A New Look at Chronic Lyme

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In the years that followed, the cluster of symptoms persisted. Crystal doggedly pushed through, completing a semester abroad, finishing college, and moving to Colorado to become a ski instructor — her lifelong dream — until it all became too much for her health. She ended up moving back to Connecticut to live with her family.

There, she sought the care of a ­naturopathic physician who sus­pected she had chronic fatigue syndrome. The condition is defined by exhaustion after exercise, unrefreshing sleep, concentration problems, and muscle pain lasting six months or more. Herbal treatments, an anti-­inflammatory diet, and acupuncture barely made a difference.

Her illness remained a mystery until 2005, the day Crystal noticed two new bull’s-eye rashes emerge spontaneously. Finally, a clue.

A Lyme-disease test proved positive, which led her physician to diagnose other tick-borne coinfec­tions. (Many persistent Lyme cases feature coinfections.) Months of IV antibiotics brought Crystal back to reasonable health. Believing she was cured, she took a job as an editor in Vermont.

Yet she remained fatigued, and working to support herself pushed her to the edge again. By 2007, at age 27, she was back home in Connecticut, in bed.

This time, with the help of her Lyme-disease specialist, Crystal approached her recovery differently. Along with antibiotics, supplements, and an anti-inflammatory diet, she pursued psychotherapy, integrative manual therapy, and neurofeedback. She regained traction, along with a new understanding that managing her illness would be an ongoing practice.

“I don’t consider myself sick,” Crystal says today — yet she also doesn’t consider herself cured. She has learned how to live with her chronic Lyme as well as symptoms from long COVID, and she is now documenting her experiences in a memoir called Long Hauler.

“I have needs from illness that come along with me, just the same way that diabetics have needs that they take along in their lives, to keep the illness in check.”

“I have needs from illness that come along with me, just the same way that diabetics have needs that they take along in their lives, to keep the illness in check.”

Crystal is one of up to 20 percent of Lyme patients whose symptoms are chronic, meaning they persist well past the initial course of treatment. In 2018, some estimates suggested there were more than 1 million Americans with chronic Lyme, or what the Centers for Disease Control and Prevention (CDC) calls posttreatment Lyme-disease syndrome (PTLDS).

Today we’re especially attuned to the long-haul fallout from COVID, where respiratory issues, brain fog, and depression hobble many patients for months. Those with chronic Lyme have faced similar hurdles for decades.

Doctors who are literate in chronic Lyme used to be rare. If you could find one, you’d likely be subjected to high doses of antibiotics and anti­malarials in harsh regimens that might’ve lasted months or years.

The success of this approach was mixed. Some chronic-Lyme ­sufferers regained their lives but endured ­grueling side effects, including ­destabilized microbiomes (see “Why Your Microbiome Matters” to learn more about this all important ecosystem that lives in you). Others suffered side effects but did not improve.

Perhaps because so many chronic Lyme cases involve coinfection, these treatments often didn’t resolve the problem.

Today, many of these same practitioners have taken a different path, a multipronged approach that combines the judicious use of drugs with more natural therapies. And many patients with intractable illness are finally getting their lives back.

When problems cascade, you must treat the whole patient before the person can clear the infection, says Lyme expert Daniel Kinderlehrer, MD, whose Denver-based integrative medical practice focuses on tick-borne disease. He starts treatment by addressing sleep and pain issues. The problem has “become so much bigger than that infection; there are so many things that are wrong that you can’t treat by just treating the infection,” he explains. “Even if you made the infection go away, you’d still have these other issues in the mix.”

The Lyme Divide

Some 30,000 Lyme cases are reported to the CDC annually, but the agency also notes that around 476,000 people are treated for Lyme each year, according to insurance claims. It’s caused by the bite of a black-legged tick, commonly known as a deer tick, which transmits the spirochete Borrelia burgdorferi (and more rarely, Borrelia mayonii) into the bloodstream.

Lyme is one of a handful of illnesses transmitted by the hard-bodied deer tick in the United States; others include anaplasmosis, babesiosis, ehrlichiosis, and tularemia; all cause significant health issues, but Lyme is the most common and best-studied.

Lyme was first reported in the Northeast and Midwest; now rising temperatures are contributing to an expanded range for ticks. (Greater awareness has also led to increased reporting.) In the most recent CDC survey, infections were reported in every state but Hawaii and Oklahoma.

