Chapter 3 Endnotes for Arthritis and Autoimmune Disease: The Infection Connection

How Infection Works

1)   Rose NR, Bona C. "Defining criteria for autoimmune diseases (Witebsky's postulates revisited)". Immunol. Today 14 (9): 426–30. (September 1993).

2)   The autoimmune theory is underscored repeatedly in immunology textbooks such as Bittar, EE and Bittar, N. Immunobiology, Elsevier (1996) pg 240, and also in various articles in Arthritis Today, the publication of the Arthritis Foundation. The original autoimmune theory appears in Rose and MacKay (3rd edition, 1986) but updated in their 4th edition (2006). An example of a more realistic view is “Interview with evolutionary biologist Paul Ewald” by Amy Proal at Also see  Also on this website are lots of useful data on Chronic Disease and the Marshall Protocol. Another good reference is

3)   Brown and Scammell (1988) pp. 78-79. Assorted childhood rheumatic infections are part of Katherine Poehlmann’s medical history (bronchitis, strep throat, pneumonia).

4)   See for paper citations, case studies, laboratory results, abstracts, and so forth. An impressive paper by Dr. Joseph M. Mercola, D.O., “Protocol for Using Antibiotics in the Treatment of Rheumatic Diseases,” can be found at The paper was presented at the 31st Annual Meeting of the American Academy of Environmental Medicine in Boston, MA in October 1996. Dr. Mercola lauds Dr. Brown’s pioneering work in mycoplasma research and tetracycline treatment. His paper essentially expands on Dr. Brown’s and Henry Scammell’s fundamental work, The Road Back. Dr. Mercola offers a description of the original protocol using minocycline in Appendix II of this book. This text is written by a physician for physicians and may be difficult for the layperson to understand. Dr. Mercola has improved upon the protocol by introducing a nutritional regimen to strengthen the immune system. See details at

5)   Blumberg, Dr. Darren R. and Sloan, Dr. Victor S. of the Robert Wood Johnson Medical School, New Brunswick, New Jersey in a letter “Classification of Reactive Arthritides.”

6)   Also see Veys E.M. and Mielants, H. “Enteropathic Arthropathies.” In: Klippel and Dieppe (1994).

7)   Sieper, J, Braun, J, “Editorial: Treatment of Reactive Arthritis with Antibiotics.” British Journal of Rheumatology, 1998, 37(7), 717-720

8)   Newkirk MM, et al. “Elevated levels of IgM and IgA antibodies to Proteus mirabilis and IgM antibodies to Escherichia coli are associated with early rheumatoid factor (RF)-positive rheumatoid arthritis.” Rheumatology (Oxford) 2005;44:1433-41.Also Ebringer A, Rashid T. “Rheumatoid arthritis is an autoimmune disease triggered by Proteus urinary tract infection.” Clin Dev Immunol. 2006 Mar;13(1):41-8.  An impressive body of research on P. mirabilis and its role in RA has been done by Alan Ebringer. E.g., and other articles on PubMed.

9)   Wilson R. “Treatment of COPD exacerbations: antibiotics.” Eur Respir Rev  2005 Sept vol. 14 no. 94 32-38. Also Hunter MH, M.D. and King DK, M.D. “COPD: Management of Acute Exacerbations and Chronic Stable Disease.” Am Fam Physician. 2001 Aug 15;64(4):603-613. Online at Also

10)   NIH Backgrounder. (Unattributed article). “Stress System Malfunction Could Lead to Serious, Life Threatening Disease” (2002)

11)   Fogoros RN, M.D. “Metabolic Syndrome.” Online at (2008)


13) (2011)


15)   Nabipour I, Vahdat K, et al. “The association of metabolic syndrome and Chlamydia pneumoniae, Helicobacter pylori, cytomegalovirus, and herpes simplex virus type 1: the Persian Gulf Healthy Heart Study.” Cardiovasc Diabetol. 2006 Dec 1;5:25. Online at

16)   Goldstone, T, et al. “Stomach hormone ghrelin increases desire for high-calorie foods.”Presentation at The Endocrine Society’s 92nd Annual Meeting in San Diego, CA, June 2010.

