White Paper on the Role of Infection in Complex Disease

Thank you for your interest in Sound Clinic. We have prepared this document to answer common questions and provide insight into our philosophy of care for patients with complex chronic illnesses. We believe that successful treatment begins with a shared understanding between patient and provider regarding the nature of these conditions, the limitations of current medical knowledge, and the strategies most likely to lead to recovery.

The patients we serve often struggle with symptoms such as fatigue, pain, cognitive dysfunction (“brain fog”), headaches, digestive issues, dizziness, sleep disturbances, heart palpitations, and other chronic health concerns that have proven difficult to diagnose or treat. Many have already consulted numerous healthcare providers and undergone extensive testing without finding satisfactory answers. Some have been told that their symptoms are unrelated, unexplained, or untreatable. Our experience suggests otherwise.

We view chronic illness through a systems-based lens. Rather than searching for a single diagnosis to explain every symptom, we recognize that illness frequently arises from the interaction of multiple factors. These may include tick-borne infections, viral reactivation, mold exposure, microbial imbalances, metabolic dysfunction, immune dysregulation, hormonal problems, nutritional deficiencies, and other stressors that can accumulate over time. While not every factor applies to every patient, meaningful recovery often requires identifying and addressing several contributors simultaneously.

Because these conditions are complex, diagnosis and treatment rarely follow a straight line. Laboratory testing can be helpful, but no test is perfect. Clinical judgment, careful observation, patient history, and response to treatment are often equally important pieces of the puzzle. For this reason, we favor an individualized approach that combines evidence-informed conventional medicine with thoughtfully-selected integrative therapies.

The purpose of this document is not to persuade you to adopt a particular viewpoint, but rather to build a shared foundation for how we think about complex illness and what you can expect if you choose to pursue care with our team. We hope this information helps you determine whether our approach aligns with your goals and expectations. If so, we look forward to partnering with you on your path toward improved health and recovery.

This document is intended to serve as a reference guide. We encourage patients to revisit specific sections throughout treatment, as many of the concepts discussed here become more relevant as the recovery process unfolds.

General Information About Our Approach to Lyme and Other Tick-Borne Infections

We strive to meet the needs of a broad spectrum of prospective patients, prioritizing effective and affordable care. Despite this focus on value, our approach may not be suitable for everyone. Tick-borne diseases, especially when not caught early, present significant challenges. Many patients find that conventional medicine has little to offer. We advocate for an aggressive and comprehensive approach that integrates pharmaceutical and botanical treatment options. While no provider or protocol can claim to offer perfect efficacy or completely eliminate adverse reactions, we are confident in our ability to balance risk and reward.

The term “Integrative Medicine” is frequently used today, often by healthcare providers offering natural alternatives to the prevailing paradigm, dominated as it is by a pharmaceutical approach. This perspective can conflict with a medical establishment that typically adheres to a limited “standard of care.” While guidelines are a good starting point, they typically exclude substantial amounts of quality research. Non-prescription solutions are often overlooked due to a lack of funding for research or marketing. When standardized recommendations do not lead to recovery, it is reasonable to explore alternative strategies, such as more individualized treatment or a broader diagnostic approach.

Persistent systemic inflammatory disease is inherently complex. And it’s natural for a sick person to pine for a magic bullet. But it’s been our experience that success usually follows from the assumption that illness emerges from multiple insults. In most cases, there are more variables than one can reasonably hope to definitively identify. This makes it practically impossible to conduct the kind of double-blind, placebo-controlled, outcome-based research that is considered the gold standard.

Lyme disease, in the strict sense of the word, is caused by a bacteria called borrelia burgdorferi. But b burgdorferi is just one of many nasty players in the extended borrelia family. For this reason, insiders increasingly prefer the term borreliosis, even though it’s less specific.

Opportunistic infections are typically caused by common and contagious microorganisms. These don’t usually cause lasting problems in healthy people but contribute to the pile-on when host immunity is compromised by something sophisticated, like borrelia. A comprehensive program that addresses borrelia, co-infections and secondary infections, while supporting detoxification, is effective most of the time. For the remaining cases, we have additional strategies.

Babesia and Bartonella are the primary co-infection families. Even harder to detect than Borrelia, they are stealthy in part because they invade cells. There is currently no test for the biotoxins that any of these infections continuously secrete to evade the immune system. Yet it is clear that for many patients, the biotoxin burden contributes more significantly to symptoms than the infections themselves.

Laboratory Testing for Tick-Borne Infections and Related Diseases

There is no perfect lab test for any of the most clinically-significant pathogens described above. But the technology has improved in recent years despite persistently bad insurance coverage. Understanding the limitations of any testing methodology requires an understanding of two terms that are used to describe test accuracy:

1. Sensitivity: The probability that a given test will yield a positive result in someone who has the disease (ie. a “true positive”). For example, a Lyme disease test with 80% sensitivity will return a positive result about 80 times if administered to 100 individuals who all have Lyme disease.
2. Specificity: The probability that a test will yield a negative result in someone who does not have the disease (ie. a “true negative”). If the same test had 90% specificity and was administered to 100 patients, none of whom had the disease, about 10 of these patients would receive a false-positive result.