Other tick-borne diseases are also on the rise. California, where standard Lyme has long been endemic, is seeing the surge of Borrelia miyamotoi, a separate spirochete that can be carried by black-legged ticks. It causes a fever disease (called “hard tick relapsing ­fever”) that is often confused with Lyme.

Overall, two types of Lyme disease now prevail:

The first features a straightforward infection, diagnosed early, with no additional immune issues. Patients typically recover after a two-to-three-week antimicrobial course. If the infection isn’t cleared on this round, the Lyme spirochetes can invade cardiac, neurologic, and joint tissue; a month or two of IV antibiotics will usually clear it.

Then there are those with Lyme (or a mix of tick-borne infections) who remain sick after the stan­dard treatment. They are usually diagnosed late and may have contracted more than one infection. This is the second type: chronic, complicated Lyme, a systemic illness so ­profound that sufferers may be too disabled to go to work or school.

A study published in the New England Journal of Medicine found a group of such patients to be as impaired as those with congestive heart failure and sicker than those with type 2 diabetes. Researchers at Johns Hopkins Medicine have also documented a striking degree of neuro­inflammation in these patients.

Chronic Lyme causes the body to fall into general instability and disrepair. Yet a Lyme diagnosis remains controversial for the persistently sick group, and many physicians are reluctant to offer it. These patients are more likely to be labeled with chronic fatigue syndrome or fibromyalgia and offered ­scattershot ­treatment.

The contro­versy may stem partly from the inadequacy of Lyme tests, which don’t reliably register Lyme anti­bodies for about six weeks. And a significant subset of people with Lyme may never test positive on standard serologies. The disease can lie dormant within tissues, and some tests can’t register certain strains of Borrelia.

Some 30,000 Lyme cases are reported to the CDC annually, but the agency also notes that around 476,000 people are treated for Lyme each year. 

Many patients and providers may never think to test for Lyme, especially if a tick bite failed to trigger the mottled red Lyme rash, erythema migrans (EM). But the rash can take many forms beyond the iconic bull’s-eye, and it may be difficult to spot, especially on darker skin. It can also fail to appear at all.

Complicating matters, many doctors rely on the CDC’s surveillance case definition, which requires a positive test or the EM rash. But the criteria were not designed for diagnosis or treatment. In 2019, the CDC released a disclaimer, which may help more patients receive treatment early on.

Still, an early course of antibiotics does not eliminate the risk of chronic Lyme for those people who remain sick after standard treatment, says physician Elizabeth Maloney, MD, president of Partnership for Tick-Borne Diseases Education. The longer a patient has been misdiagnosed, the more likely treatment will fail.


Lyme+: The Coinfection Problem

Lyme disease on its own can be debilitating, but when other tick-borne infections are also present, the problem can be exacerbated.

Zoonotic-disease expert Steven Phillips, MD, who treats a range of complex vector-borne diseases and is the coauthor of a recent book, Chronic: The Hidden Cause of the Autoimmune Pandemic and How to Get Healthy Again, calls these complex cases “Lyme+.” Treatment might be prolonged, and a cascade of other problems, incited by infection but sustained by immune dysfunction, can take hold.

These instances show that Lyme disease alone may not account for some of the most confounding cases. “Those most difficult to treat usually have more than one infection, such as babesiosis or bartonellosis,” says physician and Lyme researcher Richard Horowitz, MD, the author of How Can I Get Better? An Action Plan for Treating Resistant Lyme and Chronic Disease.

Researchers assessed 104 people with chronic-Lyme symptoms. They found that 48 percent had been infected by more than one microorganism, and 25 percent showed evidence of at least three.

The same ticks that carry Lyme-causing bacteria may also carry Anaplasma, which can cause the severe flulike anaplasmosis; the sometimes-fatal Powassan virus; and a series of other Borrelia microbes (including B. miyamotoi) that can cause relapsing fevers and other symptoms.

Bartonellosis may be the most disabling coinfection, because of its devastating neuropsychiatric impact, believe Horowitz and Kinderlehrer.  (Horowitz thinks that Bartonella can also amplify nearly every underlying Lyme symptom, including fatigue, neuropathy, muscle and joint pain, and sleep disorders.) Researchers previously doubted that bartonellosis and Lyme spread together via ticks, but some are now changing their positions. The Lyme and Tick-Borne Diseases Research Center at Columbia University now reports that “the evidence for ticks as vectors of Bartonella organisms is circumstantial but fairly strong.”

