By Dr. Kyle Warren
Edited by Meghan Feir Walker
Lyme disease: The great mimicker. The presentation of Lyme symptoms is often assumed to be autoimmune by doctors. However, Lyme has a talent for wreaking havoc in different areas of the body and merely appears to be an autoimmune disease, such as rheumatoid arthritis, lupus, IBS, or Hashimoto's. In this article, we'll be running through the similarities and differences between Lyme disease and autoimmune conditions, how Lyme disease can turn on or exacerbate preexisting autoimmune diseases, and why your doctors so frequently miss Lyme.
The Difference Between Lyme Disease and Autoimmune Disease
Many symptoms of Lyme overlap with the symptoms of autoimmune conditions. However, Lyme can also make preexisting autoimmune conditions worse or encourage your body to develop new autoimmune conditions thanks to its ongoing, massive attack on the immune system.
It's common for doctors to assume patients are suffering from an autoimmune condition when they are actually suffering from Lyme. And if the patient has an autoimmune condition, it's common for a Lyme infection to be missed.
Some of the most common autoimmune diseases that relate to Lyme symptoms include:
- Rheumatoid arthritis
- Lupus/SLE
- Multiple sclerosis
- Inflammatory bowel disease
- Celiac disease
- Sjogren’s syndrome
- Hashimoto’s disease (affecting the thyroid gland)
- Ulcerative colitis
When doctors run tests to see if their assumptions are correct, they're often extremely perplexed if the tests come back negative.
Why your rheumatologist misses Lyme disease arthritis
Have you seen a rheumatologist and been told you don’t have rheumatoid arthritis, lupus, or other pain-causing autoimmune conditions? Have you been left in the lurch without answers as to what could be the source of your pain? In this article, we’ll go over why your rheumatologist misses Lyme disease as a potential cause of your arthritis.
To watch the accompanying video, click here.
Before coming to our clinic, many of our patients have visited several doctors and specialists.
One of our patients—we’ll call her Leslie—recently said how frustrated she was with the process she had to go through before seeing us, specifically when she went to a rheumatologist.
After bouncing around the medical system for several months, she found herself in the rheumatology department to discuss her arthritic pain. The rheumatologist refused to admit Lyme disease could be a possibility.
Those suffering from Lyme disease usually relate to Leslie’s story. They are often sent to infectious disease doctors, neurologists, psychologists, cardiologists, etc., but today we’re going to focus on why rheumatologists miss Lyme disease.
Out of all the specialized areas, I would venture to guess that rheumatology departments have the most undiagnosed Lyme patients walking through their doors.
Borrelia burgdorferi and other species of Lyme disease can cause an avalanche of chronic pain issues, inflammation, and arthritis; thus, Lyme sufferers are often sent to rheumatologists. Unfortunately, they’re left without answers and are only given pain meds to dull the symptoms.
Why are rheumatologists missing Lyme disease? They shouldn’t be, especially since the CDC clearly lists Lyme arthritis as a commonly associated problem caused by Lyme disease.

How the CDC clearly showcases Lyme arthritis
On the CDC’s webpage on Lyme disease, there is a treatment section.

In the main body copy and as a sub-section on the left menu, “Lyme arthritis” is called out twice.

The CDC states, “Lyme arthritis occurs when Lyme disease bacteria enter joint tissue and cause inflammation. If left untreated, permanent damage to the joint can occur. Lyme arthritis accounts for approximately one out of every four Lyme disease cases reported to CDC.”
Under symptoms reported, they go on to mention obvious swelling of one or more joints.
“While the knees are affected most often, other large joints such as the shoulder, ankle, elbow, jaw, wrist, and hip can also be involved. The joint may feel warm to the touch or cause pain during movement. Joint swelling can come and go or move between joints, and it may be difficult to detect in the shoulder, hip, or jaw. Lyme arthritis typically develops within one to a few months after infection.”
Lyme was first discovered because of the arthritis it was causing in patients. This was long before anyone realized the various neurological problems Lyme bacteria can also cause.
Considering Lyme was first discovered in 1975, shouldn’t it be on the radar of rheumatologists by now?

