Part of our weekly "In Focus" series—stepping back, looking closer.

Rampant disagreement over what constitutes Lyme disease—in particular, who may have contracted it and how, and how long it lasts—has spawned the larger question of how best to treat it. A new study pointing to the possibility of sexual transmission of the pathogen adds fuel to the fire.

Amid the uncertainty, a patient-led lobby (the counterculture, as someone has called it) that includes doctors as well as Lyme sufferers advocates a broader definition of the disease, both for treatment and insurance purposes.

But the medical establishment asserts that too liberal a definition—and what are seen as renegade practitioners—has led to irresponsible and potentially dangerous treatment of unrelated maladies misidentified as Lyme.

It's also unknown how many people have died because of Lyme. A 2011 study found that of the 114 deaths reported over a five-year period listing Lyme as a partial or direct cause, only one was consistent with clinical manifestations described by the International Classification of Diseases.

In December 2013, the Centers for Disease Control and Prevention (CDC) confirmed that Lyme carditis—a condition in which the Lyme bacterium infects the heart—caused three deaths over the past two years. Between 1985 and 2008, only four other fatal cases were confirmed.

While the course of the illness varies greatly from person to person, initial manifestations can include a unique skin lesion known as erythema chronicum migrans, headaches, musculoskeletal pain, coughing, sore throat, conjunctivitis, and minor neurological impairment.

If the diagnosis is confirmed early enough, Lyme is treated almost exclusively with short-term antibiotics, often penicillin, which are almost 100 percent effective. But if Lyme goes untreated, symptoms can progress. (Watch related video: "The Deer Tick")

In Lyme's second stage, typically between one and several months after the initial infection, neurological abnormalities can arise, such as meningitis, encephalitis, and cranial neuritis, which can manifest as facial palsy. Some patients develop cardiac problems.

In the third stage, which can take several months to years to show up, many patients develop chronic arthritis as well as an increase in neurological and cardiac symptoms, the severity of which can ebb and flow.

Voices in the counterculture argue that Lyme's symptoms are more intense and longer lasting than the medical establishment acknowledges. They say that symptoms of chronic Lyme disease are responsible for related deaths, including suicides from depression about the disease or from the trauma of persistent debilitating symptoms such as arthritis, heart problems, and cognitive impairment.

New Developments

And now, further complicating the picture, a study published this January contends that Lyme disease may be sexually transmitted. It shows that the Lyme pathogen, Borrelia burgdorferi (Bb), has been found in both male and female sexual secretions, raising the question of whether people are at risk through intimate contact.

Bb is one of only six known spirochete bacteria, named for their coiled spiral shape. (One of the six is the bacterium responsible for syphilis.)

View Images Borrelia burgdorferi is the bacterial agent of Lyme disease. PHOTOGRAPH BY SCIENCE PICTURE CO., CORBIS

The primary vector for Bb is the deer tick—Ixodes scapularis—although other kinds of ticks have been known to transmit it, and other insects, including some mosquitoes, carry the pathogen.

A study of Bb last year revealed that it's the first known organism that doesn't need iron to survive. This allows it to evade an iron-inhibiting hormone called hepcidin, produced by the liver, which can starve intrusive bacteria.

Instead, Bb thrives on manganese, which it uses to make essential enzymes for survival—something researchers who made the discovery last year believe could play a role in ultimately combating the pathogen.

Origins: Did Ötzi Have Lyme?

In 2012, a team of researchers claimed that the 5,300-year-old mummy known as Ötzi the Iceman, discovered along the Austria-Italy border in 1991, had contracted Lyme.

Some claim that the disease first appeared in Germany in the 1880s or France in the 1920s; others say it took root in the U.S. around the time of the Great Depression.

In the summer of 1975, 39 children living relatively close to one another in Lyme, Connecticut, were recognized as sharing common symptoms consistent with juvenile rheumatoid arthritis.

Polly Murray, whose 11-year-old son, Todd, was one of those affected, alerted the state health department after the local orthopedic doctor was stumped. "He had a different answer for everybody," says Todd, who is now 49.