Evidence that coinfections add to illness continues to grow. In a study published in the European Journal of Microbiology and Immunology in 2021, researchers assessed 104 people with chronic-Lyme symptoms. They found that 48 percent had been infected by more than one microorganism, and 25 percent showed evidence of at least three.


An Integrative Approach to Treatment

The current evolution in integrative treatment still includes pharmaceuticals, but for shorter courses than the former years-long treatments. It also often involves herbal treatments and a focus on overall health, including sleep and nutrition, since a long-term infection or immune dysfunction will destabilize multiple systems in the body.

Though quite experimental, emerging integrative approaches may focus on dormant or sluggish spirochetes, which are believed to be harder to conquer than others. The research, much of it coming from university labs, is new and remains controversial, but practitioners say that these discoveries have helped move the needle for some chronically ill patients for the first time in years.

These are some of the newest approaches.

Tackling Persister Cells and Biofilms

Recent research has identified more dogged forms of the Lyme spirochete. These “persister cells” are antibiotic-tolerant variants of Lyme bacteria, meaning they are generally unresponsive to drugs.

Researchers have also begun to consider the role of biofilms: starchy, gel-like coatings made of various microbes, including Lyme Borrelia. Microbes operate symbiotically to protect themselves in these films, making it particularly hard to eliminate them.

Stanford researchers subjected persister versions of the Lyme spirochete to more than 4,000 drugs to see which ones might have an effect on Borrelia. Kenneth Liegner, MD, an internist trained in critical-care medicine, has begun treating some Lyme patients with disulfiram, a drug that has FDA approval for treating alcohol dependence and can also be a potent agent against Lyme. Disulfiram has helped some Lyme patients — and caused especially severe side effects in others.

Other researchers continue to search for treatments beyond pharma­­ceuticals. Microbiologist and immun­ol­ogist Ying Zhang, MD, PhD, has tested Lyme-containing biofilms with a broad selection of antibiotics and herbal ­substances. For instance, he and other researchers have found that ­Japanese knotweed, black walnut, sweet wormwood, and Ghanaian quinine are all effective against Lyme Borrelia.

Although these tests were in vitro and studies of human subjects have yet to be done, many practitioners treating chronic-Lyme patients have been adapting these finds on the fly, using drugs as well as herbs when necessary.

Different Drug Protocols

Horowitz has tested a drug called dapsone. It’s normally used to treat leprosy, which also involves persister bacteria. A two-month course of dapsone combined with the biofilm-buster rifampin has helped almost half of the persistently ill Lyme patients in one study to return to health.

Fruitful developments have also occurred by accident. One of ­Horowitz’s patients was in the midst of a divorce and so caught up in grief that she took quadruple the study dose for four days, before stopping cold. Though she’d been chronically ill for years, this short-term, high-dose regimen put her symptoms into full remission, which has lasted nearly a year now.

“Perhaps the answer is to hit hard for several days three or four times a year,” says Horowitz.

A few other patients signed on for the four-day treatment with significant success. Horowitz now is conducting a clinical trial to see if shorter, higher-dose treatments can do the job consistently.

Recent success with short-term aggressive drug treatments has convinced Horowitz to change the focus of his practice and eliminate long-term antibiotics for good. “Perhaps the answer is to hit hard for several days three or four times a year,” says Horowitz.

The search for safer, even more effective protocols continues.

A Gentler Approach

Other Lyme doctors choose potent herbal treatments to help patients heal. These include many essential oils that academic researchers have found to be active against persisters and biofilms: garlic, cinnamon, oregano, and clove, among others.

To suppress the inflammation that makes people feel so sick, they look to turmeric, alpha-lipoic acid, glutathione, and more.

Such strategies have worked for Kinderlehrer, whose practice focuses on tick-borne-disease patients, some of whom are unable to tolerate antibiotics, even for short periods. His protocol includes lifestyle changes, antimicrobial and anti-inflammatory herbs, CBD, and efforts to restore normal hormone function.

In many of Kinderlehrer’s patients, a formerly straightforward infection has morphed into body-wide instability. They may have developed extreme sensitivities to foods, mold, and chemicals that never bothered them before. Some experience activation of mast cells, the white blood cells close to small blood vessels, provoking dangerous allergic reactions. These reactions can trigger brain fog, mood problems, pain syndromes, and profound fatigue.

