Complex Chronic Illnesses 

 In Mind/Body

Opportunities for Mind/Body Reintegration 


One of my biggest “never say never” moments was in naturopathic medical school over 10 years ago, when I said that I would never treat Lyme disease. With my limited knowledge, I could not get behind treating someone with oral and/or intravenous antibiotics for years based on a diagnosis often established primarily on a confluence of symptoms. 

After 7 years in practice, though, my hormone and digestive patients were getting much more complicated, presenting with multi-systemic symptoms and a greater level of sensitivity to treatments that others tolerated without a hitch. These patients inspired me to dig deeper, and I opened my mind back up to chronic Lyme disease and its associated infections. As it turns out, many of my patients did end up testing positive for Lyme disease and other vector-borne infections like Bartonella and Babesia, despite these infections being excellent at evading our testing capabilities. I felt like I had cracked the code to the root cause of their symptoms, and I was ready for the challenge. 

Like many practitioners, my initial strategy was to treat the infections, but I quickly understood why these infectious diseases fell under the category of complex chronic illnesses. Treating these infections wasn’t simple at all. When I took the chronic-infectious bull by the horns under the tutelage of my mentor, I soon learned about the presence of other associated conditions including: 

  • Chronic fatigue syndrome (CFS) 
  • Chronic inflammatory response syndrome (in response to mold) 
  • Mast cell activation syndrome 
  • Electrohypersensitivity 
  • Pediatric autoimmune neuropsychiatric disorders associated with Streptococcus infection 
  • Pediatric autoimmune neuropsychiatric syndrome 

While observing these patients, I noticed these physical trends: 

  • Genetic susceptibilities for detoxification impairment 
  • Environmental exposures including infections, mold, and electromagnetic frequency (EMF) 
  • Weakened detoxification pathways as a result of both previous trends 

These trends made sense from a left-brain perspective, but what was most intriguing and compelling to me was that most of the patients had a single thing in common: trauma. It preceded the onset of significant symptomatology for most of the patients I was encountering. Many of these patients also exhibited psychosocial trends including type A personalities and struggles with boundaries and self-love. 

Complex chronic illnesses are characterized by a breach of boundaries in the physical, mental, emotional, and spiritual realms. Each patient is unique in the weight that is put in each category, and the best healing occurs when each realm is effectively addressed and supported. 

Survival of the Fittest 

One of the attributes that make humans unique is our capacity to innovate ways of being efficient. However, the cost of comfort and efficiency has come at a high price. The environment we are creating is changing at such a rapid pace that our genes are unable to adapt accordingly. 

On the other hand, microbes are rapidly adapting their strategies for survival within their everchanging environment. For example, the Borrelia species has developed several known ways of evading and disabling the innate and adaptive immune system, allowing it to flourish and spread.1 We also understand that Borrelia and its co-infections can be found in every fluid of the human body, making maternal-fetal transmission very real.2,3 Considering that stealth infections like Borrelia are extremely pervasive, we are back to the great debate of whether it is more important to focus on the germ or to strengthen the terrain. The answer likely lies in the middle, but we find that a healthy terrain makes a patient more adaptable to environmental stressors. 

Genetic Predisposition for Biotoxins 

At a foundational level, there are genetic susceptibilities affecting our body’s ability to recognize and clear toxins from mold and infections. Based off the work of Ritchie Shoemaker, MD, about 25% of the population has human leukocyte antigen (HLA) mutations that may predispose carriers to a chronic inflammatory response and development of immunologic conditions.4 In my practice, about 95% of my patients have some combination of mutations for the specific HLA gene for biotoxin illness. Such a combination cannot rule in or out a patient’s susceptibility to mold, for example, but the information can be helpful. Complex chronic illness patients are also often significantly affected by genetic defects in nutrient and neurotransmitter metabolism, including methylation. 

Over the past several decades, the population of the Western World has been getting sicker at greater numbers than genetic evolution can explain. Though genetics is a significant factor, stress also plays a major role in our immune system response to infections and toxins alike. Complex chronic cases are likely a result of the perfect storm. 