Lyme diagnosis and treatment, according to the CDC
According to the CDC, if someone is diagnosed with Lyme after getting a positive test result, doctors are supposed to administer 100 milligrams of doxycycline twice a day. If the rash is present, they should administer doxy for 10 to 14 days. However, when your brain is involved, they recommend a longer course of three weeks, and if your joints are involved, the CDC recommends a 28-day treatment duration.
Unfortunately, if this extended round of doxy doesn’t work, doctors will just start giving you other meds to help manage your symptoms, even though the infection hasn’t been eradicated. They'll give you pain meds and prednisone shots and send you to physical therapy or pain management.
Do I like this approach? No, but it’s what they do. Many Lyme patients are missed because they don't follow the standard expectation of how doctors think Lyme should behave. But right now, it's still what your doctor is told to follow. Remember, your doctor can't get in trouble for following the standard protocol, even if it is outdated and doesn't always work.
Arthritis and no positive rheumatoid arthritis or lupus test?
Get tested for tick-borne illnesses
Women are much more likely than men to develop rheumatoid arthritis, lupus, and other autoimmune conditions in general. The odds of you discovering any of these autoimmune diseases at a rheumatology appointment are statistically higher if you are a female. Men can develop these conditions, but it’s much less likely.

Both men and women can easily get Lyme and co-infections, and it’s extremely common for those with Lyme to experience arthritis.
According to Dr. Daniel Cameron, 60% of people with untreated Lyme disease may have arthritis and severe joint pain and swelling, and 40% of Lyme patients end up with long-term health problems.
If you’re experiencing signs of arthritis and a rheumatologist can’t show you a positive test for lupus or rheumatoid arthritis, getting checked for different species of Lyme bacteria and co-infections is imperative.
We're particularly concerned about Lyme being an issue if this pain developed quickly. That screams “infection.”

Sharing the knowledge: Researchers present at rheumatology conference
Rheumatologists need to know about Lyme disease and tick-borne illnesses, and they have to start testing for it. That’s why I was so glad when I heard about this presentation at a recent rheumatology conference.
In “ACR 2021: What Rheumatologists Need to Know About Lyme Disease and Tick-Borne Illnesses” from Rheumatology Advisor, it mentions a scientific session was presented titled “Lyme Disease & Other Tick-Borne Illnesses: What Every Rheumatologist Must Know.”
One of the presenters was Dr. John Aucott of Johns Hopkins University School of Medicine. For years, Dr. Aucott has been advocating for Lyme patients. In this presentation, he and other presenters discussed the prevalence of Lyme patients ending up in rheumatology departments.
This is exactly what needs to be done. Researchers and doctors who know the reality and prevalence of Lyme need to keep sharing their findings with other medical professionals.
Don’t worry about false positives; worry about false negatives
The same article from Rheumatology Advisor went on to explain how Lyme disease is tested.
“Diagnosis of Lyme disease uses 2-tiered testing that includes enzyme-linked immunoassay (ELISA) screening followed by Western blot testing… The sensitivity of 2-tiered testing for late Lyme disease arthritis is very high (97%). Polymerase chain reaction (PCR) testing of synovial fluid for the presence of B burgdorferi is also highly sensitive, but current guidelines only recommend this if needed for treatment decisions.”
The 2-tiered testing they mention is a testing protocol from the mid-90s. While ‘90s fashion came back for a time, this test should go out of style. It’s completely outdated, and there are much better tests available now.
That being said, it has great sensitivity for indicating the presence of Lyme disease arthritis. Some people say it’s too sensitive a testing method. Why are they leery of a highly sensitive test? They wonder if they can trust positive results or if there are “false positives.”
From what I’ve seen, there are very few false positives. The main problem when testing Lyme is the opposite, where you get far too many false negatives. Inaccurate tests give doctors and patients a false sense of security, causing everyone to rule out Lyme when it could be the culprit all along.
Because of this, you need to run tests on multiple species of Lyme, not just one, which is why I don't think these tests are worthwhile.
For example, if you are positive on the screener test, but you don’t meet all the criteria for the follow-up Western blot test, doctors will say you don’t have Lyme. However, I think it’s Lyme until proven otherwise when doctors don’t have a better explanation.
Doctors run these inaccurate tests, and if it doesn’t show up 100% positive for Lyme, they drop it and prescribe you some pain meds. That’s just lazy doctoring.
Doctors are supposed to take your test results, look at your history and symptoms, and come up with the most likely scenario.
I don’t think the basic course of oral doxycycline is enough after you’ve had it for longer than a month, but most people aren’t even getting the bare minimum for treatment.
Tulane study highlights the ineffectiveness of single antibiotics after 28 days
In December 2023, a study called “Combined antibiotics more effective against Lyme disease” was conducted at Tulane University.
The article highlights that a combination of antibiotics is more effective in treating Lyme disease than a single antibiotic. Research shows that chronic Lyme can develop when treatment is delayed or insufficient, especially with short courses of oral antibiotics. The study found that no single antibiotic completely eradicates the infection after 28 days, meaning that if treatment is delayed even by a couple of months, the chances of failure are high. Tulane's research emphasizes that if you're going to go the antibiotic route, multiple antibiotics are necessary to eliminate the infection once it becomes chronic. However, I wish they had included herbs in their study, which are even more effective than antibiotics once Lyme has entered its chronic state!
Fighting for the truth
When the doctor told Leslie there was no chance she was dealing with Lyme disease based on the testing (even though the screener test was positive and there were mixed messages on the follow-up blot test), she didn’t buy into it. All the rheumatoid arthritis tests were negative, yet she had a long list of symptoms.
She had arthritis pain in her knees, she lives in Minnesota, and she started getting these symptoms in the middle of the summer after a camping trip! How much more likely for Lyme can you get!?
Leslie went home extremely frustrated with the rheumatologist and quickly found research articles that backed up her case. She eventually went back and told the rheumatologist, “You can't tell me it's 100% certain that Lyme isn’t a possibility.”
Sure enough, she was right.
Leslie had gone to countless specialists who had no idea what was wrong with her, yet we were able to test and quickly ascertain the cause of her arthritis and other troubling symptoms.
Patients like Leslie—like you—should be able to have confidence in their doctors. They should be able to know their doctors are fighting for them. But patients don’t have this confidence, and for good reasons.
Too often, doctors will claim “It's not Lyme,” but they're not well educated on all the holes in testing, the most recent research, and the conditions and symptoms Lyme can mimic and produce. They don’t offer better testing or more plausible explanations, yet they stand firm in that it’s “not Lyme.” This is foolish and unhelpful and forces many patients to fend for themselves.
It's one thing if your rheumatoid arthritis tests are positive. Then it's rheumatoid arthritis. However, when you have test after test saying it’s not this, it’s not that, you have to assess the situation. What's the most probable cause?
There is always a reason for your symptoms.

