Comprehensive Guide Chronic Lyme Disease and Co-infections in Minnesota: Evidence-Based Protocols

Dr. Kyle Warren, Functional Medicine
Many of Dr. Warren's patients come to him after years of chronic Lyme disease treatment that didn't work — including care at some of the top medical centers in the country. Roughly one-third sought answers at prestigious facilities nationwide before finding a more thorough, root-cause approach.

Dr. Kyle Warren, DC, CFMP is a Lyme disease specialist based in Minnesota who treats patients virtually across the United States. With over 15 years of clinical experience and thousands of patients treated, his functional medicine background means he looks deeper — using advanced diagnostic testing across 18 known Lyme species and over 30 tick-borne infections to uncover what standard testing misses. Treatment protocols are individualized, evidence-based, and built around herbal and nutritional therapies that are easier on the body and designed to address Lyme disease and its co-infections together.

Patients report lasting improvement with virtually none* experiencing relapse — even in complex cases where previous treatment failed to provide answers.
*Individual results vary

Dr. Warren offers virtual consultations via phone or Zoom to patients across
The United States. An in-person visit is not necessary to begin testing or treatment.

Video: Why Patients Choose Dr. Warren for Lyme Disease Treatment: Success Stories and Testimonials

Watch Patient Stories - Click here 

Request Free Consultation: If you've tested "Negative" for Lyme, but still show clinical symptoms of Lyme, please get a SECOND OPINION. 

It is possible your Lyme testing was incomplete (Did the doctors check just one species of Lyme (Borrelia Burgdorferi typically) or did they check multiple species like Borrelia Mayonii, Borrelia Spielmanii, Borellia Garinii, Borrelia Afzelii, Borrelia Hermsii?).  When you get bit by a tick it is also possible you may have contracted additional co-infections - Bartonella, Babesia, Anaplasma, Ehrilichia and more. Many Lyme Doctors are uninformed or improperly test for co-infections.

Click the button below and Request Free Consultation. Virtual consultation available. Now accepting patients from all of USA

Why Chronic Lyme Disease Treatment Often Fails

Most chronic Lyme patients have been through multiple rounds of treatment before finding Dr. Warren — and after seeing and treating thousands of Lyme patients Dr. Warren explains top 5 gaps and reasons why chronic lyme treatments fail.

The most common issue is incomplete testing. Standard labs test for a single species of Borrelia, but at least 18 species are known to cause Lyme disease. Roughly one-third of Dr. Warren's patients have a species that standard testing doesn't detect, which means the infection was missed entirely despite testing.

The second major gap is unidentified co-infections. Published research shows that 93% (the vast majority) of chronic Lyme patients also carry additional tick-borne infections — Babesia, Bartonella, Anaplasma, and others — each requiring different treatment. When only Lyme is addressed, only part of the problem is being treated. This is the single most common gap in care and driver of treatment failure in Dr. Warren's clinical experience.

Third, biofilm formation plays a critical role that is rarely addressed. Within months of infection, Lyme bacteria can build protective structures that make them dramatically more resistant to standard antimicrobial treatment. What further complicates this is the fact that standard antibiotics are not particularly effective in penetrating biofilms. This explains a pattern seen frequently in chronic Lyme cases — improvement during active treatment followed by relapse once treatment stops. 

Fourth, most treatment protocols focus exclusively on killing the infection without ever supporting the immune system. No antimicrobial eliminates lyme 100%. Most reduce the bacterial load in our system. A healthy immune system is needed to finish the job. In chronic cases, immune function is often too compromised to complete the healing process — creating a cycle of partial recovery and relapse.

Finally, many patients receive a generic, one-size-fits-all protocol with no retesting or monitoring. Without ongoing evaluation, there is no way to determine whether infections are resolving, whether protocols need adjusting, or whether additional issues have emerged. Treatment without data is treatment without direction.

Dr. Warren's approach addresses all five of these gaps: Dr. Warren built his approach specifically to close these five gaps. Every patient receives comprehensive testing across all 18 known Lyme species and over 30 tick-borne infections — not just the standard panel. Protocols are individualized and evidence-based, using targeted herbal and nutritional therapies designed to penetrate biofilms and support immune recovery from the start. And unlike most treatment plans, progress is tracked through regular retesting so protocols can be adjusted based on what's actually working.
It's a fundamentally different approach — and it's why patients report lasting improvement with very few experiencing relapse, even in complex cases where previous treatment failed to provide answers.
Dr. Warren treats patients virtually across the United States via phone or Zoom. No in-person visit is needed to begin testing or treatment.

Chronic Lyme patients are some of the most informed, dedicated patients in medicine. They research, they advocate, they follow protocols carefully — and many are still sick. In our experience treating over 2,000 complex cases, the issue isn't effort or commitment. It's that the foundational assumptions guiding their care were incomplete from the start. 

 Here are some of the most common things chronic Lyme patients are told, what they come to believe, and what the research and our clinical outcomes actually show.

