A study from Johns Hopkins found that a substantial number of Lyme disease patients still had significant pain and fatigue after completing a standard 3-week course of doxycycline — and for many, symptoms persisted for 6 months or longer.
These findings raise important questions about whether 3 weeks of treatment is sufficient for all patients.
The Study: Symptoms After Standard Treatment
Bechtold and colleagues at the Johns Hopkins University School of Medicine measured fatigue, pain, and depression in patients treated with a 3-week course of doxycycline for early Lyme disease.
They used clinically validated thresholds: a Fatigue Severity Score of 36 or greater indicated high fatigue, a McGill Pain Scale score above 3 indicated high pain, and a Beck Depression Inventory score of 13 or greater indicated clinically significant depression.
The findings were striking: a substantial number of patients had high levels of symptoms immediately after completing treatment. Those with clinically significant fatigue, pain, or depression at the end of treatment continued to experience functional impact for up to 6 months.
PTLDS Underestimates the Problem
The researchers identified 6 individuals who met the IDSA case definition for post-treatment Lyme disease syndrome (PTLDS) — requiring continuous or relapsing symptoms of fatigue, musculoskeletal pain, or cognitive difficulties for at least 6 months after treatment.
But the remaining patients with severe fatigue and pain did not meet the PTLDS criteria. This is an important finding: studies of PTLDS clearly underestimate the morbidity associated with Lyme disease. Many patients who are suffering fall outside the formal definition.
Why Pain and Fatigue Persist After Treatment
Several mechanisms may explain why symptoms continue after a standard course of antibiotics:
- Ongoing immune activation and neuroinflammation
- Autonomic dysfunction disrupting energy regulation and pain signaling
- Sleep disruption preventing overnight recovery
- Undertreated co-infections such as Babesia or Bartonella
- The possibility that a single 3-week course may not fully clear the underlying infection
The authors did not discuss whether persistent infection could explain the ongoing symptoms. There are no tests to confirm that a tick-borne infection has cleared after treatment.
The Fatigue-Pain-Depression Cascade
This study illustrates how fatigue, pain, and depression compound each other. Patients with high fatigue also had greater functional impairment. Those with pain slept worse. Those who slept worse had more brain fog and cognitive difficulties.
This cascade is consistent with what we see in Lyme disease fatigue more broadly — when the underlying drivers are not addressed, symptoms reinforce each other and worsen over time.
Clinical Perspective
In my practice, I see patients every week who were told their 3-week course of antibiotics should have been enough. When pain and fatigue persist, they are often told their symptoms are unrelated to Lyme disease — or attributed to stress and depression.
This study demonstrates that clinically significant symptoms at the end of standard treatment are not rare. They warrant further evaluation, not dismissal.
Frequently Asked Questions
Is 3 weeks of antibiotics enough for Lyme disease?
For some patients, yes. But this study found that many patients still had significant fatigue, pain, and depression after completing a standard 3-week course — and symptoms persisted for months.
Why do I still have pain and fatigue after Lyme disease treatment?
Persistent symptoms may reflect ongoing immune activation, autonomic dysfunction, sleep disruption, co-infections, or undertreated infection. These drivers require further evaluation.
Does PTLDS capture all patients who are still sick?
No. This study found that many patients with significant fatigue and pain did not meet the formal PTLDS criteria, suggesting the definition underestimates the problem.
Can Lyme disease fatigue last longer than 6 months?
Yes. For some patients, fatigue persists for months to years, especially when underlying infection, co-infections, or autonomic dysfunction remain unaddressed.
Is post-treatment fatigue from Lyme disease caused by depression?
Not necessarily. While depression was present in some patients, the study showed fatigue and pain as independent symptoms with their own functional impact. Depression may be secondary to ongoing illness.
References
- Bechtold KT, Rebman AW, Crowder LA, Johnson-Greene D, Aucott JN. Standardized Symptom Measurement of Individuals with Early Lyme Disease Over Time. Arch Clin Neuropsychol. 2017;32(2):129-141.
Related Reading
- Lyme Disease Fatigue: Causes, Duration and Recovery
- Exhausted Despite Sleeping with Lyme Disease
- Persistent Pain and Fatigue After Lyme Disease Treatment
- Fatigue Can Be an Overlooked Sign of Lyme Disease
- Autonomic Dysfunction in Lyme Disease
- Lyme Disease Sleep Disorders: Why You Can’t Sleep
- Post-Treatment Lyme Disease Syndrome (PTLDS)
- Medical Dismissal and Lyme Disease
After 3 months on abx for borreliosis the pain and fatigue have never gone away. It’s been 5 years so far. I also thought I was going to die from the abx treatment. It was worse than the Lyme.
It can be so difficult.
I was on doxy then biaxin for a total of about 15 months. I still have fatigue and some other symptoms. Is this a permanent side effect or should I be looking into further treatment? I do take supplements and Chinese herbs for symptoms.
By the IDSA definition, a diagnosis of PTLDS is conferred after objective resolution of the initial Lyme disease infection, whether it was caught early or late. If LD symptoms never fully resolve, or wax and wane without complete resolution, despite active treatment for a period of many months or years, what is the the term for this clinical picture?