17)   Mårin and Farris (2005)

18)   Henley DE, et al. “Hypothalamic-pituitary-adrenal axis activation in obstructive sleep apnea: the effect of continuous positive airway pressure therapy.” J Clin Endocrinol Metab. 2009 Nov;94(11):4234-42. Online at


20)   Find a wealth of dental infection information at Also see George E. Meinig, DDS Root Canal Cover-Up (1994)  See biofilms at

21)   Baumgartner S, Imfeld T, et al. “The impact of the stone age diet on gingival conditions in the absence of oral hygiene.” J Periodontol. 2009 May;80(5):759-68.


23)   Touyz LZ. “Oral scurvy and periodontal disease.” J Can Dent Assoc. 1997 Dec;63(11):837-45. Online at

24)   Sparks SP, Desrosiers M, Donegan SJ, et al. “Tooth loss, dementia and neuropathology in the Nun Study.” J Am Dent Assoc 2007;138:1314–1322

25)   Elizabeth Kaye, MPH, PhD. “Periodontal Disease and impaired cognition.” June, 2010. Online at

26)   Liao F, Li Z, et al. “Porphyromonas gingivalis may play an important role in the pathogenesis of periodontitis-associated rheumatoid arthritis.” Med Hypotheses. 2009 Jun;72(6):732-5.


28)   Conversation with Dr. Jack Davis, a dentist practicing in Greer, SC.

29)   Dr. Aristo Vojdani’s intense interest in the study of infectious diseases began when his mother was diagnosed with RA after her dental surgery led to a bacterial infection. His California lab does comprehensive testing for autoimmunity, Lyme Disease, bacterial and viral diseases. See



32)   McCabe (1988 and 2004)

33)   Sadly, their findings and subsequent research were deliberately ignored.



36) (2008)

37)   Also see Garten (1978) for excellent information on dental infections and metal amalgams.

38)   This section includes insights from a presentation by Dr. Charles W. Stratton at the 2011 IFM international conference on infectious diseases in Bellevue, WA. Also see a comprehensive reference,“The Chlamydia Pneumoniae Handbook” at


39)   Until 2009, this organism was known as Chlamydia pneumoniae, but both names are now used interchangeably. See and use the search window with either term to find publications.

40)   Find an excellent overview of all the Chlamydiaceae family at


42)   See more about this test at

43)   Johanning (2005).

44)  (1997)

45)   This section includes insights from a presentation by Dr. David Perlmutter at the 2011 IFM international conference on infectious diseases in Bellevue, WA.

46)   Letenneur L, et al. “Seropositivity to herpes simplex virus antibodies and risk of Alzheimer's disease: a population-based cohort study.” PLoS One. 2008;3(11):e3637. Online at

47)   Itzhaki RF, Wozniak MA. “Herpes simplex virus type 1 in Alzheimer's disease: the enemy within.” J Alzheimers Dis. 2008 May;13(4):393-405. Also Wozniak MA, Mee AP, Itzhaki RF. “Herpes simplex virus type 1 DNA is located within Alzheimer's disease amyloid plaques.” J Pathol. 2009 Jan; 217(1):131-8. Statistics at

48)   Porcellini E, et al. “Alzheimer’s disease gene signature says: beware of brain viral infections.” Immunity & Ageing 2010, 7:16 . Online at

49)   Soscia SJ, Kirby JE, et al. “The Alzheimer's disease-associated amyloid beta-protein is an antimicrobial peptide.” PLoS One. 2010 Mar 3;5(3):e9505.

50)   Rubey RN. “Could lysine supplementation prevent Alzheimer's dementia? A novel hypothesis.” Neuropsychiatr Dis Treat. 2010 Oct 27;6:707-10.


52) discusses how chronically low levels of vitamin C contribute to heart disease. Tests on zoo gorillas using vitamin C supplements achieved dramatic results.