Lyme Testing

What you think: "My Lyme test came back negative — I don't have Lyme"

The reality: Standard testing checks for only 1 of 18+ known Lyme species. About a third of Dr. Warren's patients have a species that standard tests completely miss. One patient tested negative everywhere — then lit up positive for Borrelia bavariensis, a species most doctors don't even look for. A negative test doesn't mean you're negative — it may mean you weren't tested for the right thing.

Co-Infections

What you think: "I just need to treat the Lyme and I'll get better"

The reality: 93% of chronic Lyme patients have co-infections — Babesia, Bartonella, Anaplasma — and each requires a completely different treatment. One tick bite can transmit multiple infections simultaneously, creating thousands of possible combinations. It could be as simple as a single missed co-infection holding you back from 100%. If your doctor only tested for Lyme, they missed the bigger picture.

Antibiotic Treatment

What you think: "Antibiotics will cure my Lyme disease"

The reality: Antibiotics actually increase dormant Lyme forms by 270% — creating super-survivors hiding behind biofilm fortresses that are 1,000x more resistant. After 4 years of tracking outcomes, Dr. Warren found patients on antibiotics weren't getting better faster, had more side effects, and relapsed at dramatically higher rates. As Columbia University researchers noted: "We all know antibiotics never kill 100% of the infection." Your immune system has to finish the job.

Herbal Protocols

What you think:  "I tried herbs and they didn't work — herbs don't help Lyme"

The reality: The herbs didn't fail you — the strategy failed you. Johns Hopkins research proved certain herbs break through Lyme biofilms better than any antibiotic. But generic protocols from books or the internet aren't personalized to YOUR infections. Wrong infections targeted, no body preparation, conservative dosing, low-quality products, no retesting, no biofilm strategy — fix those gaps, and the same herbs that "didn't work" start working. That's the difference between a failed protocol and Dr. Warren's 85% success rate.

The Immune System

What you think: "If I just kill the bacteria, I'll be cured"

The reality: Antibiotics and herbs don't kill 100% of the bugs — they shrink the infections. Your immune system has to hold the line and finish the job. That's why no one takes antibiotics forever. But Lyme and co-infections attack different parts of your immune system, and long-term antibiotics further weaken it — wiping out gut bacteria and depleting white blood cells. Dr. Warren rebuilds your immune system while treating the infection, so your body can maintain control long-term. That's how you finish.

Herx Reactions

What you think: "Feeling terrible during treatment means it's working"

The reality: Severe Herx reactions often mean your body can't clear the toxins from dying bacteria fast enough. Most practitioners let patients "tough it out." Dr. Warren takes the opposite approach — by supporting drainage and detox pathways first, he's eliminated 80% of Herx reactions in his patients. Treatment shouldn't be a war of attrition. If you're herxing too hard, it's not a badge of honor — it's a sign your protocol needs adjustment.

Symptom Management

What you think: "I feel partially better — the treatment is working"

The reality: Partial improvement often means you killed something — but not everything. Without retesting, you're celebrating a battle while losing the war. Many patients accept 60% functionality because they've forgotten what 100% feels like. Are you measuring success by "I can get out of bed" instead of "I can live my life"? The goal isn't managing Lyme — it's finishing with Lyme. If what you're doing isn't making you consistently better, why continue it?

Treatment Approach

What you think:  "I need to treat everything at once — Lyme, gut, mold, adrenals..."

The reality: This "spray and pray" approach is too much and often unnecessary! The right approach involves properly focusing on not just Lyme, but also any co-infections. The shift happens when alongside targeting the infections there is also a focus on supporting and strengthening the immune system.

VIDEO: Breaking the Cycle of Recurrent Stubborn Lyme

Click here to watch Dr. Warren's latest video revealing why Lyme symptoms persist for some patients and effective strategies to prevent recurrence.

2025 update:  Advances in Specialized Lyme Testing 

Click here to check out the latest video from Dr. Warren, where he shares actual test results from several of his patients and gives examples of how to pick the right Specialized Lyme test for you!

Watch Patient Stories - Click here 

Why do Dr. Kyle and Dr. Paul have such good results with their patients?

This platform will help you understand if your mysterious symptoms or health issues could be from Lyme disease or co-infections related to Lyme. You will also learn about Chronic Lyme, proper and complete testing for Lyme and Lyme co-infections, and what makes the "Restorative Health Solutions Protocol" THE BEST approach for Lyme!
click below!
• How do I know for sure I have Lyme? 
Depending on your clinical symptoms, there are specific tests conducted in specific sequence that can help us assess accurately whether or not you have Lyme disease. Also, there are steps we take to avoid inaccurate test results, referred to as "false negatives." Dr. Kyle explains all of this in his video on Lyme testing.

Click here to watch the video!

• I got tested for Lyme but results came back Negative. Could I still have Lyme? 
This is a question Dr. Kyle gets asked almost every day; the short answer is YES! The long answer is, it depends if you were tested properly and if those tests were complete. Did your doctor only run the ELISA test or the Blot test? Did you get tested for co-infections? Dr. Kyle answers questions on Lyme testing in a series of videos.


