
Infection with Borrelia burgdorferi almost never occurs in isolation. Ticks that spread Lyme Disease may also transmit other infections. Some co-infections occur as a result of the immunosuppressive effects of Lyme. Co-infections can make Lyme Disease more resistant to treatment and create their own problematic symptoms. Although co-infection pathology and treatment methods are complex, here is a brief summary of the most common types of co-infections observed in Lyme Disease.

Bartonella
While conventionally associated with cat scratches, Bartonella is commonly seen in patients with Lyme Disease. Because of this, it is believed to be additionally transmitted by ticks and through the placenta. Bartonella is one of the most problematic Lyme Disease co-infections. It is a parasite to red blood cells and cells that line blood vessels, called endothelial cells. In addition to Bartonella itself, there may be Bartonella-like organisms that are impossible to test for and create similar symptoms to Bartonella infection. Bartonella is not only able to evade the immune system, it can also induce immune suppression, making Lyme Disease more difficult to treat. Some research has demonstrated that Bartonella may even be able to alter human DNA. Some of the most common symptoms of Bartonella infection include:
Fever & Lymphadenopathy: These are symptoms associated with classic Bartonella presentation.
Psychiatric Symptoms: Symptoms impacting mood and nervous system are some of the most prominent associated with chronic Bartonella infection. The psychiatric symptoms of chronic Bartonella are often the predominate symptoms. A common presentation is anxiety but Bartonella may be associated with any of the mood, motor, nerve, or neuroinflammatory deficits seen in Lyme Disease.
Skin Symptoms: Due to the effect of Bartonella on blood vessels, it can create dramatic stretch marks or red streaks on the body. While Bartonella can contribute to a wide variety of unique skin findings, common skin presentations include tender nodules and hives.
Eye Problems: These include the inflammatory presentations often associated with other chronic illnesses and Lyme Disease in general.
Chronic Fatigue & Pain Syndromes: Elevated Bartonella antibodies have been identified in people with diagnoses of Fibromyalgia and Chronic Fatigue. Pain may also impact joints.
Beside Lyme Disease, Bartonella commonly occurs with and may be a trigger for the following medical conditions:
Chronic Fatigue Syndrome
Fibromyalgia
Mast Cell activation Syndrome
POTS
PANDAS
Sjogren’s
SIBO
Gastrointestinal Dysmotility
The presence of any of these conditions may mean you need to assess for Bartonella.
Bartonella Diagnosis
Bartonella is extremely difficult to diagnose as it can shut down antibodies to itself. It can also shut down antibodies to other infections, making diagnosis of other co-infections more difficult. Up to 80% of infected individuals can test negative upon antibody testing (called IFA testing). Testing using both antibody testing and PCR may be helpful in increasing accuracy of diagnosis but Dr. Joseph Burrascano’s, a pioneer in Lyme Disease education, estimates that even this combination can miss over half of true Bartonella cases. To help overcome this obstacle, IgeneX- a lab company specializing in Lyme Disease testing, offers a test called a FISH test, which assesses for Bartonella using nucleic acid testing. The FISH test may be positive when both IFA and PCR tests are negative. When infection with Bartonella is strongly suspected, it may be helpful to run antibody, PCR, and FISH testing.
In addition to testing directly for Bartonella, you can test for immune markers that change in the presence of the infection. The following supportive lab findings may be seen in Bartonella infection:
Low VEGF - Bartonella synthesizes this vascular endothelial growth factor, which can contribute to the skin findings seen in Bartonella. If both Babesia and Bartonella infections are present, VEGF might be normal or low.
Low TNF-Alpha - If both Babesia and Bartonella infections are present, TNF alpha may be high.
Low IL-16- If both Babesia and Bartonella infections are present, IL-16 may be low, normal, or high.
Low IL-1Beta - If both Babesia and Bartonella infections are present, IL-1Beta may be low, normal, or high.
Low C3a or C4a complement
It is important to note that some of these immune markers are used to assess for the presence of Chronic Inflammatory Response Syndrome (CIRS) created by mold toxicity and the presence of mold and Bartonella can interfere with the utilization of these markers for diagnosing either.
