The Institute for Molecular Medicine




Autoimmune Illnesses and
Degenerative Diseases

Prof. Garth L. Nicolson

Rheumatoid Arthritis, Multiple Sclerosis, Lupus, Inflammatory Bowel Diseases, Scleroderma and other Autoimmune and Degenerative Diseases

Autoimmune and Degenerative Diseases are complex, multiorgan diseases of unknown etiology. Although we do not know exactly what causes Autoimmune and Degenerative Diseases, there is increasing evidence that in many patients chronic infections, particularly by certain bacteria and viruses, play an important role in these diseases along with genetic predisposition and immune dysfunction. How could infections be important in Autoimmune Diseases? They could be involved in helping to cause the illness, or they can affect patients by serving as cofactors for the illness (not causing illness on their own but serving as important factors in the disease process) or even as opportunistic infections that increase patient morbidity (sickness) and complications associated with the disease (see Nicolson et al., Antimicrobics and Infectious Diseases Newsletter, 1999).

Infections have been found in a variety of Autoimmune Diseases, particularly in Rheumatic Diseases, such as Rheumatoid Arthritis, Scleroderma, and other rheumatic disorders. We and others have gathered substantial evidence that chronic bacterial and viral infections are commonly associated with Rheumatic Diseases, and many of these patients respond to antibiotic therapy. These patients are now recovering from their illnesses after decades of inadequate diagnoses and treatments. The recovery is slow; it usually takes up to or over a year to recover, but these patients had no alternative or effective treatments for their conditions, other than the alleviation of pain.

Chronic infections are important in a variety of autoimmune and neurodegenerative diseases, such as MS, Lupus (SLE), among others, and neurodegenerative diseases, such as Amyotrophic Lateral Sclerosis (ALS). We previously proposed that many and perhaps a majority of these patients might be suffering from mycoplasmal and other infections that can cause, in part, their complex signs and symptoms. Systemic chronic infections (caused by bacteria such as Mycoplasma, Chlamydia, Borrelia, Brucella, etc. or viruses such as CMV, HHV6, EV or enterovirus, etc.) can invade virtually every human tissue and can compromise the immune system, permitting opportunistic infections by other bacteria, viruses, fungi and yeast. Mycoplasma, Chlamydia, Borrelia, Rickettsia and other pathogens can also directly damage and kill nerve cells in a process called apoptosis, resulting in nervous system degeneration.

When mycoplasmas exit certain cells, such as synovial cells, nerve cells, among others that can be infected, they can stimulate an autoimmune response. This can occur by different mechanisms. One mechanism that has intrigued us is that when certain microorganisms, such as certain species of mycoplasmas, exit from invaded cells, they carry part of the host cell membrane on their surface. This may trigger the immune system to respond to the host antigens on the foreign microorganism. Alternatively, some microorganisms display surface antigens that mimic host cell surface antigens, and these may stimulate autoimmune responses.

Other Autoimmune Diseases

Our recently published studies demonstrated a possible link between mycoplasmal infections and Rheumatoid Arthritis, since we found high frequency of multiple mycoplasmal infections in these patients (Haier et al., 1999). Previously we examined a variety of patients with chronic illnesses for the presence of mycoplasmal infections. We found that about one half other autoimmune diseases (Inflammatory Bowel Diseases, Sjögren's, Hashimoto's, Graves', Reiter's, Crohn's Diseases and others) are also associated with mycoplasmal, chlamydial, and other infections. Although these diseases have not been treated with antibiotics in large, blinded trials, there is some anecdotal evidence that antibiotics can be effective in a program with other treatments to alleviate morbidity in these patients.

New Treatments for Autoimmune Diseases

Patients with 'stealth' infections, such as caused by mycoplasmal and other bacteria, can be treated using antibiotics effective against such infections, and once they recover, their blood is no longer positive for the presence of the infection. Recent double-blind clinical studies sponsored by the National Institutes of Health indicate that some antibiotics are effective in treating Rheumatoid Arthritis. Our recent results indicate that in addition to Rheumatoid Arthritis other autoimmune diseases can be treated with antibiotics to suppress chronic bacterial infections, and antivirals to suppress chronic viral infections. Patients with such infections gain significant clinical benefits by undergoing therapies against chronic bacterial and viral infections.



