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Navigating the Complexities: How Chronic Infections Influence Our Body's Systems

What are chronic infections?

Chronic infections are prolonged infections that failed to resolve at the acute phase. They can be viral, bacterial, fungal, or parasitic in origin and they can cause persistent or recurrent health problems. Presentations of chronic infections can vary greatly depending on the type and severity of the infections. They can either cause local problems at the site of infections or more frequently, cause systemic problems and symptoms.

Common presentations of chronic/recurrent infections

  • Chronic/recurrent sinusitis

  • Chronic/recurrent otitis media

  • Chronic/recurrent vaginal infections (bacterial vaginosis, vaginal yeast infection)

  • Chronic/recurrent skin fungal infections (athlete’s foot, jock itch, toenail fungus)

  • Recurrent gastroenteritis

  • Intestinal dysbiosis

    • Intestinal bacterial, candida, and yeast overgrowth

    • SIBO (small intestine bacterial overgrowth), SIFO (small intestinal fungal overgrowth)

    • Intestinal parasitic infections

  • Lyme disease

Common impacts of chronic infections

Immune deficiency & immune suppression

  • Chronic infections can suppress our immune system and decrease our ability to fight off infections. [1]

  • Symptoms: getting cold, flu, or other types of infections more easily, and/or recovering from infections slowly.

  • Having poor immune function also increase your risk of getting infected by other pathogens (co-infections).


  • Getting infected by multiple pathogens simultaneously. [2]

  • Co-infections can further complicate and potentiate the other impacts of chronic infections.

Formation of pathogenic biofilms

  • Different pathogens can come together and form colonies, where they produce a polymer matrix to embed and protect themselves.

  • Biofilms make pathogens more resistant to our immune system's attacks, antibiotics, and antifungals. [3]

  • Biofilms are often the root cause of a chronic/resistant infection that fails to respond to pharmaceutical or herbal antimicrobials well.

  • More about biofilms.

  • In order to remove/contain these resistant infections, biofilms will need to be broken up to allow these hidden pathogens to be released and killed.


  • Chronic infections often contribute to the development of autoimmune diseases, via molecular mimicry and bystander activation [4]

Nutrient deficiency

  • Pathogens in the digestive tract can compete with us for nutrient absorption or affect the body's ability to absorb nutrients (e.g. B12 and iron deficiencies are common in SIBO). [5]

Chronic inflammation

  • Inflammation is one of our immune system's responding mechanisms to infections (e.g. immune cells produce pro-inflammatory cytokines when there's an infection).

  • When infections are prolonged, inflammation can become chronic too.

Oxidative stress

  • Our immune cells produce free radicals to help fight off pathogens in times of infection and free radicals generate oxidative stress. [6]

  • When infections become chronic, free radicals can build up and increase the overall oxidative stress load in our bodies.

  • Oxidative stress can cause damage to our DNA and our cells, and it's also a cause of chronic inflammation.

  • Oxidative stress and inflammation are related to many chronic health conditions including cardiovascular disease, diabetes, neurodegenerative diseases, autoimmune diseases, and cancer.

Endocrine dysfunction

  • Chronic infections often cause hypothyroidism (overt, subclinical, or functional), adrenal fatigue, and sex hormone imbalances.

  • Symptoms like fatigue, brain fog, hair loss, weight gain/weight loss, muscle weakness, poor immune function, and irregular or heavy menses are therefore commonly seen in people with chronic infections.

Mitochondria dysfunction

  • Bacteria and viruses are capable of hijacking and affecting mitochondrial function

  • Oxidative stress generated by infections can also cause damage to the function of mitochondria. [7]

  • Mitochondria is the "power plant" of our cells and body, responsible for most energy generation.

  • Mitochondria are also involved in several key metabolic pathways and dysfunction of mitochondria can cause fatigue, muscle weakness, neurological symptoms, digestive issues, thyroid problems, etc.

  • Conditions like chronic fatigue syndrome and fibromyalgia are commonly associated with mitochondria dysfunction and are among the common diagnoses found in people with chronic infections.

Leaky gut

  • When a chronic infection happens in the intestines, be it bacterial, fungal (Candida or yeast), or parasitic in origin; it can cause an increase in the permeability of intestinal linings, resulting in leaky gut syndrome.

  • These "gaps" in the intestinal lining allow bacteria, food particles, toxins, and drugs inside the intestines to pass through the gaps and enter the bloodstream.