Treatment of Bartonella

Like Borrelia burgdorferi, Bartonella is a persister (it creates chronic infection by living in cells and resisting treatment) and conventional treatment approaches may simply suppress rather than eradicate the infection. If using antibiotics to treat Lyme Disease, Bartonella should be treated before Babesia, as drugs used to treat Babesia can make Bartonella treatment less effective.
The most commonly used antibiotic to treat Babesia is Levaquin. Dr. Horowitz – one of the most prominent Lyme doctors, and an expert in antibiotic therapy for Lyme Disease – recommends using at least two antibiotics that target intracellular infections and up to four drugs for treating resistant patients. Intracellular antibiotics may include azithromycin, Doxycycline and Rifampin. Plaquenil, a drug traditionally used for rheumatological conditions, is often incorporated into Bartonella treatments due to its ability to increase intracellular penetration of antibiotics and slow the growth of Bartonella.
Herbal approaches to treating Bartonella may include Byron White formulas, Cordyceps mushrooms, and the herb Artemisinin. Natural products to decrease Bartonella induced damage to red blood cells and vessels may also be used. Treatment of common comorbidities should also be included in a holistic treatment approach.

Babesia
Like Bartonella, Babesia is a red blood cell parasite and persister infection. It is extremely common with Lyme Disease with as many as 66% of patients with Lyme Disease exhibiting evidence of Babesia co-infection. The two main types of Babesia assessed for with Lyme Disease are Babesia microti and Babesia Duncani. However, there are many more species of Babesia which may be able to create infections in humans. Babesia is transmitted through tick bites, vertically in pregnancy, or through infected blood. Symptoms of Babesia may occur periodically and are resistant to Lyme Disease treatment.
Symptoms include:
Fever, sweats, and chills
Fatigue
Headaches
Shortness of breath (sometimes described as air hunger)
Cough
Muscle and Joint Pain
Dizziness
Reduced mental clarity
Weight Gain
Additionally, Babesia is immunosuppressive and can worsen all symptoms of Lyme Disease.
Classically, Babesia infection creates a malaria-like illness that can be fatal. Symptoms of classic infection include hemolytic anemia, heart failure, and kidney failure.
Babesia Diagnosis
Like many other infections associated with Lyme Disease, Babesia is difficult to diagnose. Babesia microti and Babesia Duncani are the only strains routinely tested for and it has been estimated that routine labs can only detect 1-3% of Babesia infection. The rule of thumb is to rule Babesia out only if testing has been negative 10 times.
Blood smear is commonly used for Babesia testing but routinely misses Babesia, especially after the first 2 weeks of infection. IgenX offers an enhanced blood smear, which tests for multiple species of Babesia and has less false negatives than traditional smear testing. PCR testing may also be utilized; it is more accurate than smear testing for Babesia microti. FISH testing is available for Babesia and is 100x more sensitive for detecting Babesia than standard blood smears but may still miss Babesia at very low levels.
Supportive lab findings may also help with making a diagnosis of Babesia. The following changes in immune markers may be seen in Babesia migrans:
Elevated TNF alpha
Normal or elevated IL-6: Because Bartonella lowers this cytokine, it may be decreased if Bartonella infection is also present.
Normal or Elevated IL-1 Beta: Because Bartonella lowers this cytokine, it may be decreased if Bartonella infection is also present.
Low VEGF: Because Bartonella increases VEGF, if Bartonella is also present, VEGF may be normal.
Low Eosinophil Count: Because Babesia decreases the function of this type of immune cell, low count may occur in the presence of Babesia.
Elevated liver enzymes
Because Babesia decreases your ability to fight off intestinal parasites, testing for these should be performed in all patients with Babesia.
Treatment of Babesia
Treatment for Babesia is sometimes pursued when Babesia is strongly suspected but testing fails to identify it. New onset symptoms and elevations of a blood marker called eosinophilic cationic protein can suggest the presence of Babesia. According to Dr. Schaller, a full time self-funded researcher of tick borne illnesses, Babesia is almost impossible to eradicate; both conventional and alternative treatments simply reduce infectious burden. He recommends using all treatments that kill Babesia, at highest tolerated doses, for 12 weeks. Drug side effects and die off symptoms may make this exceptionally challenging for patients. Additional obstacles in treating Babesia include its ability to develop antibiotic resistance and hiding from the immune system intracellularly.
