groups estimate that only 1 percent to 2 percent of commercially produced poultry in the United States is treated with fluoroquinolone antibiotics.

“I was surprised at how little they’re used,” Lee said. “But most farmers are conservative, and they will try other things — increasing ventilation or going to market early — if they can.”

Still, the FDA isn’t taking chances. When several studies seemed to link antibiotic-resistant bacteria in humans to antibiotics used in food animals, the federal agency circled the wagons. In the fall of 2000, the agency began serious discussions about removing all fluoroquinolones from the market before any more were used to treat poultry.

As the agency awaits further studies, however, the UGA researchers are questioning whether this link truly has been established between antibiotic use on poultry diseases and human illnesses. Pointing out that natural antibiotics (such as penicillin) have been around for a long time, the scientists aren’t sure the FDA’s idea to ban existing and new antibiotics on food animals will, by itself, make a difference.

“Before we started using antibiotics, there were antibiotic-resistant genes, because this arms race has been going on forever in the microbial world,” Maurer said.

Some of the researchers even believe the studies on which FDA relied may be seriously flawed.

“We don’t have the answers, yet,” Hofacre said frankly. “We are just raising questions at this point.”

Bulletproof vests
Naturally occurring antibiotics have existed for a long time, possibly almost as long as bacteria. Most, in fact, are produced by bacteria and fungi — to kill their competitors.

“In nature, there is a brutal fight going on for limited nutrients and limited resources,” Maurer said. “To make it in that type of world, one group of organisms found ways of killing their competitors; we just call them antibiotics.”

The competing organisms evolved new genes to defend against the new antibiotic enemies. Resistance takes many forms: A gene might destroy the antibiotic or simply pump it out of the cell like a sump pump in a basement.

Whatever its methods, resistance complicates matters even as it is saving the day. When a doctor administers an antibiotic to ease a child’s earache — or, for that matter, a chicken’s respiratory ailment — the short-term relief is balanced by a potential problem. While most of the targeted bacteria die, a few sometimes remain behind, somehow resistant to the medicine. That usually happens in one of two ways. A bacterium’s DNA suddenly can change through a slight, random mutation — and it only takes a single mutation, in one bacterial gene, to resist some antibiotics’ disruptive behavior. Or, more commonly, a bacterial strain such as E. coli can acquire a special, gene-triggered enzyme that “pumps” out specific antibiotics, then share that gene with another bacterium, such as Salmonella, thereby passing its resistance along.

“There’s a lot of ‘sleeping around’ going on with certain kinds of bacteria, that’s for sure,” Lee quipped.

Even if just a handful of the infectious bacteria remain alive, they can multiply fast — and their offspring are much more likely to contain the antibiotic-resistant gene. When enough bacteria have the gene, the antibiotic will no longer be effective.

“It’s kind of like if you have 100 people in a room, and 14 have bulletproof vests,” Lee said, drawing a metaphor explaining how certain bacteria such as Campylobacter mutate, become resistant, then multiply to produce more of that resistance. “Someone starts shooting. The ones that don’t have bulletproof vests are killed, which leaves the ones that did. And those produce bulletproof vests for their offspring. What you find is that, next time, more of them are resistant.”

Maurer extends the metaphor farther to explain how other organisms transfer the genes that arm Salmonella with resistance. An E. coli bacterium passing resistant genes to a Salmonella bacterium, he said, is “like more people coming into that room, and the people there are passing extra vests to people who are completely unrelated to them.”

One way doctors try to avoid this is by giving a very long, strong course of antibiotics — a so-called “therapeutic dose” — that completely wipes out all infectious bacteria. But if patients stop taking the medicine when they begin to feel better and before the therapeutic dose is complete, the resistant bacteria are more likely to remain behind and grow.

The same thing can happen to successive generations of chickens in a broiler house. For that reason, the recent conventional wisdom has been that antibiotics must be prescribed very carefully.

But antibiotics may not be the sole source of long-term resistance. Scientists are finding antibiotic-resistant strains of bacteria in many species of wild birds and other animals — turtles and Canada geese, among others — that are never naturally exposed to any sort of antibiotic. Other researchers have punched a hole in the theory by discovering that some bacteria seem to be highly resistant to medicines that are nearly brand new.

“There’s one new antibiotic used with cattle, for instance, that’s a synthetic substance; it doesn’t exist in nature. And yet, there’s already a gene floating around that confers resistance to it,” Lee said. “This gene is out there, and it’s probably been out there for quite awhile. We can’t just go and assume that it came from the antibiotic’s use.

“Let’s say a woman used her lipstick to poke out the eyes of a mugger, and then some scientist just happened to come along and do a study of the incident. The scientist might well conclude that lipstick had evolved, or been invented, solely as a way to fight off muggers. But it didn’t; it was around all along for a different reason and just happened to be handy for the job,” she said. “This is the same.”

Unanswered Questions
All on the UGA team acknowledge that it will take years to determine whether a link exists between antibiotic use in poultry and drug-resistant bacteria that cause human ails.

By redesigning her experiments, Lee said she hopes to avoid some pitfalls of earlier bacteria research that she questions. Some of those experiments actually used antibiotics during the cultivation (bacteria-growing) step of the process, for example, potentially filling the cultures with resistant bacteria before actual testing had even begun; she’ll use a different method of culturing the bacteria.

Once they settle on experiment designs, the research team must grapple with dozens of questions. Among them:

What is the complete life cycle of Campylobacter? The bacterium lives in chicken intestines, but it doesn’t appear there until the chickens are 4 to 5 weeks old.

Why are roughly 10 percent of chickens that have E. coli infections resistant to the antibiotic chloramphenicol? The antibiotic hasn’t been used to treat any food animals in decades — and it has never been used in poultry houses — because it occasionally interrupts red blood cell production in humans, which is fatal; the drug was taken off the market in the early 1980s.

How does Salmonella bacteria manage to be especially good at acquiring resistant genes? In essence, it will take whatever it can get, wherever it can get it. There is always a tradeoff to freeloading, however, and most other bacteria don’t operate this way. Could vaccines distract Salmonella from acquiring these genes?

If fluoroquinolones are pulled off the shelves, what cost-effective replacements can be developed to replace them? After all, they are the most effective antibiotics in the poultry industry.

Their questions led to a third prong of the antibiotic resistance study. Funded by a recent $800,000 USDA grant, Hofacre will lead a research effort to investigate a group of bacteria that causes two human infections: staphylococci, the same infection in Hofacre’s thumb wound, and enterococci.

“Many researchers follow a single thread to the end,” Hofacre said. “But when we follow a thread, it might split off one way — and we have to go several different directions at once. This takes years.”

For more information, e-mail chofacre@arches.uga.edu or leem@vet.uga.edu.

Paul Karr is a prize-winning journalist and writing consultant who contributes regularly to Research Reporter.