Ideally, every test would be 100% sensitive and 100% specific, but in reality, almost none are. In many cases, it’s possible to increase a test’s specificity to reduce false positives. But ‘raising the bar’ in this way simultaneously decreases its sensitivity, leading to more false negatives. This is a major problem with conventional testing for borreliosis.

The CDC still recommends an antiquated two-tier testing process for Lyme disease. Both tests detect antibodies, proteins made to mark certain foreign proteins for destruction by the immune system. These proteins are specific to the organisms they reside on. Only those who test positive on an inexpensive screening test are then tested with an immunoblot. (This is a newer version of the Western Blot). A positive overall result requires a positive on both of the individual tests. This methodology is sensible when one test is sensitive but prone to false positives (ie. is nonspecific). In this case the second, more specific test can then be used for confirmation. Thus, a positive immunoblot confirms a positive screening test. 

Unfortunately, both tests become less sensitive over time in many individuals because antibody levels decline, even in the face of persistent infection. Since a positive overall result requires two positive tests, the problem of false negatives is compounded. By most estimates, more than half of those with longstanding Lyme disease will fail at least one of the two steps. For this reason, we do not recommend a two-tier testing approach. In fact, we don’t recommend the screening test at all. When we use tests for antibodies, we use expanded panels that bring with them different interpretation criteria. 

For many years, we favored an improved version of the Western Blot offered by a specialty lab called IgeneX. More recently, however, we have primarily utilized a urine panel from a lab called DNA ConneXions. This is occasionally followed by a more comprehensive antibody panel from an innovative lab called Vibrant America.

Immunoblot interpretation remains a complex issue. There is ongoing debate regarding the selection of antibodies for testing panels, the number of positives required to meet diagnostic criteria, and the specific cutoff points used to define a positive result. Like many Lyme-literate providers, we believe that overly restrictive interpretation criteria leads to frequent missed diagnoses. Because these standards were established over forty years ago, many patients infected with Borrelia continue to receive false-negative results. Consequently, more reasonable “alternative” interpretation criteria have been developed to address these limitations. This incremental improvement is reflected in the Vibrant Tickborne panels.

Polymerase chain reaction (PCR) is a means by which to detect very specific DNA sequences. By applying this reliable and time-tested technology to urine, a concentrated waste product, instead of blood, the DNA ConneXions lab was able to improve both the cost and dependability of tick-borne disease testing. DNA ConneXions has become our primary diagnostic tool in most cases for several reasons:

1. Comprehensiveness: DNA ConneXions does not offer a-la-carte testing; the entire panel must be ordered. This is advantageous because there are several significant tick-borne pathogen families and multiple strains in each family. 
2. Value: The DNA ConneXions “Lyme” panel includes 14 different tests. Four are used to detect Lyme (borrelia burgdorferi), and the other ten detect three strains of babesia, three strains of bartonella, two non-Lyme borrelias, a strain of ehrlichia and a strain of anaplasma. At $630, this equates to just $45 per test. (Refer to our website for the most up to date pricing.)
3. Evidence of active infection: The panel looks for infection-specific DNA instead of antibodies. The presence of antibodies is dependent on the successful function of many different facets of host immunity. This dependency opens the door to false negatives, especially in patients whose immunity has become dysfunctional. In contrast, the presence of very specific DNA, when detected in a patient’s urine, is only consistent with an active infection. This is because foreign DNA floating free in the blood is broken down by enzymes called DNAses. DNA degradation affects most samples to some degree and can lead to false negative results, as explained in the next section.
4. It’s not perfect: False negative and false positive findings are still a possibility. The urine of patients who have been infected for months or years contains only very small amounts of the DNA in question. Degradation of this already limited amount of foreign DNA — by the aforementioned DNAses — leads to ‘NPS’ and ‘IND’ designations. They’re saying that if the DNA they found had not been degraded (ie. partially digested) they would have expected to find more of it. But the probability of a false positive is very low, even in the context of NPS and IND designations. Since there is no “gold standard” for comparison, some debate is inevitable. But we think that the potential for false negative results is much greater. The detection rate for babesia is the most problematic — it seems to be lower than 70% based on our clinical suspicions. In other words, the sensitivity of the DNA ConneXions test seems to be a little below 70% for babesia, at least a little higher than that for bartonella and probably 80% or more for borrelia.

What other lab tests might be useful? We also like the Vibrant America Tickborne 2.0. This panel is a great collection of antibody tests for important human pathogens. Although it’s somewhat more expensive (around $970), it’s actually great value because of the sheer number of different tests included. They also offer a version called the Tickborne 1.0 (around $620), which only includes tests for borrelia and tick borne co-infections. We prefer the 2.0 because it includes many of the secondary infections that end up being necessary to treat. 

Ideally, we would run both the Tickborne 2.0 and DNA ConneXions test panels for every new patient. However, we typically begin with the DNA ConneXions urine PCR panel. The reason for this approach is that antibody tests, such as the Vibrant panel, do not always clearly distinguish between a previous and an active infection. Understanding this requires a distinction between two types of antibodies: IgM and IgG.