The most commonly used pharmaceutical used to treat Babesia is Atovaquone or Mepron, an anti-malarial medication. Sometimes, the less effective anti-malarial drug Mepron is also used. More thorough antibiotic protocols use other antibiotics in addition to Mepron. These drugs may include macrolide antibiotics, Cleocin, Doxycycline, Coartem, and Dapsone and most have high side effect profiles.
The most commonly used anti-Babesia treatment is Artemisia. Other herbs that may be utilized include Sida Acuta, Cryptolepis, Neem, Curcumin, and formulas by Byron White or Beyond Balance.
Babesia treatments are usually administered for a minimum of five months, since the life cycle of red blood cells (which Babesia infects) is four months. Rotating therapies can help manage relapses.
Anaplasma & Ehrlichia: Anaplasma & Ehrlichia are white blood cell parasites that can create low grade, chronic, or acute and potentially fatal disease.
Symptoms include:
Fevers and flu like symptoms
Muscle pain
Abdominal pain
Headaches
Fatigue
Acute infection is associated with low white blood cell platelet counts, elevated liver enzymes, and a rash characterized by small hemorrhages.
Diagnosis of Anaplasma & Ehrlichia is accomplished through antibody testing, blood smears or (more accurate) enhanced blood smears, and PCR. Research suggests Anaplasma like organisms may exist in tics that are not screened for by labs, that may be able to create symptoms.
These infections are usually resolved with doxycycline antibiotics. Rifampin is sometimes added to antibiotic therapy.

Mycoplasma & Chlamydia Pneumonias
Mycoplasma and chlamydia pneumonias are walking pneumonias, extremely common in primary care practice. However, research has demonstrated that both have the ability to persist intracellularly and evade immune detection. These infections can be reactivated by Lyme Disease and its co-infections. They can create chronic infections with widespread symptoms including:
Chronic Fatigue
Persistent Asthma and/or Respiratory symptoms resistant to treatment
Arthritis and Joint Pain
Skin Rashes
Neuroinflammation: Mycoplasma pneumonia is associated with neuropathies and inflammation of brain and nerve tissue as well as ALS. Chlamydia pneumonia is associated with Alzheimer’s Disease and Multiple Sclerosis.
Immune Suppression
Mycoplasma pneumonia can also create inflammatory conditions of the eyes, kidneys, and heart and promote conditions of clotting and bleeding. Chlamydia pneumonia is also associated with atherosclerosis. Both infections create generalized inflammation through the production of cytokines.
In addition to being present with Lyme Disease, both infections may also be triggered by mold illness.
Diagnosis of Mycoplasma & Chlamydia Pneumonias
These infections are usually diagnosed using serum antibody testing. Interpretation by a skilled clinician is required for diagnosis as antibody findings may reflect current re-activation of historical infection. If IgA and & IgM antibodies are present, they can help inform regarding the activity of infections. TGF-beta may be used as a marker of activity for chlamydia pneumonia, since it is up-regulated by infected immune cells called macrophages. However, this marker is not specific for chlamydia pneumonia and may also be elevated in cases of mold toxicity.
Because the infections can also evade immune detection, they may not show up on antibody testing until after treatment has been initiated. It is important to work with a well educated doctor to determine if suspicion for these infections is high before initiating treatment.
Treatment of Mycoplasma & Chlamydia Pneumonias

Because these pneumonias are bacterial persisters, they often require long term, combination antibiotic therapy. One of the best antibiotic therapies for chlamydia pneumonia is the Stratton Protocol, developed by Dr. Charles Stratton, a chlamydia pneumonia researcher at Vanderbilt University. His protocol entails a combination of amoxicillin, azithromycin or doxycycline, rifampin, and metronidazole. These antibiotics are supported with a number of natural products to help increase efficacy, reduce treatment side effects, and decrease inflammation. Antibiotic therapy for Mycoplasma pneumonia includes a combination of azithromycin, doxycycline, and Levaquin or Ciprofloxacin. Dr. Horowitz, an expert in Lyme Disease treatment, uses antibiotics for Bartonella to treat the walking pneumonias. I treated my own Chlamydia pneumonia persistent infection with the Dr. Stratton protocol and have used it in clinical practice with success. While effective, side effects can be difficult and limit patients’ willingness to complete treatment.
