By Dr. Kyle Warren
Edited by Meghan

How high is the risk of developing chronic Lyme disease, and are doctors missing Lyme as the cause of your symptoms? Have you had acute Lyme disease and were treated for it, but you continued having or developing symptoms?

We’re going to walk through a March 2022 study conducted by the Johns Hopkins Lyme Disease Research Center that highlights how many people may be slipping through the cracks of the medical system and developing chronic Lyme or post-treatment Lyme disease syndrome (PTLDS). 

Are doctors missing Lyme as the cause of your symptoms?

Why the standard CDC protocol for Lyme disease isn’t always enough

The Johns Hopkins study we’re taking a look at today titled “Risk of post-treatment Lyme disease in patients with early diagnosed and promptly treated Lyme disease: A prospective cohort study” should have a great impact on the way doctors and patients approach Lyme disease.

As mentioned in the study, “This is the largest peer-reviewed prospective controlled study in the US that specifically focuses on the longer-term outcomes of early diagnosed and promptly treated Lyme disease patients.”

This study shows that even if a patient catches a Borrelia burgdorferi (Lyme disease) infection immediately and is put on the standard CDC-recommended antibiotics promptly, those patients are still at risk for developing ongoing symptoms and infection. 

This raises many questions, including what the risk percentage may be for people who are not diagnosed right away. 

Are doctors missing Lyme as the cause of your symptoms?

Lyme patients often have a frustrating journey

There is no doubt the diagnosing and treatment journeys of most Lyme patients are frustrating. Patients often try to seek answers for years and even decades before they are properly diagnosed. Unfortunately, many patients never get a proper diagnosis, only get treated for symptoms, or are misdiagnosed as having another disease. 

For these reasons and many others, we are incredibly thankful for the research Johns Hopkins, Columbia, and other institutions are doing to help shed light on the inner workings of Lyme disease and its co-infections. When notable institutions dismantle long-held, false beliefs about a disease like Lyme, they can help change and improve how doctors diagnose and treat patients in the future. It may take years longer, but it’s a step in the right direction. 

This research can help wake up the rest of the medical community in realizing how big of an issue Lyme disease and co-infections are and how often they are an underlying cause of major problems.  

That being said, let’s dive into this study in greater detail. 

Study highlights risk of PTLDS: Still nearly 10% even with ideal, prompt treatment

The study setting

In this particular Johns Hopkins study, they were using 234 patients who had acute Lyme disease, presented the classic erythema migrans rash, had no other specific co-morbidities, and were given the standard acute Lyme antibiotic protocol (meaning, they found the infection right away and treated it within the first 3 months of getting the infection). 

The researchers then monitored all 234 patients over the next 6-12 months following their initial diagnosis and treatment to see who, if any of them, developed chronic symptoms or still had chronic symptoms after being treated with the appropriate CDC-recommended treatment protocol. 

The study results: Standard protocol not nearly as effective as previously claimed

It has been said for years that the CDC-recommended treatment protocol is about 99% successful for those with acute Lyme disease. 

However, the results of this study showed that the standard protocol is not nearly as effective as previously claimed by the medical community.

Results showed that functionally impairing persistent symptoms occurred in 10-14% of the early treated Lyme disease patients. Once again, this means 10-14% of people who found the bug on them, caught the infection, and got on antibiotics right away still developed long-term symptoms. 

The most common of these long-term symptoms included severe fatigue, body pain, and cognitive challenges.

Patients with persisting symptoms fall through the cracks

When the standard protocol has already been administered, what do patients do and where do they go for help if symptoms persist or develop later? 

Unfortunately, most doctors tell them their Lyme infection should no longer be active. These patients then get sent down the rabbit hole with referrals to pain clinics, neurologists, rheumatologists, psychologists, dermatologists, and other specialists. They often get placed on medications that can only partially mask the symptoms, if at all. And they’re left with more questions than when they first got Lyme disease.

People are frequently falling through the cracks of the medical system, suffering and left without answers. 

All doctors, particularly neurologists and rheumatologists, need to be extremely aware that they could often be getting patients sent to them who really have Lyme disease (that either has been totally missed and no one’s found it, or they treated it and the treatment didn’t work). Unfortunately, I do not see neurologists and rheumatologists stepping up to the plate and recognizing that this is a problem. 

Are doctors missing Lyme as the cause of your symptoms?

Lyme disease: The ongoing battle for your health

The researchers also noted in this study that the battle for those with Lyme is often significant. They indicate symptoms were not just mild fatigue and the pain of everyday living. Rather these patients were dealing with severe fatigue and pain that dramatically impacted their quality of life. 

This is what Lyme patients, like you, are battling on a regular basis. 

When Lyme enters into a chronic state, it usually isn’t as life-threatening as it can be in the acute stage. However, it causes ongoing, severe symptoms that can make life almost unbearable for some. It affects the lives of everyone dealing with it. It affects marriages and other relationships, work life and productivity, sleep and relaxation, mental health, and every other aspect of one’s life and everyday activities.

If a patient is experiencing major fatigue, pain and/or neurological problems that are impacting their lives, Lyme disease should be looked into (with thorough testing) as a possible and probable cause. 

How High is the Risk of Developing Chronic Lyme Disease?

Lyme disease: A growing public health concern

While Lyme disease and co-infections are just a few of the many possible causes for these symptoms and many others, their prevalence is growing and they are already a huge cause of symptoms in diagnosed and undiagnosed people. 