• Could a Lyme test be run differently between one doctor's office and another?
Yes, this happens all the time! Most major Lyme organizations, such as the CDC (Centers for Disease control and Prevention) and the IDSA (Infectious Disease Society of America), differ in their recommendations on how to test for Lyme! The biggest risk for a patient is to work with a doctor who does not understand these issues and runs incomplete testing for Lyme, and then tells that patient they don't have Lyme disease when, in fact they do. Dr. Kyle has seen this many times in his practice! 



Dr. Kyle Warren,
DC, CFMP
(Functional Medicine, Doctor of Chiropractic)
specializes in Functional Medicine, putting together the big picture of a person’s health. His specialties include Chronic Lyme, Lyme testing, Lyme co-infections, Immune and Environmental Toxicity.

Challenges patients face when it comes to Lyme disease.

click below!
• Are Lyme co-infections common in Minnesota?  
In Minnesota, Lyme co-infections are very common. What's sad is that most doctors will test for Lyme, and only if it is positive, will test for co-infections. That's the wrong approach! 


• I got tested and treated for Lyme. Could I still have co-infections?   
In Minnesota, the answer is Yes! Lyme co-infections are very, very common. The approach differs depending on the type of co-infection. So If you were treated and are still not feeling like your old self, please do get tested for co-infections. These tests can make all the difference  in your recovery.


• What are the common co-infections in Minnesota?
 Babesia, Bartonella, and Anaplasma are the ones we often see and recommend testing for in Minnesota. We may also test you for Ehrilichia and Powassan Virus.

Cat Scratch fever or Bartonella is another very common infection. Many times patients come into Dr. Kyle's office thinking they have Chronic Lyme when in-fact they have Bartonella. To learn about Bartonella, please click below.

Bartonella testing and Protocol

• Is the approach the same regardless of 
the co-infection or combination of co-infections?
No, it is not! As these unique infections, viruses, parasites, and bacteria live in different cells and parts of your body and work differently; there is not a one-size-fits-all approach to effectively resolve them all. But there are protocols for all (each) of them, and they can be dealt with successfully. 



click below!
• What is the BEST way to treat Chronic Lyme?  
Dr. Kyle and Dr. Paul have developed one of the BEST protocols to address Chronic Lyme. In a series of videos, he answers patient questions on the controversy around chronic Lyme and the best way to manage it.


• Why is Chronic Lyme so controversial? Why do some doctors don't even know how to test for it? What makes it so complicated?
Many Chronic Lyme patients have been given the run-around within our healthcare system.  Any where from 6-21 % still develop chronic Lyme even after standard meds. That's where conventional Western Medicine falls short with Chronic Lyme. Through a series of videos, Dr. Kyle explains the controversy around chronic Lyme, why it is hard to diagnose, and what's the best way to treat it.


•How long until I start feeling better?
Dr. Kyle and Dr. Paul have shown improvement for these patients in as little as 3-6 months! If you do in fact have Chronic Lyme, and depending on additional co-infections, it may take up to 12-18 months, but not to worry; you should see improvement much quicker than that in your symptoms and in your quality of life. Dr. Kyle discusses the essential steps in The (BEST) Chronic Lyme Protocol.



•Why doctors don't believe in Chronic Lyme? Why is there controversy?   
In this video, Dr. Kyle explains the controversy about Chronic Lyme and why it's so hard for patients. He describes how their protocol at RHS (Restorative Health Solutions) is unique, offering great results for patients working with them on Chronic Lyme.


•Are there natural herbs and products that can help my Lyme Disease? 

Yes, absolutely. Many natural herbs are proven safe and useful  in Chronic Lyme Patients. Examples include Cryptolepis, Japanese Knotweed, Cat's Claw, Skullcap, Black Walnut, Artemisia and more. I don't recommend you just start taking these. The dose also varies in each patient. We have to run some baseline analysis to know which to use on you and how. Request Free Consultation if you have any questions.
click below!
60% of Chronic Lyme patients experience Neuroborreliosis which is Lyme in the brain. In the video below at the link below, Dr. Kyle Warren, DC, CFMP explains the neurological issues and associated nerve damage caused in Chronic Lyme patients

Click the image below to watch the video

• Why do people develop so many neurological symptoms with Lyme disease? 
Unfortunately, Lyme loves the brain and therefore causes severe neurological damage over time that can manifest in different ways. 
The neurological effects of Lyme include POTS (Postural orthostatic tachycardia syndrome), Headaches, Migraines, different kinds of pains, Facial Palsy, strange sensations in the body, including Fibromyalgia and Brain Fog.

Watch Patient Stories - Click here 

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HOW COMMON IS LYME DISEASE IN MINNESOTA?
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Order the NutriRestore Acute Lyme (Just Got Bit Kit) here...

This kit is for anyone recently (within the past three months) bit by a tick and is taking or has recently completed standard care.
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or a second opinion?
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