Most medical students are taught that within a few weeks of exposure to an infectious disease, the body starts to make IgM antibodies. Then, weeks to months later, after the immune system eradicates the infection, it switches to make an IgG version of the same antibodies. This turns out to be a big simplification and an even bigger generalization. The reality is much more variable, especially if the infection doesn’t get completely eradicated. Some chronically-infected patients keep making IgM antibodies indefinitely. But most eventually switch to IgG, even if the infection isn’t totally gone. A few don’t maintain detectable levels of either.

Unfortunately, there’s no way to predict which of these three groups a person will fall into. But IgM antibodies are really compelling evidence of active infection. Given that chronic infection is the norm for tick-borne infections (if a person isn’t given antibiotics within a few weeks) IgG antibodies are suspicious at the very least. Furthermore, a negative antibody test doesn’t completely rule an infection out. For these reasons, it’s necessary for the provider to integrate all of the available information. That includes things like symptoms, history and tests for other diseases. It may seem like putting the cart before the horse, but sometimes the most definitive diagnostic evidence comes in the form of a favorable response to treatment. 

There is no substitute for taking a comprehensive patient history. While symptoms are often less specific than expected, valuable information can be gathered by observing how they evolve over time in the context of treatment. For those open to the approach, Autonomic Response Testing (ART) serves as an efficient tool to determine which patients are most likely to benefit from any given treatment while minimizing the risk of side effects.

What is ART and How Does It Work?

As described above, even modern diagnostic testing often falls short when it comes to detecting chronic infections. Increasingly, healthcare providers in this field utilize “muscle testing” to develop effective and well-tolerated treatment plans. This method, an adjunct to more traditional medical information gathering, was first documented in the 1950s by Dr. George Goodheart Jr. Dr. Goodheart observed that touching a diseased body part could decrease in apparent muscle strength in other parts of the body. The phenomenon was more subtle than flinching in response to pain, but not categorically different. He integrated acupuncture and clinical nutrition into a system he called Applied Kinesiology, or AK.

It’s worth noting that computer-aided skin conductance, also known as “electrodermal” testing is believed to observe the same underlying neurological phenomena as AK. 

A deep understanding of this topic involves graduate-level physics and physiology, with some aspects remaining theoretical. However, most people have an intuitive sense of the difference between “fight or flight” and “rest and digest.” Acupuncturists observed this duality thousands of years ago, referring to it as Yin and Yang. Today, students recognize these as the sympathetic and parasympathetic branches of the autonomic nervous system (ANS).

Beginning in the 1980s, Dietrich Klinghardt, MD, PhD, built upon Goodheart’s foundation. He recognized that the muscle weakening he observed was reflective of changes in the patient’s ANS. Most people have experienced the way stress can cause muscle tension, especially in the neck and shoulders. This is mediated by autonomic nerves embedded in tendons. Structures known as ‘Golgi tendon organs’ measure tension and send that information back to the brain. But they’re also hooked up to the ANS such that changing the amount of stress in the system influences the threshold at which the Golgi organs begin to fire.

Making sense of muscle testing also requires some understanding of electromagnetic fields. As owners of cell phones, we are all aware of the capacity for invisible information exchange. Most people are unaware that electromagnetic fields are generated by all matter, or that substantial published research suggests that dozens of living things, including humans, can perceive electromagnetic frequencies. This lack of awareness stems from the fact that the perception in question usually occurs subconsciously. For a deeper dive, read ‘The Field’ by Lynne McTaggart.

Examples of electromagnetic field perception in action include the ability of sharks to hunt in dark or murky waters – though underwater cables have a way of tripping their senses. Birds and turtles navigate with an instinctive sense of direction and location. While the exact mechanism for how this information translates into a neurological response remains unclear, scientists at the University of Tokyo have recently observed subtle cellular changes that may explain these abilities.

Another key principle relates to the physiological changes that stress creates in the body. Stress begins in the central nervous system, and its effects can be measured elsewhere, as in a polygraph or lie-detector test. Similarly, electrodermal practitioners use the fact that exposure to specific frequencies emitted by antibiotics and nutritional supplements causes temporary changes in skin conductivity, observable with a voltmeter. Muscle testing is another way to observe these changes. Although it may seem less scientific than using computers and voltmeters, it is more practical and efficient. This difference is mostly about relative amounts of signal and noise. 

When a patient is exposed to the electromagnetic frequency that is unique to an active infection, they go into a state of increased stress. This could also be described as “increased sympathetic tone.” The body does not respond the same way to resolved infections or pathogens that it hasn’t been exposed to. This makes ART a great way to infer what’s making a person sick, as distinct from what they’re merely hosting. Conversely, exposure to the frequency of the right therapeutic agent reverses the change by increasing parasympathetic tone. Once the correct remedy is applied to the biofield, the stress response disappears and the muscle regains its strength.

Klinghardt was able to enhance the practical application because he understood electromagnetic science and autonomic physiology. His “signal enhancers” (quartz-like blocks) amplify the frequencies of various substances, allowing for more reliable testing. He likens this to one vibrating tuning fork causing another identical fork to start vibrating when placed nearby. Owing to their optical properties, these blocks appear to resonate at the electromagnetic frequency of various things that are placed in close proximity.