Lyme cases continue to increase
In the aforementioned rheumatology article, they note that untreated Lyme disease arthritis can continue showing up months or years after the onset of the infection.
They also highlight that there are 450,000-500,000 new estimated Lyme cases per year and that “The incidence of Lyme disease and its distribution in the US and Canada are increasing.”
With a 10-20% fail rate, 50-100,000 Americans aren’t getting help for their Lyme disease from the medical system and are ping-ponging from one uninformed specialist to the next. They aren’t getting solutions or accurate explanations for their symptoms. That’s a ridiculously high number of people left to fend for themselves, and it’s unacceptable.
In Minnesota alone, around 10,000 Lyme patients are falling through the cracks of the medical system every year. It’s a major problem, and I think rheumatologists are seeing Lyme sufferers routinely.
If you ask a rheumatologist how many times they diagnosed a patient with Lyme in the last year, the answer should never be zero. There are a certain number of people who are walking in with what looks like rheumatoid arthritis, and it may be Lyme disease. But this is being missed and contributing to people’s prolonged suffering.

What can you do if you have Lyme?
If you suspect or know you have Lyme disease and you were unable to catch it early enough for doxycycline to eradicate the infection, don’t fear; you can still recover from Lyme disease and other tick-borne illnesses.
While taking multiple antibiotics simultaneously can work to fight Lyme, it’s hard on the body, particularly when you have to take multiple antibiotics for long periods.
Patients who come to our clinic have often already tried using multiple antibiotics to kill Lyme, and it failed. This is one of the reasons why I prefer to take a more holistic road to recovery, where we use herbals and nutraceuticals to support the body as we kill harmful pathogens. It’s easier on your body, more supportive for your immune system and other organs, produces far fewer Herxheimer reactions, and has a much lower rate of infection reoccurrence compared to the multiple-antibiotics route. We have more video and article resources that touch on this topic.
Lyme gets missed on so many levels. It gets missed by countless neurologists, psychologists, cardiologists, and rheumatologists in particular.
Specialists encounter Lyme disease patients frequently, yet they rarely look into tick-borne illnesses as a potential cause of a patient’s distress, even when they can’t figure out what’s causing their problems. Lyme mimics many conditions, including rheumatoid arthritis, lupus, and other autoimmune conditions, so specialists must start checking for Lyme and other tick-borne illnesses with modern, thorough testing.
Please, doctors and patients, be Lyme aware.
Watch the video and follow RHS
To view the accompanying video on this topic, click here.