  • Role of Chronic Bacterial and Viral Infections in Neurodegenerative, Neurobehavioral, Psychiatric, Autoimmune and Fatiguing Illnesses: Part 1, by Prof. Garth L. Nicolson and Jörg Haier, British Journal of Medical Practitioners 2009; 2(4): 20-28. pdf doc

  • Role of Chronic Bacterial and Viral Infections in Neurodegenerative, Neurobehavioral, Psychiatric, Autoimmune and Fatiguing Illnesses: Part 2, by Prof. Garth L. Nicolson and Jörg Haier, British Journal of Medical Practitioners 2010; 3(1): 301-311. pdf doc

  • Mycoplasma and other intracellular bacterial infections in rheumatic diseases: comorbid condition or cause? by Prof. Garth L. Nicolson, Open Journal of Tropical Medicine 2017; 1: 016-017. pdf_doc

  • Chronic Bacterial and Viral Infections in Neurodegenerative and Neurobehavioral Diseases by G.L. Nicolson, Laboratory Medicine 2008; 39(5): 291-299 pdf doc

  • An integrative model of chronically activated immune-hormonal pathways important in the generatin of fibromyalgia, by P.C. Breeding, N.C. Russell and G.L. Nicolson, British Journal of Medical Practitioners 2012; 5(3): a524-a534. pdf_doc

  • Mitochondrial dysfunction and chronic disease: treatment with natural supplements, by Nicolson G.L. Alternative Therapies in Health & Medicine 2014; 20(Suppl 1): 18-25. pdf_doc

  • Chronic Mycoplasmal Infections in Gulf War Veterans' Children and Autism Patients by G.L. Nicolson et al., Medical Veritas 2005; 2:383-387. pdf doc

  • High Frequency of Systemic Mycoplasmal Infections in Gulf War Veterans and Civilians with Amyotrophic Lateral Sclerosis (ALS), by G.L. Nicolson et al., Journal of Clinical Neuroscience 2002; 9: 525-529. pdf doc

  • Identification And Treatment Of Chronic Infections In CFIDS, Fibromyalgia Syndrome And Rheumatoid Arthritis, by Prof. Garth Nicolson, CFIDS Chronicle 1999; 12(3): 19-21 pdf doc

  • The Pathogenesis And Treatment Of Mycoplasmal Infections, by G.L. Nicolson et al., Antimicrob. Infect. Dis. Newsl. 1999; 17(11) : 81-88 pdf doc

  • Mycoplasmal Infections in Chronic Illnesses: Fibromyalgia and Chronic Fatigue Syndromes, Gulf War Illness, HIV-AIDS and Rheumatoid Arthritis, by G.L. Nicolson et al., Medical Sentinel 1999; 4:172-176 pdf doc

  • Detection of Mycoplasmal Infections in Blood of Patients with Rheumatoid Arthritis, by J. Haier et al., Rheumatology - 1999: 38: 504-509 pdf doc

  • Membrane Lipid Replacement—a functional approach to repairing cellular membranes, reducing symptoms, and restoring function, by Prof. G.L. Nicolson. Functional Food Science 2022; 2(8): 198-204. pdf_doc

  • Microbial translocation disorders: assigning an etiology to idiopathic illnesses, by Sfera A, Hazan S, Klein C, Zapata-Martin del Campo CM, Sasannia S, Anton JJ, Rahman L, Andronescu CV, Sfera DO, Kozakidis Z, and Nicolson GL.. Applied Microbiology 2023; 3(1): 212-240. pdf_doc

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  • The Vaccine Controversy. Why Full Informed Consent Must be Instituted for All Vaccines. by G.L. Nicolson and N.L. Nicolson,  Criminal Politics, 2003 pdf doc

  • Chronic Co-Infections in Rhematoid Arthritis, Chronic Fatigue Syndrome, Fibromyalgia Syndrome and Other Chronic Illnesses, by Prof. Garth Nicolson, The Intercessor Newsletter, The Road Back Foundation, 2002 pdf doc

  • Identification and Treatment of Chronic Infections in Rheumatoid Arthritis and other Chronic Diseases, by Prof. Garth Nicolson, The Intercessor Newsletter, The Road Back Foundation, 2001 pdf doc

  • Autoimmune Neurological and Rheumatic Diseases: Role of Chronic Infections in Morbitity and Progression, by Garth Nicolson and Nancy Nicolson, Proc. 13th Intern. Symp. Integrative Medicine 2001; 13: 104-112. pdf doc


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