For testing young children, “surrogate muscle testing” emerged by necessity. The surrogate acts as an intermediary. This may appear strange at first, but it helps to remember that humans are electromagnetic beings, constantly emitting and perceiving information. While close proximity enhances this communication, skin-to-skin contact isn’t strictly necessary. Surrogate testing has other advantages: a healthy surrogate can enhance reliability by preventing untrained patients from consciously resisting weakening effects, reducing the operator’s preconceived notions, buffering the operator’s own health issues, and even preventing muscle fatigue or injury during direct testing.

What to Expect Once in Treatment

At Sound Clinic, we do not require patients to purchase expensive package deals; however, we do recommend a six-month commitment to treatment. We estimate that approximately two-thirds of our patients remain in treatment for 12 to 18 months, while others may require shorter or longer durations. Some patients respond almost immediately, while others see significant improvements only after several months. While prognosis can be difficult to estimate, factors such as the duration of illness, patient age, and severity of symptoms are significant predictive factors.

Patients researching Lyme disease may encounter information regarding the “Herx” response, short for ‘Jarisch-Herxheimer reaction’. Originally described by a physician treating syphilis at the dawn of penicillin, a Herx is characterized by an exacerbation of existing symptoms, usually within a week of beginning effective treatment. Like syphilis, Lyme disease is caused by a type of bacteria called a spirochete. Killing these bacteria releases endotoxins, increasing the body’s toxic burden. As many symptoms are secondary to these toxins, the die-off of microbes can worsen symptoms. The term “Herx” now also describes treatment-related reactions to the death of fungal, parasitic, and sometimes even viral infections. 

A more nuanced alternative is worth mentioning here: Imagine a bacteria attempting to defend itself in the face of an antibiotic. It might have the capacity to increase the rate at which it releases the biotoxins it is already making to manipulate its host’s immunity. It’s a bit like poking the bear. This is a little different than the same bacteria dying en masse in the streets and stinking up the whole town. Both versions are characterized by the exacerbation of preexisting symptoms. And both can be alleviated by stopping treatment. But a patient who is poking the bear might actually fare better with more aggressive treatment. Conversely, a person who is feeling worse because of a major herd-culling event might want to try again at half dose a few days later once their detox pathways catch up.

The most effective way to manage a Herx reaction is to take a break from treatment. Pausing antimicrobial therapy in the context of an exacerbation of symptoms is different from stopping the amoxicillin ahead of schedule because the sore throat is gone. In most cases, it only takes a day or two for the body’s detox pathways to catch up. Treatment can then be resumed, usually with little in the way of additional Herxing. But it isn’t a race. Aspirin, ibuprofen, or diphenhydramine (Benadryl) can help treat Herx reactions. So can a hot bath in Epsom salt. Various detox and/or drainage supplements are helpful in reducing Herx severity and duration. Glutathione is the body’s master detox molecule. It’s our go-to agent for patients who repeatedly run into the Herx barrier. However, its benefits are much more apparent when it’s administered intravenously. 

Although unpleasant, a Herx response confirms the diagnosis of a chronic infection. Medicinal agents almost always have some potential to trigger side effects like nausea, diarrhea, or rash. This could also be described as intolerance. If an antimicrobial agent exacerbates an existing symptom or symptoms within a week, it’s safe to assume a Herx is occurring and the treatment is working. Classic symptoms include pain, fatigue, or cognitive impairment. However, a Herx can take the form of almost any symptom or cluster of symptoms, including a flu-like illness.

Generally speaking, sicker individuals experience more pronounced and protracted Herx reactions. Minimally symptomatic patients may not have a Herx at all, while sicker patients may struggle to tolerate sub-therapeutic doses. The goal is to find a balance between a debilitating symptom exacerbation and an overly passive approach. We want to avoid emergency room visits. Taking a break from treatment, even at the first sign of adversity, is completely acceptable. In addition to glutathione, we offer intravenous hydration and anti-inflammatory medicine. In most cases, we can offer these services on short notice.

Even within the Lyme community, opinions vary on the acceptable severity and duration of a Herx reaction. While we believe some degree of Herxing is almost inevitable, it can be detrimental if it becomes excessive or prolonged. If you are struggling, please take a break, but do not give up. We are often surprised by how much smoother the process becomes after a few days off.

Since most patients are on multiple agents, it’s desirable to figure out which one is triggering the Herx. If you think you may be Herxing but aren’t sure which medicine is the trigger, consider the following protocol: Begin by stopping all therapeutic agents — especially antimicrobial herbs or antibiotics that were started within a week of the Herx. Symptoms generally return to baseline in 1-3 days. Then reintroduce them one at a time, adding a new one every 4 days. Don’t get too hung up on the reintroduction sequence. If you think you know which one triggered you, consider making it the last one you try to reintroduce. If something triggers you a second time, put it aside until you can discuss your experience with your provider at the time of your follow-up appointment.