As the study notes, “With 476,000 new cases annually in the US, the ‘long haul’ impact of Lyme disease is clearly a substantial public health concern.”

Remember: At least 10-14 percent of people who received treatment are still slipping through the cracks, so we can assume the percentage of people who are undiagnosed is exasperatingly greater. 

They noted that their study undoubtedly underestimates the accurate rate of those with persistent symptoms “since this study of early diagnosed and treated patients does not account for the substantial number of misdiagnosed and delayed diagnosed cases experienced in a non-study setting where prolonged illness risk would be expected to be greater.”

Many of my patients have come to our clinic after having Lyme for years. Their battle was exhausting and devastating and it took them years of research and jumping from one doctor or specialist to another to get an accurate diagnosis. 

They are part of the group of patients who didn’t catch Lyme disease early. Their persistent symptoms cannot be ignored, but they are a much harder group to do studies on accurately because they often don’t know when they first were infected.  

Additional study findings on Lyme disease

Along with conducting their research on the fail rates of treating acute Lyme, the researchers also discovered additional information that can better help us understand those with a greater risk of developing chronic Lyme disease.

  • Participants with prior Lyme disease were approximately 5 times as likely to meet symptom and functional impact criteria for post-treatment Lyme disease compared to those without prior Lyme disease. 
  • They also had higher joint pain, memory problems and depression and 2-3 times as high odds of reporting moderate or severe fatigue and muscle pain. 
  • Results were highly statistically significant and indicate symptoms were not just the mild fatigue and pain of everyday living but rather severe fatigue and pain that impacted the quality of life.
  • Females were 4 times as likely as males to meet post-treatment Lyme disease criteria than return to health criteria. 
  • For each increase in a potentially traumatic life event, the risk of meeting post-treatment Lyme disease criteria increased by 30%. 
  • More research is needed to determine if female sex and/or increased exposure to traumatic life events impact the initial biologic response to Borrelia burgdorferi infection and increase the risk for persistent symptoms.

Dr. Warren’s Thoughts on the study

In my opinion, this study did a great job highlighting that the current CDC treatments for Lyme are not adequate in many cases. Also, what they recommend is similar to the approach we take in our clinic. 

Johns Hopkins has been highlighting for years that the standard approach isn’t enough, and I think it’s the correct approach. 

In their own words, “More research is needed to determine if there are common mechanisms of inflammation and immune response dysregulation, autonomic nervous system dysfunction, or pathogenic or antigen persistence.”

Immune system support for inflammation

In order to best go after Lyme they want more research done on patients’ immune systems. 

Whenever inflammation is present, it’s important to look at immune system function. A healthy immune system should have been able to kill the initial infection, especially with the help of antibiotics. When the help hasn’t been enough, it’s important to look at how the immune system is functioning and how the immune system can be best supported. 

Nervous system dysregulation

They also mention that it’s important to look at nervous system dysregulation playing a part. I will extend that and say every system in the body should be assessed. Whatever area of the body has been hurt by Lyme disease needs to be repaired.

This is frequently the nervous system but it also frequently affects joints, muscles, mitochondria, the heart, and the liver. All the areas of your body that have been damaged by Lyme disease need support and time to repair.  

Pathogen and antigen persistence 

Lastly, they bring up that other pathogens and antigens can persist and wreak havoc on the body as well, making it much harder to get rid of the Lyme infection. 

In our clinic, we would call these Lyme co-infections. In other articles, we discuss these. 

It’s not just about killing the initial log phase of Lyme (learn more about the phases of Lyme in this article). Once Lyme enters these different forms, whether it’s in a spirochete and log form or a  cyst and stationary form, we find that the later forms of Lyme are much more antibiotic-resistant, can cause more severe symptoms, and respond better to other substances.

To watch the accompanying video, click below.

“How High is the Risk of Developing Chronic Lyme Disease?” Summary

As this study clearly indicated, ongoing problems from Lyme disease are much more common than previously thought. 

In this article, we also highlighted these Johns Hopkins findings:

  • Thinking that treating acute Lyme is as simple as taking a round of doxycycline and that it works for everyone is flawed. The current CDC treatments for Lyme are not adequate in many cases.
  • Patients with persisting symptoms are getting brushed aside, and this is a huge problem.
  • Even in the best of circumstances, it works 86-90% of the time.
  • Many other factors can put a person at a higher risk of developing PTLDS/ chronic Lyme disease and co-infections.
  • In order to handle chronic Lyme the best, you must take a look at inflammation, support the immune system, rehab the body, and address persisting forms of Lyme disease and co-infections. 

We’re thankful for the research being done at institutions Johns Hopkins as they illustrate how big of a problem Lyme disease is and how much more research is needed.


John N. Aucott MD1, Ting Yang PhD1, Isaac Yoon MD2, Debra Powell MD3, Steven A. Geller MD4, Alison W. Rebman MPH1. Risk of post-treatment Lyme disease in patients with ideally-treated early Lyme disease: A prospective cohort study. International Journal of Infectious Diseases, Volume 116, 230 – 237. doi:

Free Consultation
close slider
  • Please provide your contact information and we will contact you to schedule your free consultation.
  • Restorative Health Solutions
    7701 York Ave S #230
    Edina, Minnesota 55435
  • This field is for validation purposes and should be left unchanged.