On 2018 Feb 04, Sin Hang Lee commented:

The medical profession, including medical schools and hospitals, is now a part of the health care industry, and implementation of editorial policies of medical journals is commonly biased in favor of business interests. PubMed Commons has offered the only, albeit constrained, open forum to air dissenting research and opinions in science-based language. Discontinuation of PubMed Commons will silence any questioning of the industry-sponsored promotional publications indexed in PubMed.

On 2017 Jun 24, Sin Hang Lee commented:

Jorge Cervantes proposed a new theory to argue against the existence of chronic Lyme disease with persistent infection [1]. According to this theory, “after antibiotic eradication of Bb, its DNA is able to persist in anatomical locations that coincide with sites of inflammation.” He assumed that the free, naked and water-soluble DNA molecules released from the dying Borrelia burgdorferi spirochetes remain in the extracellular matrix of the patient’s tissues. However, under section “3. Borrelia DNA persistence” of his article, the references cited did not test for free borrelial DNA at all, and therefore do not back up his theory. For examples, in the reference by Li et al. [2], the authors concluded that the DNA detected was in moribund or dead B burgdorferi cells, not in free form. In the reference by Schmidt et al. [3] and the reference by Aberer et al. [4], borrelial DNA was detected in the pellet of patients’ urine samples after centrifugation at 14,000 x g and 36,000 × g, respectively. Since soluble free DNA molecules cannot be pelleted by such a low centrifugal force, the borrelial DNA detected by these authors must be still bound to bacterial cells or cell fragments in the urine. In the reference by Kubanek et al. [5], the authors actually showed by electron microscopy that the tissues tested positive for borrelial DNA clearly contained borrelial bacteria, not free DNA.

Free, extracellular, naked bacterial DNA is very prone to decay. Foreign DNA experimentally introduced into a mammal is degraded and eliminated from the host’s blood within 48 hours [6]. But the stability of extracellular DNA still depends on its form or even on the sequence of its nucleotide bases. Circular plasmid DNA is more stable in vitro than a segment of linear chromosomal DNA after release from the bacterial cell. Even DNase I does not cleave DNA randomly although not base nor sequence specific. Extracellular bacterial 16S rDNA is known to be degraded much more rapidly in the environment than those bound to cell fragments [7]. Borrelial 16S rDNA extracted by ammonium hydroxide stored in TE buffer is stable, but is degraded rapidly in human serum at room temperature (unpublished personal observation). DNA sequencing-confirmed detection of borrelial 16S rDNA in the pellet of serum or plasma samples derived from patients’ venous blood constitutes solid molecular evidence of spirochetemia in Lyme borreliosis [8, 9]. Whether spirochetemia in chronic Lyme disease needs to be treated with prolonged antibiotics is an important heath care issue which should be further discussed. To push an elusive DNA-binding AMP treatment of chronic Lyme disease can only direct the attention away from the real issue of how to define Lyme disease, acute or chronic, as an emerging infectious disease, like Ebola and Zika, for proper patient management. There is no evidence that free naked borrelial DNA has been demonstrated in any patient samples.

The author should also cite a reference to back up his claim that human macrophages can remove extracellular Bb DNA. The reference by Brencicova and Diebold [10], cited by the author, clearly stated “Endosomal TLR are situated in the membrane of the endolysosomal compartment of APC and sample the content of these compartments for the presence of nucleic acid agonists. Pathogens or dead cells gain access to the compartment by endocytosis. Alternatively, infection-induced autophagy can shuttle viral nucleic acids and antigens into the endolysosomal compartment and allow for recognition of replicating virus within infected cells by endosomal TLR.” Free DNA was not mentioned.