The Symptom Questionnaire

Dr. Joseph Burrascano, a Lyme pioneer, developed a symptom questionnaire based on his experience treating thousands of Lyme patients. This questionnaire uses a 5-point scale, where ‘5’ indicates very severe symptoms, and ‘Never had’ or ‘Resolved’ both count as zero points. In these cases, please mark a ‘0’ instead of leaving the question blank. Tracking changes in your symptom scores helps us gauge your response to treatment. Pursuant to the previous section, it’s common for scores to initially increase before decreasing. Please score your symptoms based on your average experience over the last week to accurately reflect recent trends, as opposed to more distant history. The questionnaire also helps us efficiently document medical necessity and guides future treatment decisions.

A Note About Forms and Disability

We recognize that Lyme patients often experience legitimate and severe symptoms that can be disabling. While we are usually effective at helping patients recover, we are less equipped to assist with disability applications. The burden of proof for disability is high, and many deserving applicants are denied. Disability insurers, especially private companies, prioritize their financial interests and are inclined to deny claims whenever possible. They focus on objective evidence rather than subjective experiences. So specialized lab tests definitely play a role here. 

Patients diagnosed with more verifiable conditions, like neuropathy confirmed by EMG, are more likely to be approved. A diagnosis based on subjective symptoms, like anxiety, is harder to prove. However, if that’s the foundation of a disability application, the diagnosis should come from a certified psychiatrist. Specialized legal representation should be involved early on in the process. So please don’t just ask for a disability letter. Even the completion of forms for short-term FAMLI leave requires a dedicated appointment. Patients should arrive at that type of appointment being familiar with the forms and having a clear sense of what accommodations they believe are necessary.

The Team-Based Approach to Lyme

To maximize the number of patients we can assist, Shauntae, Ara, and Dr. Naylor work together as a team. This collaborative approach often involves different team members managing various aspects of a patient’s care. Please note that Dr. Naylor does not offer hormonal interventions or annual preventive medicine encounters. These services require separate appointments, which are typically scheduled with Shauntae, Ara, or another member of our integrative primary care team.

General Information About Antibiotic Therapy

Patient concerns about antibiotic use seem to be increasing. While it’s true that they can affect intestinal microbial diversity, antibiotics play an important role. The reality is that most patients come to us already suffering from a dysfunctional relationship with the microbial world. The gut is a type of ecosystem and restoring balance usually begins and often ends with effective suppression of unfriendly actors. Accordingly, oral antibiotics remain a mainstay in treatment. Having said that, the therapeutic value of botanical antimicrobials is often underestimated. For most patients, they are indispensable for the management of secondary infections. Even tick-borne co-infections — at least those not dominant or ascendant at any given time — should be managed with herbs in most treatment intervals. Plants have to constantly defend themselves against pathogens and their extracts contain dozens of powerful compounds working in concert.

Drug companies are heavily regulated. That’s a good thing. But their small-print inserts are seldom read. The potential side effects listed for most drugs is very long because it must include all adverse reactions reported during clinical trials. These effects are usually mild and almost always resolve within days upon discontinuation of the drug. It is not feasible to review complete lists of possible side effects at the time of an office visit. It’s even been shown that discussing a side effect increases the likelihood of a patient experiencing it. Nevertheless, a few key points warrant consideration:

Antibacterial therapy increases the risk of diarrhea. Sometimes antibiotic-associated diarrhea can be caused by resistant bacteria called clostridium difficile, or c diff for short. One study estimated the risk of c diff infection in the context of cefdinir to be 6.22 per 10,000 prescriptions. Other preferred agents like azithromycin and doxycycline are even safer, boasting less than one case per 10,000 prescriptions. Concurrently using medications that block stomach acid further increases the risk, likely because c diff spores that a patient ingests while on treatment are more likely to survive in a less acidic stomach environment. Some people are c diff carriers, meaning don’t know they have it and may or may not be symptomatic because of it. Exposure to this bacterium is more common in healthcare settings. So please wash your hands with soap or use hand sanitizer when entering and exiting any clinic, hospital, or nursing home. Vancomycin is an antibiotic that is very effective for c diff. Patients with this infection often report light-colored, unformed stools and malaise. These symptoms warrant a prompt call to our office.

Candida overgrowth is harder to diagnose but probably more common. For many with tick-borne diseases, yeast is a problem even before antibiotic treatment begins. Antifungals, be they botanical or pharmaceutical, are an important part of overall recovery. Accordingly, they are independently necessary and not just a management strategy for an unintended consequence of antibacterials. 

A third factor in gastrointestinal dysfunction, often overlooked, is chronic intestinal parasitosis. Protozoa is a useful word that is used to describe single-cell parasites. The most well-known protozoa is giardia, but cryptosporidium commonly blooms into developed-world water treatment facilities. Workers shock the pools but invariably a few survive and find their way into tap water. Our patient population experiences diminished immunity. That makes them more vulnerable to chronic protozoal infections, and also more likely to be symptomatic because of them. 

While this discussion is technical, it’s an important part of weighing the risks vs benefits of antibacterial treatment. Medical autonomy is a fundamental right, and we do our best to meet our patients where they’re at. However, an aversion to antibiotics decreases the probability of recovery. As described above, c diff is rare and treatable; candida independently requires treatment and we consider protozoa within our scope of expertise. Practitioners who don’t have prescribing rights are at a disadvantage in all of these areas, which may contribute to perspectives that sometimes stand in the way of effective treatment.