53) (2004) and

54)   Personal communication with Dr. Garth Nicolson, January 2002.

55)  (2010)

56)   “Mycoplasmal Infections,” a well-documented, detailed overview, is provided without charge to Institute for Molecular Medicine visitors to   

57) and - a0199  

58)   About 3 Tbs per day of coconut oil (lauric acid) would suffice to dissolve microbes’ lipid envelopes in the gut, lymph system, and blood.

59) (2009)

60)   Simmons WL and Dybvig K. “Mycoplasma Biofilms Ex Vivo and In Vivo.” FEMS Microbiol Lett. 2009 June; 295(1): 77–81. Online at

61)   Research conducted primarily by Dr. Albert Sabin, who worked with Dr. Brown at the Rockefeller Institute during the 1930s. Also see Simecka, J. W., et al. “Mycoplasma Diseases of Animals.” in Maniloff (1992) section V, chapter 24.

62)   All quotes attributed to Drs Baseman and Tully in this chapter may be found at

63)   Toppo (1986), p. 52. Also Pelton, R. et al., Drug-Induced Nutrient Depletion Handbook. Lexi Comp, Inc. 2001.

64)   Murray, et al. (2009) Chapter 6 (Bacteriology by Dr. Gene Mayer. Online at

65)   Cassel, G.H and Mekalanos J. “Development of Antimicrobial Agents in the Era of New and Reemerging Infectious Diseases and Increasing Antibiotic Resistance.” JAMA Feb 7 2001; 285(5), 601-5.

66)   Scammell (1998) p. 132.

67)   Hunter MH, M.D. and King DK, M.D. “COPD: Management of Acute Exacerbations and Chronic Stable Disease.” Am Fam Physician. 2001 Aug 15;64(4):603-613. Online at Also

68)   Wilson R. “Treatment of COPD exacerbations: antibiotics.” Eur Respir Rev  2005 Sept vol. 14 no. 94 32-38.

69)   McManus TE, et al. “High levels of Epstein–Barr virus in COPD.” Eur Respir J 2008; 31: 1221–1226

70)   Drs Baseman and Tully (1997): .”..pathogenic mycoplasmas are among the most difficult microorganisms to grow from clinical specimens and remain frequent contaminants of primary and continuous eucaryotic cell lines and tissue cultures. In some instances, mycoplasma contamination is obvious since infected eucaryotic cells exhibit aberrant growth, metabolism, and morphology. However, mycoplasmas often establish covert and chronic infections of target cells that lead to either invalid and misleading data or introduction of mycoplasmas or their products into reagents dedicated to therapeutic or research purposes.”

71)   Engelhard, Victor H. “How Cells Process Antigens.” Scientific American, August 1994. Also “The Immune System–Overview”(2011) at immunity/immune-overview.html.

72)   Personal communication with Dr. Garth Nicolson, January 2002.

73)   Garrett (1995) pp. 572-5.

74)   Ataoglu, H.; Goksu, N.; Kemaloglu, Y.K.; Bengisun, S.; and Ozbilen, S. “Preliminary Report on L-forms: Possible Role in the Infectious Origin of Secretory Otitis Media.” Annals of Otology, Rhinology and Laryngology. June 1994; 103:6, 434-8.

75)   Watson, P., Voss, L., et al. “The Microbiology of Chronic Otitis media with Effusion in a Group of Auckland Children.” New Zealand Medical Journal. May 1996;109:1022, 182-4.

76)   Mel'nikoava NN, Mokrousova IV. “Study of rifampicin resistance in L-forms of Mycobacterium tuberculosis, by analyzing rpoB gene mutations.” Probl Tuberk Bolezn Legk. 2006;(11):22-4.  [in Russian]

77)   Nicolson, Garth L.; Nasralla, Marwan Y.; and Nicolson, Nancy L. “The Pathogenesis and Treatment of Mycoplasmal Infections.” Antimicrobics and Infectious Disease Newsletter. 1999;17(11): 81-8.