View Images Ötzi the Iceman, a 5,300-year-old mummy, may have had Lyme disease. Photograph by The Bridgeman Art Library, Getty

As his mother began drawing attention to the strange epidemic, a doctor at Yale University named Allen Steere began sleuthing the problem.

In a 1977 paper in the medical journal Arthritis and Rheumatism, Steere identified a new disease transmitted by ticks. He called it Lyme arthritis, and soon after it became known as Lyme disease.

Lyme ticks are active year-round, other than during subfreezing weather, but spring is the most dangerous season. That's when the baby ticks, or nits—so tiny as to be almost invisible—are born.

One theory—compelling but controversial—about the sudden emergence of the disease in Connecticut blames the accidental release of infected ticks during experiments at Plum Island Animal Disease Center, on Long Island Sound about eight miles south of Lyme.

Originally operated by the U.S. Army, then by the Department of Agriculture, and now by the Department of Homeland Security, the facility's official mandate is defense research relating to agricultural bioterrorism.

A book by Michael Carroll called Lab 257 cites post-World War II experiments on Plum Island that involved using ticks as disease vectors for germ warfare.

Officials have denied the allegations, but Carroll and others—including former Minnesota Gov. Jesse Ventura—allege the government has used the facility to develop various diseases intended for delivery as biological weapons.

When Is Lyme Lyme?

For his discovery of Lyme and subsequent work on the disease, Allen Steere started out as the counterculture's golden boy. But he came to believe that too many symptoms were being labeled chronic Lyme without proof. He says he's now a pariah to advocacy groups and Lyme sufferers, and he avoids involvement in the increasingly polarized controversy.

Gary Wormser, head of infectious diseases at New York Medical College in Valhalla, agrees that misdiagnosis of Lyme is rampant. "I don't think it's helping patients. I don't think it's helping science," he says.

Lyme, Wormser says, has become a catchall for a constellation of symptoms that elude diagnosis: "If I can't figure out what you have, it must be Lyme disease."

He puts some of the blame on medical science's failure to find answers to a range of symptoms that include headaches, joint and muscle aches, depression, chronic fatigue, irritable bowel syndrome, and cognitive impairment. These ailments often seem to be subjective, with no physiological cause.

"For a lot of people who are not feeling well, those people are the most vulnerable to turning to the types of practitioners that don't follow mainstream practices," Wormser says.

"I'm not saying there aren't some [Lyme] patients that have been debilitated by some of these symptoms, but it seems to be a really small percentage—far less than you'd be led to believe."

Todd Murray, one of the original Lyme children, grew up to be an emergency department physician. He believes he still suffers from symptoms relating to the original infection.

"I have weird things I attribute to Lyme," he says, including a permanent heart condition diagnosed in 1989.

As a doctor, Murray recognizes the dilemma of anecdotal evidence. "I can see both sides, because physicians have to go on evidence-based medicine. So to try to use therapies which have not been shown to be beneficial in clinical studies doesn't make sense."

He cites, for instance, hormone replacement therapy for post-menopausal women, which was ultimately shown to increase coronary artery disease, stroke, and breast cancer. "A lot of things in medicine would seem to intuitively make sense. However, when they're studied, the outcomes may be found to be different than expected," Murray says.

Challenges of Treatment

Identification of Lyme usually begins with the telltale bull's-eye rash. But patients don't always present with the rash, or sometimes it has a different shape and appearance, which means the disease can progress before a course of antibiotics is prescribed.

In Lyme's later stages, antibiotics are still used, with dosages and duration increased. But there's disagreement as to whether antibiotics should ever be administered for longer than three months, even in extreme cases.

"The ideology of the counterculture," Steere says, "is to simply treat symptoms with antibiotic therapy, [and] the Infectious Diseases Society of America [IDSA] has said in essence that's not correct." The IDSA notes that "using antibiotics for a very long time [months or years] does not offer superior results and in fact can be dangerous, because it can cause potentially fatal complications."