I am not getting that this proves that the pain and fatigue were caused by the ABX and not the infection unless the patients studied had zero fatigue, pain and depression at the initiation of the ABX treatment. I continued to decline after the 3 weeks of ABX until I found a Lyme doc who prescribed a combination of ABX that was appropriate. It took 4.5 YEARS of treatment before the symptoms that had all presented BEFORE ABX treatment began to resolve. Yes this is hard but denying treatment with multiple antibiotics for those who can handle it is criminal. In response to Mary Ann above, your Lyme must not have been close to what I was dealing with. It would have killed me and I was willing to try any treatment that had a chance of saving my life.
Dr. Cameron
5 weeks after bite, I still have a tiny raised scab surrounded by red skin. Thinking of seeing my dermatologist who might excise it completely. Your thoughts? Thanks, Robin
It could be just the chemical and physical reaction to the tick bite rather than an infection.
I agree with Patricia’s statement.
Is this saying the antibiotics caused the pain and fatigue?
If we didn’t have it before Treatment why would we have gone to a doctor?
Some of my first symptoms were just those, and the only drugs I had taken was lisprinerol.
So then it would be lisprinerol that caused my issues?
Pain and fatigue persisted despite having prescribed 3 weeks of antibiotics. A persistent infection is one of the considerations.
My son was treated for Lyme disease when he was 10, in 1990 before much was known about the disease. He probably had had it for at least 2 years before we realized the relationship between the rash we had earlier seen and his present symptoms. Finding a doctor who was knowledgeable in Lyme Disease back then was difficult. We finally found a doctor who was willing to treat him and told us to keep him on antibiotics until they symptoms went away. We would stop at intervals and the symptoms would return so he would go back on antibiotic treatment again. He had to stay on antibiotics for 3 years before he could successfully go off without symptoms returning. He is now 38 years old and has never had a recurrence and is healthy in every way. I know that some of the spirochetes will go into hiding when confronted with the antibiotics and then come out in all their glory when antibiotics are stopped. Just a few weeks of antibiotic therapy is sometimes just not enough. I wonder if “pulse therapy” might be more effective.
I am glad your son has done well despite the treatment delays. I favor daily antibiotics if treatment becomes necessary.
Hello!! I was on doxycycline for 1.5 month for acne. I stopped it because I had fatigue symptoms. I recovered(not full) after 25 days but after 20 days fatigue started again. I work and workout every day. Is this normal about doxycycline? Doctor said i damaged my gut but without any specific test. Just blood tests which showed nothing.
Thanks in advance.
i find doxycycline for acne can interfere with the tests and prevents some of the finding e.g., a rash.
Was recently diagnosed with the erythema migrans rash above ankle. I did not know what it was and went to my podiatrist who has prescribed 6 weeks of doxycycline. The rash was the only indication. I don’t have exaggerated symptoms, mostly joint aches and fatigue. If I did progress to worse disease, I cannot expect my podiatrist to continue treating. My dermatologist and primary care physician do not treat Lyme or know really anything about it.
I live in Northern California. The local county vector office advised to find an infectious disease MD. Do you have any recommendations?
There are sites that suggest names if needed e.g., LymeDisese.org or ILADS
I developed the EM rash on my back. It grew to over 12″ before I was given Doxycycline. I took the Doxy for 3 weeks 2ce a day. The day after I stopped taking it, my spine began to hurt. I would say about 10 of my vertebrae. What would this be an indication of?
I would encourage you to be evaluated by your doctor to look for evidence of a persistent infection or co-infection or look for another illness. Call my office at 914 666 4665 in Mt. Kisco, New York if you have any questions.
My mate recently finished a 21 day treatment of doxycycline for a lyme disease diagnosis. This morning was his last dose. He developed the EM rash 6, possibly 8 weeks before going to the doctor. He has pain in his back that seems to move around a bit. It’s intermittent and he can’t actually desribe what it feels like. He has terrible anxiety, so much that he went to the er this weekend because he was convinced there was a tumor growing in his body. A ct scan didn’t present anything of the like. He remains in a constant state of Malaise.
I look for other causes during and after treatment. I also typically use other antibiotic treatment regimen if the symptoms remain.
I had lymes disease as a toddler. I was never treated for it.
I am now 21 years old. I experienced hair thinning/ loss, fever, neck pain on the left side, and extreme fatigue. I went to my doctor and she told me I had a new infection of Lymes Disease. I took Doxy twice a day for 3 weeks straight. It is now 2 months post-treatment, I am back to feeling extremely fatigued, my hair is still falling out, and the pain on the left side of my neck still persists. Do you advise further treatment?
I have patients who benefit from treatment. Some doctors disagree. Only one of three NIH sponsored Lyme disease trials showed benefits of retreatment. I have seen patients with a new infection who also had an unresolved previous infection.
Hello , I’ve been misdiagnosed for 2 years . Now have neuropathy, vertigo. The Dr gave me 2 rounds of doxy. Felt little better. He says it’s dead after 10 days and refused to believe I feel bad still . Its post Lyme treatment syndrome. I finally got appointment with neurologist but it’s 5 months away and the neurological issues are worse. I asked for one more round of doxy to get through but they refuse. They say all in my head . They say I can’t be tested again bc I’ll show positive for next 5 years bc of antibodies. Please help me anyway possible to give me hope. Thank you and God bless
A positive test supports the diagnosis of Lyme disease. A positive test for Lyme disease after Lyme disease does not mean the infection is over. You many consider consulting a doctor experienced in treating chronic manifestations of Lyme disease.