In my own practice, I begin treatment of persistent walking pneumonias with herbal and oxidative therapies which have less side effects and good results. I use similar treatments for both infections. My therapy begins with Olive Leaf extract, adequate levels of oral and nebulizer glutathione, and nebulized medical grade hydrogen peroxide with iodine. I also ensure patients have adequate levels of immune supportive nutrients, which can be depleted by these infections, and I often dose Cordyceps to helps support the immune system. Other natural approaches may include Byron White formulas and therapies aimed at reducing inflammatory cytokines associated with these infections. Magnesium deficiency is common with Mycoplasma and Chlamydia pneumonias and should be addressed to help reduce side effects of treatment.

Other Tick Borne Illnesses
This category of co-infections includes a variety of illnesses that are transmitted by ticks other than the classic Ixodes scapularis, or deer tick. These illnesses may be endemic to certain geographical areas and can occur with Lyme Disease and have similar symptoms. Infections include:
Tick Borne Relapsing Fever: Symptoms characterized by episodic flu like illness with drenching sweats and shaking chills, cough, abdominal pain, skin rashes, and a variety of neurological symptoms. Complications include lethal clotting diseases, airway distress syndrome, inflammation of heart wall leading to long term cardiovascular side effects, and enlargement of liver and/or spleen.
Tick Paralysis: This potentially lethal tick borne illness can be spread by approximately 400 different tick species. It begins as a non-specific viral illness followed by distal paralysis, often mimicking Guillain-Barre Syndrome.
STARI/Master’s Disease: This tick borne illness begins with the classic erythema migrans rash and can lead to long term symptoms of arthritis and Lyme carditis.
Rocky Mountain Spotted Fever: Rocky Mountain Spotted Fever is transmitted by several species of the Lone Star tick and can only survive inside the cells of another organism. Symptoms are characterized by flu-like illness and commonly a rash called a petechial rash caused by micro-bleeds under the surface of the skin.
Infections Associated with Immunocompromised Status
Some co-infections seen in Lyme Disease are not transmitted through tick bites but are present due to the immunocompromisation created by Lyme. These infections include:
Candida Infections: These may be oral, vaginal, or systemic. They may be secondary to Lyme Disease, mold illness, or antibiotic therapy used for treatment.
Viruses: Viral illnesses are extremely common in chronic illness and can be a trigger for many types of auto-immune conditions. Many viruses can persist as chronic infections with periods of dormancy and reactivation.The presence of viruses can make Lyme Disease more difficult to treat and the presence of Lyme Disease can make viruses more difficult to treat. The presence of viral infections can also worsen symptoms of a flare. Viruses to screen for in Lyme Disease include Epstein Barr Virus, Human Herpesvirus 6, Cytomegalovirus, Parvovirus, and West Nile Virus. Other viruses that may be tested for in Lyme Disease patients include Dengue Fever, Japanese Encephalitis, Equine Encephalitis, Chikungunya Virus, Possowan Encephalitis, Heartland Virus, and Bourbon Virus.
Toxoplasmosis gondii: Exposure to toxoplasmosis occurs through consumption of undercooked meat or infected cat feces (e.g. you change the litter box and hands don’t get washed well enough).. Risk of infection is greater when infection with parasites is also present. Most people infected never develop symptoms but those who do may experience flu-like illness. Toxoplasmosis has risk for serious complications in the severely immunocompromised.
Brucellosis: This infection is spread through ingestion of infected animal products and can create chronic infection mimicking Lyme Disease. It may occur with Mycoplasma pneumonia. If all treatment options have been exhausted and common co-infections and toxicities have been ruled out while Lyme Disease symptoms persists, testing for Brucellosis may be helpful. However, testing may produce false positives.
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