The principle of empiric treatment also deserves to be mentioned. It’s defined as medical care that is based on clinical experience, observation, and educated guesses. Even something as seemingly simple as sinusitis is rarely possible to confirm with swabs or cultures. Strep throat lends itself better to this technology but it’s common to treat empirically, even if the rapid swab is negative, because sometimes the culture reveals a different answer. Sometimes, the culture is also negative but by the time it comes back, the patient, having been on antibiotics for a few days, is feeling much better. 

The degree to which a healthcare practitioner is comfortable with empiric treatment could be said to define how liberal or conservative they are in their approach to patient care. For reasons described above, a conservative approach may be poorly suited to the needs of the complex patient population.

Most of the agents we prescribe have a low probability of triggering side effects. It may be convenient to think of them as occupying a first tier, where special precautions aren’t considered necessary. Below are two examples of important pharmaceuticals that we think of as being on a second tier where there is more risk but it can be mediated by awareness or monitoring. A third tier is reserved for refractory cases and is beyond the scope of this document. Use of disulfiram, for example, invariably involves a conversation at the time of an appointment.  

Doxycycline (“doxy”): This effective and inexpensive antibacterial agent is sun-sensitizing, meaning it can cause sunburn-like rashes even with normal sun exposure. Consider this a preventable tropical vacation failure. But it can sometimes strike even on the backs of the hands of gardeners or road-trippers. Fair-skinned individuals are more susceptible; sunscreen helps. It can also upset the stomach and should be taken with food, even if your pharmacist advises otherwise. Minocycline is similar; it seems less likely to trigger nausea or sunburn but more likely to trigger vertigo.

Tinidazole (Tindamax) and metronidazole (Flagyl): These drugs are crucial for borrelia persisters. Alcohol must be avoided, as they can significantly amplify hangover effects. Occasionally, patients may need to add alcohol-based tinctures to hot tea before consuming them. In rare cases, these drugs need to be discontinued because of symptoms like numbness or tingling. We have not seen these symptoms last but we always recommend discontinuation of the medication if it happens. Because these medications can sometimes irritate the liver, we usually check liver enzyme levels with a simple blood test 10-14 days into treatment. We typically prescribe these medications at about half the usual dose, which seems to significantly reduce the already low probability of these unintended consequences. We prefer tinidazole as its potential side effects appear less frequent than those of metronidazole.

Allergic reactions to medications are always possible, with some medications being more allergenic than others. Herx rashes and allergic rashes can be difficult to distinguish. Both are unpleasant but ultimately self-limiting. Benadryl often helps but causes sedation, whereas second-generation antihistamines like loratadine (Zyrtec) are less sedating but seem to be less effective. Anaphylactic reactions are very rare in our practice but potentially very dangerous, as swelling of the tongue and/or throat can obstruct the airway. If you have experienced an anaphylactic reaction in the past, you should have an EpiPen on hand, especially when starting a new medication. If you need a prescription for a new EpiPen, we are happy to provide one. If you suspect you are having an anaphylactic reaction, do not hesitate to use your EpiPen; if you do not have one, call 911 immediately.

Do I need to take probiotics?

Probiotics are beneficial for treating and preventing antibiotic-associated diarrhea. While prevention is generally preferable to treatment, discontinuation of treatment is what matters most. For that reason, routinely recommending probiotics to every patient may not be cost-effective. Having said that, probiotics have bonafide medical applications. 

What dietary changes should I make?

Refined carbohydrates, especially sugar and flour, are increasingly recognized as major contributors to lifestyle-related metabolic diseases like obesity, diabetes, and heart disease. Minimizing these ‘empty calories’ benefits nearly everyone, regardless of health status.

Wheat sensitivity affects many of our patients, ranging from mild intolerance to Celiac disease. Negative Celiac test results don’t rule out less severe sensitivities. For those on this spectrum, strict avoidance is often more effective than mere reduction, since an inflammatory response to gluten can easily last several days. Food allergy testing is unreliable so an elimination diet remains the gold standard. It’s a straightforward protocol: Start by strictly avoiding wheat for a month. If you feel better, you have your answer. If unsure, reintroduce something like pasta and observe for symptoms like abdominal cramping, pain, indigestion, fatigue, or cognitive impairment.

Avoiding wheat and reducing sugar eliminates most refined, nutrient-poor foods. This reduces inflammation and is sufficient restriction for most. For stubborn Candida overgrowth or weight loss, a stricter “Candida diet” (no sugar, starch, alcohol, caffeine or dairy) may be necessary. Starch is a term that applies to all flour, potatoes, and rice. Alternatively, “eat like a caveman” aligns with paleo diets, acknowledging our limited adaptation dietary changes wrought by the agricultural revolution. Asian populations have adapted to rice but Africans and indigenous people, being more recent hunter-gatherers, are often more vulnerable to diabetes and obesity related to consumption of refined foods. There’s also a lot of individual variability — some people feel better and have better cholesterol on high-fat ketogenic diets. Others swear by low FODMAP diets. There aren’t any good ways to predict which of these diets will work best for any given person; some food restriction trial and error is usually necessary for those who are reactive to foods.