References [1] Cervantes J. Doctor says you are cured, but you still feel the pain. Borrelia DNA persistence in Lyme disease. Microbes Infect 2017 Jun 15. pii: S1286-4579(17)30090-4. doi: 10.1016/j.micinf.2017.06.002. [Epub ahead of print] Review. [2] Li X, McHugh GA, Damle N, Sikand VK, Glickstein L, Steere AC. Burden and viability of Borrelia burgdorferi in skin and joints of patients with erythema migrans or lyme arthritis. Arthritis Rheum 2011;63: 2238-47. [3] Schmidt B, Muellegger RR, Stockenhuber C, Soyer HP, Hoedl S, Luger A, et al. Detection of Borrelia burgdorferi-specific DNA in urine specimens from patients with erythema migrans before and after antibiotic therapy. J Clin Microbiol 1996;34:1359-63. [4] Aberer E, Bergmann AR, Derler AM, Schmidt B. Course of Borrelia burgdorferi DNA shedding in urine after treatment. Acta Derm Venereol 2007;87(1):39-42. [5] Kubanek M, Sramko M, Berenova D, Hulinska D, Hrbackova H, Maluskova J, et al. Detection of Borrelia burgdorferi sensu lato in endomyocardial biopsy specimens in individuals with recent-onset dilated cardiomyopathy. Eur J Heart Fail 2012;14:588-96. [6] Schubbert R, Renz D, Schmitz B, Doerfler W. Foreign (M13) DNA ingested by mice reaches peripheral leukocytes, spleen, and liver via the intestinal wall mucosa and can be covalently linked to mouse DNA. Proc Natl Acad Sci U S A. 1997;94:961-6. [7] Corinaldesi C, Danovaro R, Dell'Anno A. Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Appl Environ Microbiol 2005;71:46-50. [8] Lee SH, Vigliotti JS, Vigliotti VS, Jones W, Shearer DM. Detection of borreliae in archived sera from patients with clinically suspect Lyme disease. Int J Mol Sci. 2014;15:4284-98. [9] Lee SH. Lyme disease caused by Borrelia burgdorferi with two homeologous 16S rRNA genes: a case report. Int Med Case Rep J. 2016;9:101-6. [10] Brencicova E, Diebold SS. Nucleic acids and endosomal pattern recognition: how to tell friend from foe? Front Cell Infect Microbiol 2013;3:37.

On 2017 Jun 24, Sin Hang Lee commented:

Jorge Cervantes proposed a new theory to argue against the existence of chronic Lyme disease with persistent infection [1]. According to this theory, “after antibiotic eradication of Bb, its DNA is able to persist in anatomical locations that coincide with sites of inflammation.” He assumed that the free, naked and water-soluble DNA molecules released from the dying Borrelia burgdorferi spirochetes remain in the extracellular matrix of the patient’s tissues. However, under section “3. Borrelia DNA persistence” of his article, the references cited did not test for free borrelial DNA at all, and therefore do not back up his theory. For examples, in the reference by Li et al. [2], the authors concluded that the DNA detected was in moribund or dead B burgdorferi cells, not in free form. In the reference by Schmidt et al. [3] and the reference by Aberer et al. [4], borrelial DNA was detected in the pellet of patients’ urine samples after centrifugation at 14,000 x g and 36,000 × g, respectively. Since soluble free DNA molecules cannot be pelleted by such a low centrifugal force, the borrelial DNA detected by these authors must be still bound to bacterial cells or cell fragments in the urine. In the reference by Kubanek et al. [5], the authors actually showed by electron microscopy that the tissues tested positive for borrelial DNA clearly contained borrelial bacteria, not free DNA.

Free, extracellular, naked bacterial DNA is very prone to decay. Foreign DNA experimentally introduced into a mammal is degraded and eliminated from the host’s blood within 48 hours [6]. But the stability of extracellular DNA still depends on its form or even on the sequence of its nucleotide bases. Circular plasmid DNA is more stable in vitro than a segment of linear chromosomal DNA after release from the bacterial cell. Even DNase I does not cleave DNA randomly although not base nor sequence specific. Extracellular bacterial 16S rDNA is known to be degraded much more rapidly in the environment than those bound to cell fragments [7]. Borrelial 16S rDNA extracted by ammonium hydroxide stored in TE buffer is stable, but is degraded rapidly in human serum at room temperature (unpublished personal observation). DNA sequencing-confirmed detection of borrelial 16S rDNA in the pellet of serum or plasma samples derived from patients’ venous blood constitutes solid molecular evidence of spirochetemia in Lyme borreliosis [8, 9]. Whether spirochetemia in chronic Lyme disease needs to be treated with prolonged antibiotics is an important heath care issue which should be further discussed. To push an elusive DNA-binding AMP treatment of chronic Lyme disease can only direct the attention away from the real issue of how to define Lyme disease, acute or chronic, as an emerging infectious disease, like Ebola and Zika, for proper patient management. There is no evidence that free naked borrelial DNA has been demonstrated in any patient samples.