The Loaded Bucket of Toxins 

Chronic infections increase the demand on our immune system and inflammatory and detoxification pathways. With prolonged and increased exposure to environmental toxins, patients often become more sensitive to their surrounding environment. 

When supporting the body in the treatment of chronic infections, it is imperative to eliminate environmental triggers and adequately support detoxification pathways. Patients must be even more proactive about clean air, water, and food to minimize inflammation, immune dysregulation, and oxidative stress in the body. In addition to reducing exposure to pesticides, chemicals, and metals, the situations to address before initiating antimicrobial treatments are: 

  • Mold/mycotoxins 
  • Mast cell activation syndrome 
  • EMF exposure 

It is important to enlist the support of specialists when assessing a home for mold and/or EMF exposure. For water damage to homes, the International Society of Environmentally Acquired Illnesses (ISEAI) maintains a list of professionals known as Indoor Environmental Professionals (IEPs). For EMF exposure, the Building Biology Institute has a list of professionals known as Building Biologists. Assessments by these professionals have been invaluable in helping patients to understand their environment and reduce the load of chronic physical triggers. 

Opening the Drain 

Treatments in an effective antimicrobial protocol will elicit a cascade of inflammatory substances including endotoxins, exotoxins, mast cell degranulation products, and pro-inflammatory cytokines.5,6 It is therefore imperative in the treatment of complex chronic conditions to regulate inflammation, mast cell activation, immune function, and the body’s pathways of elimination – the liver, kidneys, skin, lymphatics, and digestive tract. Areas of consideration for adjunctive physical support include: 

  • Detoxification support with appropriate herbs and binders 
  • Coffee enemas for detoxification and vagus nerve stimulation 
  • Mast cell stabilizers 
  • Anti-inflammatories 
  • Methylation support 
  • Th1/Th2 balance 
  • Anticoagulants 
  • Regular movement 

These tools often vary in effectiveness from patient to patient, but creating a strong foundation greatly improves the progression of treatment. 

The Mental/Emotional Tipping Point 

Our minds are integrally connected with our physical body. In nurturing the physical body, many find the ability to better access the transformations needed on a mental/emotional level. For others, their journey starts conversely: supporting the mental and emotional body must take place before eliciting physical improvement. 

Most patients can identify a point in their journey where the direction of their health took a noticeable turn for the worse, where they could not ignore the nudges any longer. This shift often occurs when their mental, emotional and/or physical compensations have been overpowered. Patients experiencing chronic illness often experience stress as shown in Table 1.7 

Table 1. Manifestations of Stress 

Categories of Stress Description Examples 
Stressful event sequences Will eventually come to an end, but timing is uncertain Loss of spouse, major natural disaster; these events give rise to a series of related challenges 
Chronic stressors Significant change in social role Traumatic injury, caring for a disabled spouse/child 
Distant stressors Occurred in the distant past yet have potential for long-term damage Being sexually assaulted, witnessing traumatic death 

Trauma and Healing 

The amygdala is the part of the limbic brain that scans the environment for danger. After trauma, this area of the brain becomes hypervigilant and overreactive to stimuli. The medial prefrontal cortex (mPFC) typically assists the amygdala by helping to reestablish a sense of safety. Unfortunately, with trauma, this connection between the amygdala and mPFC can be impaired. Trauma can significantly impact how we process, learn, and react to our environment.8 

Gabor Maté, MD, an expert in trauma, explains that trauma “is a psychic wound that hardens you psychologically and then interferes with your ability to grow and develop…Trauma is not what happens to you, it’s what happens inside you as a result of what happened to you. Trauma is that scarring that makes you less flexible, more rigid, less feeling, and more defended.”9 Studies show that the rigidity Maté mentions is unfortunately also experienced physically by our immune systems when it, too, experiences a loss of self that results in chronic diseases including autoimmune diseases.7 

The good news is that our brains are plastic, and pathways can be rewired to regain normal function. Knowing there is no silver bullet, the challenge lies in finding the right modality. This is where you really must work with your patient, provide them with options and allow them to explore a starting point or their next step. Consider the following options for your patients. 