78)   See (2000). Also Carvalho JR, Filipe L, et al. “Detailed analysis of expression and promoter methylation status of apoptosis-related genes in prostate cancer.” Apoptosis. 2010 Aug;15(8):956-65.

79)   Gdoura R, et al. “Assessment of Chlamydia trachomatis, Ureaplasma urealyticum, Ureaplasma parvum, Mycoplasma hominis, and Mycoplasma genitalium in semen and first void urine specimens of asymptomatic male partners of infertile couples.” J Androl. 2008 Mar-Apr;29(2):198-206. Online at

80) shows a detailed history of the development of the Marshall Protocol, with hot links to many informative publications and research findings.

81)  (2003)

82)   Park, H. J., Lee, S.H., et al. "Antiarthritic Effect of Bee Venom: Inhibition of Inflammation Mediator Generation by Suppression of NF-êB Through Interaction With the p50 Subunit." Arthritis & Rheumatism, November 2004; 50:11; pp. 3504-3515.

83)   Rothfeld, Glenn, M.D. “About Bee Venom Therapy.” Online, with many references to scientific literature on bee products, bee venom, and other types of venom, at

84)   Roberts, MC. “Antibiotic Resistance.” in Maniloff (1992), section V, chapter 31.

85)   Brandt DB, et al. “The Promise of a Tetracycline Antibiotic for Treating Osteoarthritis.” Arthritis & Rheumatism. 2005;52(7):2015-2025. Online at

86)   Hunter MH, M.D. and King DK, M.D. “COPD: Management of Acute Exacerbations and Chronic Stable Disease.” Am Fam Physician. 2001 Aug 15;64(4):603-613. Online at

87)   Wilson R. “Treatment of COPD exacerbations: antibiotics.” Eur Respir Rev  2005 Sept vol. 14 no. 94 32-38.


89)   Appendix: “Antibiotics: Efficacy Against Susceptible Pathogens.” Physician’s Drug Handbook (2007).

90) (2008)

91) lists herb and vitamin interactions with tetracycline.

92)   See

93)   Malley, Beth A. “The Use of Minocycline in the Treatment of Rheumatoid Arthritis.” For a PDF of this article, click here or Google “encognitive townsend letter minocycline”

94)   BC Tilley, GS Alarcon, et al, “Minocycline in Rheumatoid Arthritis: a 48 Week, Double-Blind, Placebo-Controlled Trial,” Ann Int Med, 1995; 122:2, pg 81 -89.

95)   O’Dell, J.R.; Paulsen, G.; Haire, C.E.; et al. “Treatment of Early Seropositive Rheumatoid Arthritis with Minocycline: Four-year Followup of a Double-blind, Placebo-controlled Trial.” Arthritis and Rheumatology 1999;42:1691-1695.

96)   See “Arthritis Treatments.”


98)   Haier J, Nasralla M, Franco AR, and Nicolson GL.“Detection of mycoplasmal infections in blood of patients with rheumatoid arthritis.” Rheumatology 1999;38(6): 504-509.

99) (2010)

100) (2005)

101) (2011)

102)   See This is an excellent and comprehensive website with many informative articles on chronic illnesses.

103)   Scammell (1998) p. 212.

104)   Mandell (1983) chapter 5.

105)   Brown and Scammell (1988) chapter 15.


107)   Ongoing microbiology research by Dr. Stuart Levy, Tufts University.

108)   “Functional Anatomy of Prokaryotic and Eukaryotic Cells.” Chapter 4 of textbook by Tortora, et al (2006). Online at

109)   Sánchez-Vargas FM, Gómez-Duarte OG, “Mycoplasma pneumoniae—an emerging extra-pulmonary pathogen.” Clinical Microbiology and Infection. Volume 14, Issue 2, pages 105–115, Feb 2008. Online at

110)   Baum (2005)

111)   Brown and Scammell (1988) chapter 23.

112)   See for Dr. Mercola’s comprehensive three-part program. He has helped thousands of his patients who make a commitment to this admittedly difficult but ultimately rewarding dietary plan.

