Kaleigh Ahern was twelve years old when a tick bit her. She noticed it “perched” on her shoulder when she was taking a shower one morning. “I thought it was your average, everyday bug,” Ahern told me recently. But, when she tried to brush it off, the tick wouldn’t budge. “The legs wiggled but it was embedded in my skin. I freaked out and started screaming.” Kaleigh’s mother, Holly Ahern, came running and removed it. “I took the kid and the tick to the doctor,” she said. “I told him, Here is my kid, here is the tick, and there is the place where it was attached to her.” That was in 2002. The Aherns live near Saratoga Springs, New York, where Lyme disease has been endemic for years. The infection is transmitted by tick bites, so Ahern assumed that the doctor would prescribe a prophylactic dose of antibiotics. But he said that he wasn’t going to treat it. “If a rash develops or she starts to have flulike symptoms, bring her back,” he told her. At the time, Ahern, an associate professor of microbiology at SUNY Adirondack, didn’t know much about tick-borne illnesses. She took Kaleigh home and watched for the signature symptom of Lyme disease: a rash that begins with a bright-red bull’s-eye around the tick bite.

No rash developed, and Kaleigh was fine—strong enough to become an all-American swimmer both in high school and at Union College. There were times during high school when she felt mentally hazy and not quite right physically, which she attributed to allergies or a teen-age bout of mononucleosis. But at the end of her freshman year in college she found herself crippled by anxiety, depression, and insomnia. She was beset by searing headaches, her muscles often felt as though they were on fire, and her brain seemed wrapped in a dense fog. Kaleigh tested positive for Lyme disease. Like most physicians, her doctor followed the standard medical practice, endorsed by public-health officials throughout the United States, and prescribed a three-week course of antibiotics. “I was so happy to know what was wrong with me,” Kaleigh said. “For a while, I didn’t mind the pain.”

The drugs didn’t work, though. At her mother’s insistence, the doctor extended the prescription three more weeks, but Kaleigh only got sicker. This brought the Aherns to a clinical impasse. The Centers for Disease Control and Prevention has established highly specific criteria for the diagnosis of Lyme disease: an acknowledged tick bite, the appearance of a bull’s-eye rash, and, for those who don’t live in a region where Lyme is common, laboratory evidence of infection. Most people who fit the profile respond well to antibiotics, even months or years after the initial infection. Many Lyme specialists, however, believe that short-term antibiotic therapy may suppress symptoms but rarely cures the disease. Kaleigh switched doctors and began a course of antibiotics that lasted eight more months.

There was no change. Furthermore, there is no evidence that prolonged antibiotic therapy helps patients with Lyme disease, so insurance companies almost never pay for it. “I realized that my parents were shovelling thousands of dollars into these antibiotics,” she said. “After the oral approach failed, I was recommended to go onto I.V. treatment, but I had had enough.” Kaleigh’s condition had become so grave that she withdrew from school. “I would have episodes where I would just lie on the ground writhing. And my parents could do nothing but watch. I wish they had taken videos and put them online, so people would know.”

Kaleigh turned to alternative treatments often recommended by Lyme patients with similar experiences. She took herbs—turmeric and ginger, which are thought by some to strengthen the immune system—and she gave up gluten, grains, refined foods, and sugar. The goal was to reduce inflammation caused by her body’s production of insulin and to inhibit the growth of the bacterium that causes Lyme. She also began treatments with a Rife machine, an electromagnetic device invented in the nineteen-twenties which emits radio signals that, some researchers suggest, can destroy harmful bacteria. Although thousands of people are convinced that Rife therapy has helped them with Lyme and other diseases, little empirical evidence exists to demonstrate that it works. Nonetheless, Kaleigh began to feel better. She still has headaches and severe muscular pain at times, but she returned to Union a year ago and graduated this spring. She knows that her approach to Lyme disease is controversial and acknowledges that the improvements might be due to her dietary regimen or to Rife treatments or to a placebo effect. She doesn’t mind; after enduring such pain, she has found that fine points don’t matter.

Lyme disease is the most commonly reported tick-borne illness in the United States, and the incidence is growing rapidly. In 2009, the C.D.C. reported thirty-eight thousand cases, three times more than in 1991. Most researchers agree that the true number of infections is five to ten times higher. Although some of that increase is due to heightened awareness, transmission is rising in areas, like New England, where the disease is well established, and is spreading to regions as far south as Florida, through changes in climate and the movements of infected animals.

The disease is caused by the bacterium Borrelia burgdorferi. In the Northeast and the Midwest, B. burgdorferi is transmitted by the bite of a black-legged tick, Ixodes scapularis. (In the Western United States, a related tick, Ixodes pacificus, prevails, and in Europe the main vector is Ixodes ricinus.) Lyme was all but unknown until 1977, when Allen Steere, a rheumatologist at Yale, produced the first definitive account of the infection. The condition was initially thought to have been an outbreak of juvenile rheumatoid arthritis in and around Lyme, Connecticut. In 1982, Willy Burgdorfer, a medical entomologist at the National Institutes of Health’s Rocky Mountain Laboratories, determined that the infection was caused by the previously unknown spirochete borrelia. As is common in scientific practice, the bacterium was named for him: Borrelia burgdorferi.

Those facts are undisputed. But nearly everything else about Lyme disease—the symptoms, the diagnosis, the prevalence, the behavior of the borrelia spirochete after it infects the body, and the correct approach to treatment—is contested bitterly and publicly. Even the definition of Lyme disease, and the terminology used to describe it, has fuelled years of acrimonious debate. The conventional medical assessment is straightforward: in most cases, the tick bite causes a skin rash, called erythema migrans, which is easily identified by its bull’s-eye. If left untreated, the bacteria can spread to muscles, joints, the heart, and even the brain. Public-health officials say that a few weeks of antibiotic treatment will almost always wipe out the infection, and that relapses are rare. In this view, put forth in guidelines issued by the Infectious Diseases Society of America, Lyme is normally easy to treat and easy to cure.

For many people, though, the clinical situation is far more complicated. Some who have been infected with borrelia don’t notice the rash. Others—up to a quarter of those with Lyme, including Kaleigh Ahern—never even get one. Most troubling, some patients who are treated continue to suffer from a variety of symptoms long after their therapy has ended. Nobody really knows why they fail to get better. Infectious-disease experts refer to the phenomenon, which can affect up to twenty per cent of patients, as Post-Treatment Lyme Disease Syndrome. Researchers have attempted to resolve the mystery in experiments with monkeys, mice, and dogs; human studies are also under way. As the number of infections grows, so does the number of people struggling to figure out what is wrong with them.

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Many of these patients say that medical officials pay little attention to their persisting symptoms, and that Lyme disease is anything but easy to treat or to cure. They believe that the bacteria can hide in the body for years, potentially causing harm long after treatment ends. This condition, they say, is pernicious, difficult to diagnose, rarely cured, and widely ignored. Moreover, at least four pathogens, in addition to the Lyme bacterium, can be transmitted by the black-legged tick: Anaplasma phagocytophilium, which causes anaplasmosis; Babesia microti, which causes babesiosis; Borrelia miyamotoi, a recently discovered genetic relative of the Lyme spirochete; and Powassan virus. Some of these infections are more dangerous than Lyme, and more than one can infect a person at the same time. Simultaneous infection, scientists suggest, may well enhance the strength of the assault on the immune system, while making the disease itself harder to treat or recognize.