The Dynamic Neural Retraining System (DNRS) 

Through integrating cognitive behavioral therapy, cognitive reappraisal, and behavior modification, this system helps patients redirect thought patterns while they exercise being in an elevated state throughout the day. DNRS may be tremendously helpful for patients with issues related to overactive limbic systems, especially multiple chemical sensitivity. 

The Gupta Program 

Utilizing components like neurolinguistic programming, inner child work, and parts therapy, this program also capitalizes on neuroplasticity to support patients so they may heal from chronic illnesses like CFS, fibromyalgia, environmental sensitivities, and more. 

Mindfulness Meditation and the Vagus Nerve 

A small study on mindfulness meditation over 8 weeks showed a reduction in inflammation, improved immune function, and elevated glutathione levels in circulation.10 There are many resources in this arena, so it is easy and affordable for patients to access a meditative practice that speaks to them. An example is Stanley Rosenburg’s book Accessing the Healing Power of the Vagus Nerve: Self-Help Exercises for Anxiety, Depression, Autism and Trauma, which offers many self-directed tools for fortifying the parasympathetic nervous system. 

Further therapies 

For more advanced and assisted therapies for mind-body reintegration under the supervision of a medical provider, patients may also explore: 

  • Brainspotting 
  • Eye movement desensitization and reprocessing 
  • Psychedelic assisted therapies 
  • Somatic Experiencing 
  • Traditional shamanism 


Illness can both reinforce and be a result of the disconnection of mind and body. Over time, it becomes challenging and foreign to truly be inside one’s body and spirit. A crucial role as health providers is to lovingly guide our patients to reinhabit their bodies so they may create new relationships and dynamics on all levels. 


  1. Anderson C, Brissette CA. The Brilliance of Borrelia: Mechanisms of Host Immune Evasion by Lyme Disease-Causing Spirochetes. Pathogens. 2021;10(3):281. 
  1. Schlesinger PA, Duray PH, Burke BA, et al. Maternal-fetal transmission of the Lyme disease spirochete, Borrelia burgdorferi. Ann Intern Med. 1985;103(1):67-68. 
  1. Markowitz LE, Steere AC, Benach JL, et al. Lyme disease during pregnancy. JAMA. 1986;255(24):3394-3396. 
  1. Walker A. Chapter 6: External Health Stressors. In: The Trifecta Passport: Tools for Mast Cell Activation Syndrome, Postural Orthostatic Tachycardia Syndrome and Ehlers-Danlos Syndrome. United States: Kindle Direct Publishing; 2021:165-166. 
  1. Butler T. The Jarisch-Herxheimer Reaction After Antibiotic Treatment of Spirochetal Infections: A Review of Recent Cases and Our Understanding of Pathogenesis. Am J Trop Med Hyg. 2017;96(1):46-52. 
  1. Bertani B, Ruiz N. Function and Biogenesis of Lipopolysaccharides. EcoSal Plus. 2018;8(1):10.1128/ecosalplus.ESP-0001-2018. 
  1. Segerstrom SC, Miller GE. Psychological stress and the human immune system: a meta-analytic study of 30 years of inquiry. Psychol Bull. 2004;130(4):601-630. 
  1. The Wisdom of Trauma, Companion Booklet via Adapted from Katie McLaughlin, Stress and Development Lab, University of Washington. 
  1. Caparrotta M. Dr Gabor Maté on childhood trauma, the real cause of anxiety and our ‘insane’ culture. HumanWindow. Published September 24, 2020. Accessed June 17, 2022. 
  1. Rodrigues de Oliveira D, Wilson D, Palace-Berl F, et al. Mindfulness meditation training effects on quality of life, immune function and glutathione metabolism in service healthy female teachers: A randomized pilot clinical trial. Brain Behav Immun Health. 2021;18:100372. 

Thalia Hale, ND, is a naturopathic doctor in the San Francisco Bay Area. Dr Hale has been practicing for over 10 years. Treating chronic digestive and hormonal conditions led her to specialize in complex chronic patients presenting with mast cell activation, mold-related illness, and Lyme disease and its coinfections. 

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