For most people, it’s enough to start by reducing portions, avoiding refined foods at the grocery store, and making better choices at restaurants. Be mindful of sugar in beverages, including sports drinks, coffee, and juice. Don’t give up if you slip; disciplined grocery shopping once or twice a week is more effective than constantly resisting temptations that are already in the pantry. 

So what replaces the restricted foods? Vegetables. In abundance. Try not to overcook them. Learning how to make them palatable is an underrated life skill! Include some protein with every meal, especially breakfast. Consider pea protein powder or collagen peptides with fruit, plain Greek yogurt, and frozen kale for breakfast or as a meal replacement. Quinoa is a more nutritious and less allergenic grain option.

The therapeutic power of dietary interventions is significant. We often hear dramatic stories from patients who have cut out both dairy and gluten. Since removing both simultaneously can be challenging, and since dairy is nutrient-dense, we recommend starting with “no-gluten, low sugar.” For those ready for more, a trial of dairy avoidance is worthwhile. Dietary changes are low-cost, low-risk interventions.

What about exercise?

Exercise offers powerful health benefits, but too much can be detrimental. Listen to your body: if recovery takes two days, you’ve overdone it. Walking provides many benefits with less injury risk than more demanding activities. Lifting light weights with high repetitions has many proven benefits.

What are the risks of treatment?

Nearly every intervention carries some risk; Even the safest medicines have potential side effects. Our patients are often more sensitive to medications, increasing the likelihood of adverse reactions. While ART reduces adverse reactions, it doesn’t eliminate them, especially when it comes to ‘Very Sensitive’ patients. With most patients attempting dozens of medicines over the course of treatment, it’s probable that something won’t go well. 

Another phenomenon to be aware of is the development of intolerance to a medication when it has exhausted its usefulness. There is little overlap between medicines that are working and medicines that are causing side effects. So if you’re experiencing side effects, don’t be a hero. If a medicine was well-tolerated and then started causing nausea or diarrhea or a rash, it probably stopped working around that time and the body figured that out and stopped absorbing it. Go ahead and discontinue it.

The best way to avoid drug interactions is to get all your medications from the same pharmacy. Since that isn’t always possible, please maintain your own complete medication list and share it with all prescribers and each pharmacy whenever there is a change.

Where does all the controversy come from?

Those new to the Lyme debate often attribute failures in diagnosis or treatment to government or commercial entities like the CDC, FDA, Big Pharma, or health insurance. While there’s enough blame to go around, there’s no question that the guidelines published by the Infectious Diseases Society of America have been disastrously influential.

No study has attempted to diagnose or treat patients in a manner that addresses tick-borne co-infections, let alone opportunistic secondary infections. Furthermore, none has attempted to manage persisters using a sequential antibiotic strategy. Part of the problem is structural: Ethical and financial considerations make it difficult to study human subjects. Additionally, large study groups are necessary to study multiple variables simultaneously. 

The research problem is only compounded by the subjective nature of symptoms like fatigue, pain and brain fog. Similarly, patients are much more observant of acute worsening of symptoms than they are of slow improvement. And, unfortunately, rodents won’t tell you anything at all. However, the main issue with the IDSA guidelines is their casual dismissal of treatment-resistant and/or chronic infection. This problem mostly maps to different limitations associated with each of the three main diagnostic tools: culture, DNA amplification (PCR) and antibody detection. 

Borrelia is very difficult to grow in culture. As with most bacterial infections, the sensitivity only gets worse in the context of treatment with antibacterial agents. Even in ideal circumstances, positive results become much rarer after just a few doses of antibiotics. For instance, taking amoxicillin for strep throat would be expected to make borrelia undetectable by culture testing for months or even years. PCR testing, as discussed above, isn’t bad when applied to urine instead of blood. However, that approach is still considered experimental. Antibody testing usually doesn’t distinguish previous from active infection. For similar reasons, it’s not a good test of cure. 

Collectively, these problems make it hard to know who to enroll in your study and even harder to define the outcome in a meaningful way. Yet despite these limitations, there’s a mountain of published data showing that borrelia can survive antibiotic therapy. Experienced clinicians agree that most patients with longstanding symptoms require individualized treatment with many medications. To make the necessary changes at the right times, providers need more time and experience than they are likely to get within a paradigm increasingly dominated by corporate interests.

What’s my prognosis?

Every patient wants to know if they’re going to get better. And, every doctor knows that there are exceptions to every generalization. Outcomes are less predictable when the disease is multifactorial and complex. In most cases, it’s reasonable to estimate an 80% chance of an 80-100% recovery in 12-18 months of treatment. For insured patients with average coverage, that typically translates to out-of-pocket expenses ranging from $5,000 to $10,000. 