The author should also cite a reference to back up his claim that human macrophages can remove extracellular Bb DNA. The reference by Brencicova and Diebold [10], cited by the author, clearly stated “Endosomal TLR are situated in the membrane of the endolysosomal compartment of APC and sample the content of these compartments for the presence of nucleic acid agonists. Pathogens or dead cells gain access to the compartment by endocytosis. Alternatively, infection-induced autophagy can shuttle viral nucleic acids and antigens into the endolysosomal compartment and allow for recognition of replicating virus within infected cells by endosomal TLR.” Free DNA was not mentioned.

References [1] Cervantes J. Doctor says you are cured, but you still feel the pain. Borrelia DNA persistence in Lyme disease. Microbes Infect 2017 Jun 15. pii: S1286-4579(17)30090-4. doi: 10.1016/j.micinf.2017.06.002. [Epub ahead of print] Review. [2] Li X, McHugh GA, Damle N, Sikand VK, Glickstein L, Steere AC. Burden and viability of Borrelia burgdorferi in skin and joints of patients with erythema migrans or lyme arthritis. Arthritis Rheum 2011;63: 2238-47. [3] Schmidt B, Muellegger RR, Stockenhuber C, Soyer HP, Hoedl S, Luger A, et al. Detection of Borrelia burgdorferi-specific DNA in urine specimens from patients with erythema migrans before and after antibiotic therapy. J Clin Microbiol 1996;34:1359-63. [4] Aberer E, Bergmann AR, Derler AM, Schmidt B. Course of Borrelia burgdorferi DNA shedding in urine after treatment. Acta Derm Venereol 2007;87(1):39-42. [5] Kubanek M, Sramko M, Berenova D, Hulinska D, Hrbackova H, Maluskova J, et al. Detection of Borrelia burgdorferi sensu lato in endomyocardial biopsy specimens in individuals with recent-onset dilated cardiomyopathy. Eur J Heart Fail 2012;14:588-96. [6] Schubbert R, Renz D, Schmitz B, Doerfler W. Foreign (M13) DNA ingested by mice reaches peripheral leukocytes, spleen, and liver via the intestinal wall mucosa and can be covalently linked to mouse DNA. Proc Natl Acad Sci U S A. 1997;94:961-6. [7] Corinaldesi C, Danovaro R, Dell'Anno A. Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Appl Environ Microbiol 2005;71:46-50. [8] Lee SH, Vigliotti JS, Vigliotti VS, Jones W, Shearer DM. Detection of borreliae in archived sera from patients with clinically suspect Lyme disease. Int J Mol Sci. 2014;15:4284-98. [9] Lee SH. Lyme disease caused by Borrelia burgdorferi with two homeologous 16S rRNA genes: a case report. Int Med Case Rep J. 2016;9:101-6. [10] Brencicova E, Diebold SS. Nucleic acids and endosomal pattern recognition: how to tell friend from foe? Front Cell Infect Microbiol 2013;3:37.

On 2018 Feb 04, Sin Hang Lee commented:

The medical profession, including medical schools and hospitals, is now a part of the health care industry, and implementation of editorial policies of medical journals is commonly biased in favor of business interests. PubMed Commons has offered the only, albeit constrained, open forum to air dissenting research and opinions in science-based language. Discontinuation of PubMed Commons will silence any questioning of the industry-sponsored promotional publications indexed in PubMed.