View Images Lyme disease is often accompanied by a bull's-eye rash. Photograph by Kallista Images, Getty

Counterculture doctors treating patients whom they believe have chronic Lyme will recommend not only long-term antibiotic treatment but also various other therapies, such as holistic curatives, physical therapy, and counseling.

Because some people who have Lyme elude detection, "you have to ask the right questions when you make a diagnosis," Murray says. "I think there needs to be a standardized, reliable protocol for testing."

Culturing the Lyme spirochete, Bb, to determine the presence of Lyme would provide a definitive answer. But it's costly and time-consuming, and therefore rarely done.

Instead doctors usually check for the presence of Lyme antibodies through a blood test. According to the CDC's recommendations, if the test, known as an enzyme-linked immunosorbent assay (ELISA), proves negative for the antibodies, no further test is recommended. If it comes up positive, a second test—an immunoblot test—is recommended to confirm Lyme.

Murray says ELISA and blots in tandem are currently the best method, along with more complicated cerebrospinal fluid tests in cases where symptoms are apparent but the first two tests are negative.

But with these methods, false negatives are still a significant possibility. It's also possible that Lyme cells can alter their outer surface protein and escape detection, and that different spirochetes can cause symptoms that look like Lyme but aren't. All this, Murray says, means research must be targeted toward finding better tests for the disease.

Follow the Leaders—Or Off With Your Head!

Daniel Cameron, president of the International Lyme and Associated Diseases Society, speaks for the counterculture. He believes that "thought leaders" in the medical community prevent acceptance of what he considers strong evidence that Lyme is both underreported and ineffectively treated. "Who wants to question Dr. Wormser?" he says.

"Even though the evidence is accumulating [that Lyme can be chronic], doctors have a tendency to have to wait for a thought leader to change their mind, otherwise they'll get criticized, or the medical board might drop the ax on you," he says. "Off with your head! So it becomes high risk to become a doctor who treats chronic Lyme. Most doctors don't want to have to."

View Images Ticks are easily picked up on hikes through wooded areas, like the trails seen here in Parfrey's Glen in Wisconsin. Photograph by Jeffrey Phelps, Aurora Photos/Corbis

Cameron says many state medical boards are pursuing lengthy "chart-by-chart" investigations of doctors using long-term antibiotic treatment for Lyme. These can continue for years prior to legal action by boards aimed at revoking a doctor's license.

But five states—California, Connecticut, Massachusetts, New Hampshire, and Rhode Island—have passed laws protecting physicians from reprisal or harassment when treating Lyme patients with long-term antibiotics.

While he's careful not to use the word "cure," Cameron says that with long-term treatment, patients who have had Lyme for years can go into remission and be symptom-free.

He's not particularly impressed with the CDC's latest announcement that the number of Lyme cases in the U.S. is likely ten times the 30,000 or so generally reported each year.

"In epidemiology, every time you have a surveillance system, you always at least have a tenfold underreporting. There have been studies that show it might be as much as 40 times that."

He also questions the fact that 95 percent of the reported cases come from just 13 states, mostly in the Northeast, along with Minnesota, Virginia, and Wisconsin. People in other states are less likely to report cases if the official view is that Lyme is rare and geographically restricted, according to Cameron. "That's a little bit of a reporting problem."

Could the CDC's admission of greater numbers be related to the preparation of a new Lyme vaccine?

"They had one vaccine," Cameron says—LYMErix, which was available for about five years until 2002. It was then shelved because of low sales and, some say, questionable effectiveness. (Ironically, Lyme vaccines are available for dogs but not humans.)

"The buzz on the street is that, of course, one of the reasons the CDC recognized more cases is that in order to get a vaccine through the pipeline, you have to have a problem," Cameron says.

Game Changer

Raphael Stricker, a San Francisco–based internist who co-led the sexual transmission study, says the possibility of Lyme spreading that way would "change the whole picture." It means that potentially ticks aren't the only culprits.

"What I think this is going to do is that it's going to move treatment to another level," he says.