Patients often come to us feeling dismissed by the conventional paradigm or failed by natural medicine providers. They may be overwhelmed by their illness or they may have burned out their support system. Sometimes all of these things are true. However, just as things can always get worse, there’s always hope for recovery. Just as the body’s true complexity sometimes seems infinite, there are only so many things that can go wrong. In fact, it’s safe to say that almost everything we see can be attributed to inflammation. While patients increasingly complain of “inflammation,” this isn’t technically a symptom. But it’s true that if you’re bothered by something, it’s probably inflamed. And it’s useful to think of inflammation as invariably mediated by the immune system. The immune system is triggered by a finite number of things: 

1. Physical trauma: In chronic cases not preceded by acute injury, this can be ruled out. 
2. Metabolic disease:. The new GLP-1 drugs have revealed that problems related to the conversion of fuel to energy are driving more inflammation than previously thought. These drugs are doing things that can’t be done with diet alone. 
3. Allergy: Mast Cell Activation Syndrome is a trendy diagnosis, but that doesn’t make it a wasteland. Antihistamines can be useful even if they don’t always get to the underlying problem. We’re comfortable with both the natural and pharmaceutical antihistamine medicines. 
4. Autoimmunity. Thought leaders are increasingly highlighting how a threatened immune system can overreact to innocuous triggers, including allergens and the body’s own proteins. While there have been significant advancements in biological drugs like Humira, there is also a general consensus that infections trigger autoimmune responses. We believe the role of low-grade infections in perpetuating autoimmunity is frequently under-appreciated. Consequently, we remain skeptical of nonspecific autoimmune diagnoses. However, we recognize that specific autoimmune conditions often exist in conjunction with the other factors we are monitoring.
5. Infection: Microscopic threats can be divided into four categories: bacteria, viruses, parasites and fungus. There are herbal and pharmaceutical medicines that we use to treat microorganisms from each of these kingdoms. And even when we can’t completely kill them, sometimes we can help the immune system learn to live with them using something called Low Dose Immunotherapy (LDI).

Thinking about inflammation as being driven by these factors helps us narrow in on the right treatment options. No two people recover in exactly the same way, but most of them do get their lives back. Fortitude, patience, perseverance and open-mindedness are key attributes of successful patients and practitioners alike. 

Conclusion

Complex chronic illness rarely yields to simplistic explanations or one-size-fits-all solutions. While modern medicine has achieved remarkable advances, many patients continue to struggle with symptoms that are difficult to explain, diagnose, or treat within conventional frameworks. Our experience has taught us that meaningful recovery often requires a broader perspective—one that considers the cumulative effects of infection, immune dysfunction, environmental exposures, metabolic health, nutrition, and individual biological variability.

At Sound Clinic, we approach these challenges with humility, curiosity, and determination. We do not claim to have all the answers, nor do we believe that any single test, medication, supplement, or protocol can fully explain or address the complexity of human illness. Instead, we rely on a combination of careful listening, clinical experience, ART, evolving scientific evidence, and individualized treatment strategies to help patients move toward better health.

Recovery is rarely a straight line. Progress often comes in stages, with setbacks, adjustments, and unexpected discoveries along the way. The patients who achieve the greatest success are often those who remain engaged in the process, communicate openly with their care team, and maintain patience as their bodies heal. While the journey can be challenging, we have witnessed countless individuals regain function, restore hope, and reclaim meaningful parts of their lives that once seemed lost.

We appreciate the trust our patients place in us and recognize the responsibility that comes with that trust. Whether you are just beginning your search for answers or have spent years navigating a complex medical journey, our goal is to serve as a knowledgeable guide, an attentive partner, and a steadfast advocate for your recovery. We look forward to working together toward a healthier future.

References

Videos: 

1. Under Our Skin: The Hidden Story of Lyme Disease. This documentary was shortlisted for an Oscar nod.
2. Under Our Skin 2 – Emergence: The sequel to Under Our Skin returns to discover that the patients in the original are recovering in the context of treatment.
3. The Quiet Epidemic: A young Brooklyn girl and a Duke University scientist deal with a disease the medical establishment has long said doesn’t exist.

Books 

1. Why Can’t I Get Better? Solving the Mystery of Lyme and Chronic Disease, by Dr. Richard Horowitz
2. Cure Unknown: Inside the Lyme Epidemic, by Pamela Weintraub

Scientific Review Articles

1. Counterpoint: Long-Term Antibiotic Therapy Improves Persistent Symptoms Associated with Lyme Disease, by Raphael B. Stricker. http://cid.oxfordjournals.org/content/45/2/149.full
2. Lyme disease: The Next Decade. Raphael B Stricker and Lorraine Johnson. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108755/
3. Persistent Borrelia Infection in Chronic Lyme Disease: A Review of the Medical Literature by Raphael B. Stricker, Melissa C. Fesler, Lorraine Johnson. https://www.scirp.org/journal/paperinformation?paperid=149133

Original Peer-Reviewed Research

1. Persistence of Borrelia burgdorferi in Rhesus Macaques following Antibiotic Treatment of Disseminated Infection, by Embers et al. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029914

Top Websites

1. Patient advocacy and general information: lymedisease.org
2. The leading professional association: http://www.ilads.com
3. Advanced clinical knowledge: http://www.betterhealthguy.com
   1. A dense synopsis can be found here.