When Lyme Disease Doesn’t Go Away

It’s tick season. Here’s what Brian Fallon, the director of Columbia’s Lyme & Tick-borne Diseases Research Center, has to say about combating chronic Lyme disease.

Carla Cantor
April 29, 2019

Brian A. Fallon, (VP&S ’85, MPH ’85) spent his early career working with patients whose medical symptoms were a mystery. The Columbia University Irving Medical Center psychiatrist became one of the foremost researchers of hypochondria and somatic disorders, or psychological illness that manifests as physical symptoms.

He might have stayed with that specialty had he not begun in the early 1990s to see a surge in referrals of patients with chronic, unexplained symptoms who had all been healthy—until they got Lyme disease. These patients suffered from chronic pain, fatigue and cognitive problems that had a debilitating effect on their lives. They all had been treated with antibiotics with partial response but then relapsed.

Since such persistent infection was considered impossible, they were told they were hypochondriacs.

“At the time, the medical community was saying that initial antibiotic therapy led to a cure,” Fallon said. “I found this hard to believe given the suffering among these patients. We needed to look further.”

Since 2007 Fallon has headed Columbia’s Lyme & Tick-borne Diseases Research Center, a joint effort by the Global Lyme Alliance, the Lyme Disease Association and the Columbia University Medical Center Board of Trustees. It is the first such academic research center in the country, and its mission is to tackle the core clinical questions of the disease and identify better diagnostics, biomarkers and treatments.

Fallon discusses why this is a pivotal time in the world of Lyme disease.

Book cover of Conquering Lyme Disease

Q. Lyme disease was first reported in the United States in 1977 in the town of Old Lyme, Connecticut.  How far have we come?

A. We still have many unanswered questions, but there has been tremendous progress. We now know the cause of the disease, a bacterium called Borrelia burgdorferi, and its multi-system manifestations. We know many of the biologic tricks the organism uses to evade the human immune response and we know its genetic makeup, as it has been fully sequenced. We know that while most Borrelia are easily eradicated with a standard course of antibiotics, some persist despite treatment. We briefly had a vaccine on the market, which is no longer available, but a new vaccine is now in clinical trials. Despite advances in some areas, there remain serious problems, most prominently that the epidemic of Lyme disease continues to expand both geographically and in the number of new cases—an estimated 400,000 in the United States each year.

Q. What are the symptoms of chronic Lyme disease and how is it diagnosed? What percentage of Lyme sufferers go on to have chronic problems?

A. Most patients do well if the infection is recognized and treated early. In about 10 to 20 percent of cases, patients develop a more severe disease whose symptoms can include debilitating pain, fatigue, headaches, mental fog causing difficulty with memory or finding words, irritability and  sleep disorders. Unfortunately, because our blood tests are antibody-based and can remain positive for years even when infection is no longer present, it is hard to determine whether a patient’s recurrent symptoms are due to persistent infection, a new infection or a post-infectious disorder.

Q. Why does post-treatment Lyme disease affect some people and not others?

A. This is an important question for which we have only preliminary answers. Infection by a more invasive strain of the Borrelia microbe, rather than one that only causes skin manifestations, increases the risk of more severe disease. Certain genetic markers increase the risk of chronic Lyme arthritis. Patients with a history of multiple physical illnesses and other life stressors may have less resilience to infection. And because the tick may transmit other microbes, some patients may have two or more infections.

Q. What are the current treatments for persistent Lyme disease?

A. There are multiple approaches to the treatment of lingering symptoms, but there haven’t been any new, large clinical trials in the U.S. on chronic Lyme-related symptoms in over 10 years. Studies in Europe of early Lyme disease indicate that some of these patients improve without further treatment over the course of one year after initial antibiotic therapy. Patients with chronic symptoms need a personalized approach based on the cause of their symptoms.

Q. Is there hope of finding a cure?

A. Absolutely. With precision medicine approaches, biomarkers are now emerging that appear able to predict who might respond to standard antibiotic therapy and those who might not. This provides an opening for testing new treatment approaches for the latter group, leading to improved long-term outcome.

Dr. Fallon is co-author of Conquering Lyme Disease: Science Bridges the Great Dividewith Dr. Jennifer Sotksy ( VP&S’16,) a fourth-year psychiatry resident at Columbia University Irving Medical Center. (Columbia University Press, 2017 hardcover,  2019 paperback)

For media inquiries or more information, contact Carla Cantor at 212-854-5276 or



  • Again, the erroneous percentages of 10-20% of patients going on to develop persistent symptoms is inaccurate.  There’s a whole lot more of us out here in Lyme-land than that.  Please read:  In a nutshell, microbiologist Holly Ahern points out that the 10-20% the CDC calls PTLDS only includes those patients diagnosed and treated early.  It does not and should not include a large subset of patients (30-40%) diagnosed and treated late.  When you add the two groups together, you get 60% of patients going on to struggle with persisting symptoms.  This is an important detail as it shows the vast numbers struggling as well as the need for high priority research studying this issue.  


  • He discusses strains of borrelia.  I learned something the other day – that borrelia (Lyme) is unique in that bacteria are typically only allowed 1 species name, but due to honoring Willy Burgdorfer, all borrelia are “Lyme.” This little fly in the ointment is a huge reason many are not getting diagnosed.  Current 2-tiered testing only tests for 1 strain. I was told by a researcher to think of the Borrelia burgdorferi sensu lato complex as an umbrella, and the 23 genospecies are dangling from it (soon to be 24, BTW!) This may be why Southerners struggle with getting a diagnosis. STARI may be one of these borrelia that doesn’t fit into the box researchers have created for this night-mare.



  • He also found IV’s give much higher blood levels of drugs than orals, and that the following variables necessitated IV treatment:
    1. Spinal tap shows high inflammation (high protein)
    2. High Sed rate and synovitis (inflammation of synovial membrane)
    3. People sick for more than 1 year
    4. Age over 60
    5. Acute carditis
    6. Immune deficiency
    7. Those who used immunosuppressants
    8. Failed oral treatment


  • If you study this for 1 second you begin to appreciate the complexity of treating this which mainstream doctors still haven’t even accepted.


  • The fact that there haven’t been any new, large clinical trials in the U.S. on chronic Lyme-related symptoms in over 10 years is unacceptable when you consider that this is two times more prevalent than breast cancer.  HELLO?  Where’s the green ribbons and huge institutions raising funds for Lyme research?  Oh, yeah, I remember, our researchers are using their own microscopes in their basements!  MacDonald is shown in the documentary, “Under Our Skin.”  


  • BTW: when MacDonald presented his culture findings (direct testing) at a meeting of the NY State medical society where there were many detractors from Yale & Stoneybrook who didn’t want their patented serological tests to be usurped. They accused him of falsifying his results.  Dr. McDonald then went on to prove conclusively it was Lyme by morphology, silver staining, monoclonal antibodies staining, DNA PCR and finally electron microscopy.  Frustrated, he quit the field and moved to Texas leaving all his old files in Burrascano’s basement until twenty years went by and he became interested again due to Alzheimer’s research & picked up his old files.