113) This site lists several doctors who will administer the antibiotic protocol:

114)   This section represents insights obtained at the Institute for Functional Medicine’s 2011 international symposium “The Challenge of Emerging Infections in the 21st Century.” Notably, Dr. Michael Ash’s presentation “Living with the Host:  Immune Programming and Clinical Implications.”

115)   Dubois, B, et al. “Sequential role of plasmacytoid dendritic cells and regulatory T cells in oral tolerance.” Gastroenterology. 2009 Sep. 137(3): 1019-28.

116)   Maynard, CL, Weaver, CT. “Intestinal T cells in health and disease.” Immunity 2009 Sep 16:31(3);388-400. Review.

117)   The chemicals in Lavoris® mouthwash have been known to kill the bacteria that cause GERD. These are zinc oxide, sodium hydroxide, and citric acid..

118)   A procedure called Transnasal Esophagoscopy (TNE) gives physicians a new and more effective way to detect esophageal tumors.  (2011) Dr. Jonathan Aviv has demonstrated the technique on the Dr. Oz Show.

119)   Presentation by Dr. Sandra Macfarlane at the 2011 International IFM conference in Bellevue, WA

120)   One example is Macfarlane S, Dillon JF. “Microbial biofilms in the human gastrointestinal tract.” J Appl Microbiol. 2007 May;102(5):1187-96. Online at

121)   See “Gut Bacteria and Health Countermeasures” at health.htm (2011)

122)   Protocol for Antibiotic Therapy, from The Road Back Foundation at

123)   Murray, et al. Medical Microbiology, 2005, chapter 40.

124) (2008)

125) (2006) Also search on keywords “disbacteriosis” and “dysbiosis” at

126)   See details at  (2009)

127)   See “A Revolution in Our Understanding of Oils and Nutrition” at

128)   This short subsection is not intended to be prescriptive. There are a great many health texts which give detailed information on a balanced diet specifically for countering yeast infections.  See, for example, Crook (1986, 1995) and also (2011) and (use the search window on this website).

129)   Communication with nutritionist Dr. Victoria Arcadi, who states that 60-80% of her patients have systemic yeast overgrowth.


131) (2007)

132)   There are many books and informative websites on this topic, e.g., and Harsh laxatives are not recommended.

133)   Waling, E. “Apple Cider Vinegar is Effective Treatment for Candida.” (2009). Online at

134)   Lawson, C. “Cure Yeast Infection Naturally With Garlic.” The American Chronicle. (2009).

135)   Crook ( 1986) and Crook (1995)


137)   Cho SS and Finocchiaro T. (2010)

138)   Find a complete list at

139)   Find details at

140)   See


142)   Overview with many references:


144)   Find details at

145)   Painter, FM. “Bromelain Monograph.” Altern Med Rev Aug 1998:3(4)302-30. Online at Overview with many scientific references.

146)   Cichoke and Hoffer (2000)

147)   Fraser R, Ingram MC, et al. “Cortisol Effects on Body Mass, Blood Pressure, and Cholesterol in the General Population.” Hypertension. 1999;33:1364-1368.  Online at

148)   Diagram online at


150)   Bergman, J. “ATP The Perfect Energy Currency for the Cell.” Creation Research Society Quarterly, Vol 36, No.1. 1999. Online at Excellent overview with diagrams.

151) Textbook overview with diagrams.

152)   Mevalonate pathway mechanism at

153)   Unattributed article. “Cholesterol-Reducing Drugs May Lessen Brain Function, Says Researcher.” ScienceDaily (Feb. 23, 2009) Online at


155)   O’Riordan, M. “Statin-induced myopathy reflects structural muscle damage, new study shows.” 7/6/2009. Online at

156)   Details at

157)   Article by the late Dr. H.A. Nieper on serrapeptase and carotid artery blockage: Also see the forum on serrapeptase at 

158)   Sharma AK. “A Preliminary trial of Serratiopeptidase in patients with Carpal Tunnel Syndrome.” J Assoc Phy India. 2000;48:1130.