Still other patients suffer from immune suppression, which likely occurs when Borrelia invade the lymphatic system, interfering in the process where antibodies are generated and sustained, according to University of California, Davis, immunologist Nicole Baumgarth, DVM, PhD.

This lowering of the guard, notes Kinderlehrer, could enable reactivation of yet other infections, such as the Epstein-Barr virus, as well as endocrine or neurological disruption. (Experts are also seeing this same reactivation happening in many patients with long COVID.)

Because no two chronic-Lyme patients are the same, treatments must be highly individualized.

Integrative physician Erica Lehman, MD, is another practitioner who now treads more softly in her treatment of Lyme patients. “A ­decade ago, I was more heavy-­handed with antibiotics,” she recalls. But a retrospective analysis of her patients’ outcomes has made her rethink her approach.

She still uses antibiotics, including IV treatment to reduce the load of infection, but then she switches to lower doses and herbs as soon as possible. “Slow and steady wins the race,” Lehman says.

Years of experience have helped her recognize patient clusters: those with neurologic disease versus illness that hits the gut, the endocrine system, joint tissue, and more. Each cluster has a different treatment protocol and separate path to wellness; though their problem may have started with a tick-borne disease, they face other issues now. (Much of her approach is informed by MyLymeData, a patient-powered Lyme-disease research project.)

Because no two chronic-Lyme patients are the same, treatments must be highly individualized.

Bill Rawls, MD, author of Unlocking Lyme, couldn’t agree more. He was almost 50 when he experienced a devastating descent into illness that was diagnosed as Lyme. After weeks of antibiotics, he was sicker than before. Ultimately, Rawls — who sought training in herbal medicine after his Lyme diagnosis — developed an herbal therapy protocol aimed at slowly killing tick-borne microbes while helping his immune system heal.

“Most of my patients don’t recall a tick bite,” he explains. Instead, they got sick after some extreme stress: a toxic exposure, head injury, overwork, or a traumatic life event. All can weaken the immune system and allow under-the-radar infections to gain purchase.


Each Journey Is Unique

Many of the healthcare providers who specialize in chronic Lyme end up doing so because they’ve experienced it themselves. Like Rawls, naturopathic physician Mac Toohey, ND, was bitten by a tick in 2007. She was lucky enough to have a bull’s-eye rash, an incontrovertible sign of the disease. (Though not everyone who gets Lyme will have the rash, nearly everyone who has the rash ends up with Lyme.) Despite early diagnosis and treatment, she developed neurological symptoms.

When her stomach could no longer tolerate antibiotics after a yearlong course, she turned to herbs, such as Japanese knotweed and skullcap. That plus a shift to a more plant-based diet aided her in turning the corner.

Then she contracted Lyme again in 2015, and the same treatments didn’t help. Toohey soon learned she had yeast overgrowth and small-intestinal bacterial overgrowth (SIBO), which had to be treated first.

Based on what she learned, she now treats chronic-Lyme patients with IV antibiotics, addresses microbiome imbalance, and focuses on patients’ overall nutrition and sleep habits.

Toohey’s experience has shown her that when a tick-borne disease causes a patient to remain ill for months or years, it is always a journey of one. Much depends on the infections involved and the person’s own biology: Complex chronic illnesses damage different systems and present in unique ways. Practitioners like Toohey, trained in the integrative arts, gently strip the layers of illness, relying on research to guide the way.

Many other practitioners have taken note. Some of the most aggressive, antibiotic-focused Lyme doctors have begun to adapt their treatment protocol, creating new hope in the chronic-Lyme community. The long-term, heavy-dose pharmaceuticals these physicians offered have been controversial, harsh, and costly to maintain. Lyme patients who couldn’t tolerate them often sought support in the world of alternative care, where they may have faced quackery and scams, such as the groundless promotion of malaria treatments.

Today, a well-considered integrative approach is backed by a growing body of peer-reviewed research. Though more clinical studies are still necessary to validate treatments and elevate the level of care for chronic Lyme, the integrative world is a good place to turn when the fallout from tick-borne illness just won’t end.

And as the rates of other complex chronic illnesses, like long COVID, continue to climb, the hard-won experience of chronic-Lyme survivors may be able to provide a road map for us all.

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