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Summary
- Borrelia burgdorferi and other species of Lyme disease can cause an avalanche of chronic pain issues, inflammation, and arthritis; thus, Lyme sufferers are often sent to rheumatologists.
- Lyme mimics many conditions, including rheumatoid arthritis, lupus, and other autoimmune conditions.
- The CDC clearly lists Lyme arthritis as a commonly associated problem caused by Lyme disease.
- The CDC states, “Lyme arthritis occurs when Lyme disease bacteria enter joint tissue and cause inflammation. If left untreated, permanent damage to the joint can occur. Lyme arthritis accounts for approximately one out of every four Lyme disease cases reported to CDC.”
- The CDC also says that while knees are affected the most frequently, “other large joints such as the shoulder, ankle, elbow, jaw, wrist, and hip can also be involved. The joint may feel warm to the touch or cause pain during movement. Joint swelling can come and go or move between joints, and it may be difficult to detect in the shoulder, hip, or jaw. Lyme arthritis typically develops within one to a few months after infection.”
- Lyme was first discovered because of the arthritis it was causing in patients.
- Women are much more likely than men to develop rheumatoid arthritis, lupus, and other autoimmune conditions in general.
- According to Dr. Daniel Cameron, 60% of people with untreated Lyme disease may have arthritis and severe joint pain and swelling, and 40% of Lyme patients end up with long-term health problems.
- If you’re experiencing signs of arthritis and a rheumatologist can’t show you a positive test for lupus or rheumatoid arthritis, getting checked for different species of Lyme bacteria and co-infections is imperative.
Questions to ask yourself
- Are you in a Lyme-endemic state, like Minnesota or Wisconsin?
- Did you start experiencing relatively quick symptoms of arthritis?
- Are tests negative for rheumatoid arthritis and lupus?
- If the extended round of doxycycline doesn’t work, doctors will just start giving you other meds to help manage your symptoms, even though the infection hasn’t been eradicated.
- Researchers recently presented the case for Lyme disease at a recent rheumatology conference.
- The 2-tiered testing method they mention in the article is outdated. There are much better tests available now that should be used.
- Don’t worry about false positives, even with sensitive testing methods. Worry about false negatives. Those are much more prevalent and give doctors and patients false reassurance that tick-borne disease isn’t the issue.
- Many doctors aren’t well educated on all the holes in testing, the most recent research, and the conditions and symptoms Lyme can mimic and produce.
- If a doctor doesn’t offer better testing or more plausible explanations, yet they stand firm in that it’s “not Lyme,” it’s foolish and unhelpful and forces many patients to fend for themselves.
- If your rheumatoid arthritis tests are positive, it's rheumatoid arthritis. However, when you have test after test saying it’s not RA or lupus, what’s the most probable cause? (Hint: Many diagnosed with “seronegative RA” or “undifferentiated connective tissue disease” actually have Lyme!
- Tulane researchers note that untreated Lyme disease arthritis can continue showing up months or years after the onset of the infection.
400,000-500,000 new Lyme cases per year
- They also highlight the 450,000-500,000 new estimated Lyme cases per year and that “The incidence of Lyme disease and its distribution in the US and Canada are increasing.”
- With a 10-20% fail rate, 50-100,000 Americans aren’t getting help for their Lyme disease from the medical system and are ping-ponging from one uneducated specialist to the next. They aren’t getting solutions or accurate explanations for their symptoms.
- Lyme gets missed by countless specialists: neurologists, psychologists, cardiologists, and rheumatologists in particular. Specialists encounter Lyme disease patients frequently, yet they rarely look into tick-borne illnesses as a potential cause of a patient’s distress, even when they can’t figure out what’s causing their problems.
- Specialists must start checking for Lyme and other tick-borne illnesses.
- If you have Lyme or suspect you do, don’t lose hope. You can get better and live your life to the fullest!
- My patients have often already tried using multiple antibiotics to kill Lyme, but it failed. This is one of the reasons why I prefer to take a more holistic road to recovery, where we use herbals and nutraceuticals to support the body as we kill harmful pathogens.