159)   Unattributed article. “Serrapeptase Insect-Derived Enzyme Fights Inflammation.” Online at (2001)

160)   Selan L, Berlutti F, et al. “Proteolytic enzymes: a new treatment strategy for prosthetic infections?” Antimicrob Agents Chemother. 1993; 37(12):2618-21.

161)   See

162)   Ma G and Allen HC. “New Insights into Lung Surfactant Monolayers Using Vibrational Sum Frequency Generation Spectroscopy.” Photochemistry and Photobiology, 2006, 82: 1517–1529. Online at

163)   Howell (1995)

164) (2005)


166)   Howell (1995)

167) This reference and information guide is comprehensive and useful. Although it appears on a commercial vitamin/supplement site, citing the guide does not mean that Dr. Poehlmann receives any compensation or endorses any products sold on the website.


169)   More detail at and


171)   Brown and Scammell (1988) chapter 7.

172)   A good rule of thumb: every pound of excess weight exerts 4 pounds of pressure on knee and ankle joints.

173)   Maksymowych, W.P.; Ikawa, T.; Yamaguchi, A.; Ikeda, M., et al. “Invasion by Salmonella typhimurium Induces Increased Expression of the LMP, MECL, and PA28 Proteasome Genes and Changes in the Peptide Repertoire of HLA-B27.” Infection & Immunity. 66: 4624-32, 1998.

174)   Ikawa, T.; Ikeda, M.; Yamaguchi, A.; Tsai, W.C., et al. “Expression of  Arthritis-causing HLA-B27 on Hela Cells Promotes Induction of C-Fos in Response to in vitro Invasion by Salmonella typhimurium.” Journal of Clinical Investigation. 101: 263-72, 1998.

175)   Adams JS, Lee G. “Gains in bone mineral density with resolution of vitamin D intoxication. Ann Intern Med 1997;127:203–6. Online at

176) shows a detailed history of the development of the Marshall Protocol, with hot links to many informative publications and research findings.

177)   Olszewski (1987) pp. 123-127. See also Vinh, DC, Embil, JM "Severe skin and soft tissue infections and associated critical illness". Curr Infect Dis Rep 9 (5): 415–21, September 2007.


179)  and The last is a commercial site but the article presented is useful and informative. Dr. Poehlmann does not support or endorse any commercial products. Her efforts are completely nonprofit. Google “Enig fats oils” to find many of her papers and online references.



182)   Kandasamy P, Zarini S, Chan ED, et al. “Pulmonary surfactant phosphatidylglycerol inhibits Mycoplasma pneumoniae-stimulated eicosanoid production from human and mouse macrophages.” J Biol Chem. 2011 Mar 11;286(10):7841-53

183)   See Properties & Their Role in Autoimmune Diseases/index.htm  (August 1999 presentation by Dr. Harold Clark as a lecture series)

184)   Connor, J.F., DVM. “Early Pig Vaccination Disease Breakthrough Mycoplasmal Pneumonia Vaccine for Young Pigs Shows Promise.” (2009). Online at


186)   See

187)   Michaud (1989) chapter 9. Also “The Immune System–Overview”(2011) at

188)   Culhane, Kari W. “Allergy Antidotes for Kids.” Natural Health, March/April 2000.

189)   Michaud (1989) pp. 64-5.

190)   Mandell, Dr. Marshall (1988) Megadoses of any vitamin are not recommended over time. The large amounts he suggests are for a specific and intense allergic reaction, not for daily intake, even as a preventive measure.

191)   Personal communication with Dr. Garth Nicolson, January 2002.


193)   Ullman D and Frass M. “A Review of Homeopathic Research in the Treatment of Respiratory Allergies.” Alternative Medicine Review, Vol 15, Number 1. (2010). Online at Also see .

194)   Visit, enter the homeopathic remedy in the search window to find details of conditions to which it applies. The site contains many informative articles and references. Also search by condition to find applicable natural remedies.



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