  • These substances that shouldn't exist in the bloodstream will cause systemic and widespread problems, including headaches, anxiety, food allergies/intolerance, joint pain, itchy skin, skin rashes/hives, acne, chronic inflammation, autoimmunity, leaky blood-brain barrier, etc.

Leaky blood-brain barrier (leaky brain)

  • The blood-brain barrier (BBB) separates the brain from the circulating blood to allow only selective substances like hormones and nutrients to enter the brain, thereby protecting the brain and the central nervous system (CNS) from harmful substances or pathogens.

  • Systemic inflammation, oxidative stress due to infections, and an imbalance of the gut microbiome can disrupt the blood-brain barrier (BBB), causing "leaky brain" and leading to neuroinflammation. [8]

  • When the integrity of the BBB is compromised; pathogens, toxins, and chemicals from the bloodstream can now get into the brain.

  • Leaky brain can cause symptoms like anxiety, depression, brain fog, memory loss, headaches, migraines, numbness, and tingling.

  • Leaky brain is also associated with neurological conditions like autistic spectrum disorder, dementia, Alzheimer's disease, Parkinson's disease, and schizophrenia.

How to recover from chronic infections?

Depending on the severity and duration of the chronic infections, this can be a short or extensive list:

  • Identify which pathogens are involved (different pathogens exhibit different "personalities" and may be more susceptible to different antimicrobials)

  • An anti-inflammatory diet or specific diet for specific types of infections (e.g.: anti-candida diet for intestinal/vaginal fungal infection, elemental diet, or SIBO-specific diet for SIBO)

  • Pharmaceutical or herbal antimicrobials to help eliminate or control the infections

  • Boost and regulate the immune system

  • Address biofilms

  • Remove underlying obstacles that can affect the healing process

    • E.g.: heavy metals, environmental hormones, mycotoxins, psychological stress

    • Mold and mycotoxin illnesses can be common in resistant and persistent infections

  • Support the endocrine system

    • Suboptimal thyroid, adrenal, and sex hormones can further affect our immune function and the body's ability to fight off infections

  • Support mitochondria function

  • Reduce oxidative stress and inflammation

  • Repair and optimize gut microbiome

  • Repair blood gastrointestinal barrier and blood-brain barrier

  • Replenish nutrients

Chronic infections are frequently present in people with chronic health conditions and therefore other factors like environmental toxins, allergies, mental and emotional stress, and structural problems often co-exist. To heal from chronic infections effectively, it's crucial to seek advice from a health professional to address all the underlying root causes and heal the body from all levels (body, mind, spirit).


  1. Bonagura, Vincent Robert, and David Walter Rosenthal. “Infections that cause secondary immune deficiencym's Immune Deficiencies (2020): 1035–1058. doi:10.1016/B978-0-12-816768-7.00049-1

  2. Bonagura, Vincent Robert, and David Walter Rosenthal. “Infections that cause secondary immune deficiency.” Stiehm's Immune Deficiencies (2020): 1035–1058. doi:10.1016/B978-0-12-816768-7.00049-1

  3. Bjarnsholt, Thomas. "The role of bacterial biofilms in chronic infections." Apmis 121 (2013): 1-58.

  4. A M Ercolini, S D Miller, The role of infections in autoimmune disease, Clinical and Experimental Immunology, Volume 155, Issue 1, January 2009, Pages 1–15,

  5. Bures, Jan, et al. "Small intestinal bacterial overgrowth syndrome." World journal of gastroenterology: WJG 16.24 (2010): 2978.

  6. Pohanka, Miroslav. "Role of oxidative stress in infectious diseases. A review." Folia microbiologica 58.6 (2013): 503-513.

  7. Meeus M, Nijs J, Hermans L, Goubert D, Calders P. The role of mitochondrial dysfunctions due to oxidative and nitrosative stress in the chronic pain or chronic fatigue syndromes and fibromyalgia patients: peripheral and central mechanisms as therapeutic targets? Expert Opin Ther Targets. 2013 Sep;17(9):1081-9. doi: 10.1517/14728222.2013.818657. Epub 2013 Jul 9. PMID: 23834645.

  8. Obrenovich, Mark E M. “Leaky Gut, Leaky Brain?.” Microorganisms vol. 6,4 107. 18 Oct. 2018, doi:10.3390/microorganisms6040107


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