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Lyme disease, or borreliosis, is an emerging infectious disease caused by bacteria from the genus Borrelia. The vector of infection is typically the bite of an infected black-legged or deer tick, but other carriers (including other ticks in the genus Ixodes) have been implicated. Borrelia burgdorferi is the predominant cause of Lyme disease in the U.S. and Borrelia afzelii and Borrelia garinii are in Europe.
The disease presentation varies widely, and may include a rash and flu-like symptoms in its initial stage, then musculoskeletal, arthritic, neurologic, psychiatric and cardiac manifestations. In a majority of cases, symptoms can be eliminated with antibiotics, especially if treatment begins early in the course of illness. Late or inadequate treatment often leads to "late stage" Lyme disease that is disabling and difficult to treat. Controversy over diagnosis, testing and treatment has led to two different standards of care.
Additional recommended knowledge
The acute phase of Lyme disease infection is a characteristic reddish "bulls-eye" rash, with accompanying fever, malaise, and musculoskeletal pain (arthralgia or myalgia). The characteristic reddish "bull's-eye" rash (known as erythema chronicum migrans) may be seen in up to 80% of early stage Lyme disease patients, appearing anywhere from one day to a month after a tick bite. The rash does not represent an allergic reaction to the bite, but rather a skin infection with the Lyme bacteria, Borrelia burgdorferi sensu lato.
The incubation period from infection to the onset of symptoms is usually 1–2 weeks, but can be much shorter (days), or much longer (months to years). Symptoms most often occur from May through September because the nymphal stage of the tick is responsible for most cases. Asymptomatic infection exists, but is uncommon.
Other, less common findings in acute Lyme disease include cardiac manifestations (up to 10% of patients may have cardiac manifestations including heart block and palpitations), neurologic symptoms (neuroborreliosis may occur in up to 18%), as well as simple altered mental status as the sole presenting symptom has been reported in early neuroborreliosis.
Untreated or persistent cases may progress to a chronic form most commonly characterized by meningoencephalitis, cardiac inflammation (myocarditis), and frank arthritis. It should be noted, however, that chronic Lyme disease can have a multitude of symptoms affecting numerous physiological systems: the symptoms appear heterogeneous in the affected population, which may be due to innate immunity or variations in Borrelia bacteria. Late symptoms of Lyme disease can appear months or years after initial infection and often progress in cumulative fashion over time. Neuropsychiatric symptoms often develop much later in the disease progression, much like tertiary neurosyphilis.
In addition to the acute symptoms, chronic Lyme disease can be manifested by a wide-range of neurological disorders, either central or peripheral, including encephalitis or encephalomyelitis, muscle twitching, polyneuropathy or paresthesia, and vestibular symptoms or other otolaryngologic symptoms, among others. Neuropsychiatric disturbances can occur (possibly from a low-level encephalitis), which may lead to symptoms of memory loss, sleep disturbances, or changes in mood or affect.
Lyme disease is caused by Gram-negative spirochetal bacteria from the genus Borrelia. At least 37 Borrelia species have been described, 12 of which are Lyme related. The Borrelia species known to cause Lyme disease are collectively known as Borrelia burgdorferi sensu lato, and have been found to have greater strain diversity than previously estimated.
Until recently it was thought that only three genospecies caused Lyme disease: B. burgdorferi sensu stricto (predominant in North America, but also in Europe), B. afzelii, and B. garinii (both predominant in Eurasia). However, newly discovered genospecies have also been found to cause disease in humans. "There are over 300 strains of Borrelia world wide". It is presently unknown how many of these cause lyme, but many of them may.
Hard-bodied ticks of the genus Ixodes are the primary vectors of Lyme disease. The majority of infections are caused by ticks in the nymph stage, as adult ticks do not become infected through feeding.
In Europe, the commonly known sheep tick, castor bean tick, or European castor bean tick (Ixodes ricinus) is the transmitter.
In North America, the black-legged tick or deer tick (Ixodes scapularis) has been identified as the key to the disease's spread on the east coast. Unfortunately, only about 20% of persons infected with Lyme disease by the deer tick are aware of having had any tick bite, making early detection difficult in the absence of a rash. Another possible vector is the lone star tick (Amblyomma americanum), which is found throughout the southeastern U.S. as far west as Texas, and increasingly in northeastern states as well. These tick bites usually go unnoticed due to the small size of the tick in its nymphal stage, as well as tick secretions that prevent the host from feeling any itch or pain from the bite.
On the west coast, the primary vector is the western black-legged tick (Ixodes pacificus). It was once thought to be a vector, although recent studies demonstrate that this tick species is not a competent vector of Borrelia burgdorferi sensu lato.
While Lyme spirochetes have been found in insects other than ticks, reports of actual infectious transmission appear to be rare. Sexual transmission has been anecdotally reported; Lyme spirochetes have been found in semen and breast milk, however transmission of the spirochete by these routes is not known to occur.
Due to the difficulty in culturing Borrelia bacteria in the laboratory, diagnosis of Lyme disease is typically based on the clinical exam findings and a history of exposure to endemic Lyme areas. The EM rash, which does not occur in all cases, is considered sufficient to establish a diagnosis of Lyme disease even when serologies are negative. Serological testing can be useful, but is not diagnostic.
Clinicians who diagnose strictly based on the U.S. Centers for Disease Control (CDC) Case Definition for Lyme are in error, as the CDC explicitly states that this definition is intended for surveillance purposes only, and is "not intended to be used in clinical diagnosis."
Importantly, virtually no controlled studies of late lyme encephalopathy have been performed, and the CDC diagnostic criteria were not formulated for use on this entity. Once lyme disease is well established in the brain, it can occur as a very disabling diffuse encephalopathy which however is difficult to diagnose using standard serological or intrathecal testing for reasons outlined below. Lyme is a deep tissue infection and by the time encephalopathy is established, few if any CSF antibodies can be detected, and PCR is unreliable. Seronegative disease can occur for the same reason that this phenomenon occurs in neurosyphilis, with incomplete or intercurrent antibiotic treatment abrogating the serum antibody response, but not eliminating the infection.
It is in this context that advanced imaging studies like SPECT or PET can provide objective evidence of global brain dysfunction. Resort is often made to neuropsychological testing, but a normal result does not rule out the illness, which can be very subtle and manifest as a disabling mood disorder accompanied by massive and debilitating fatigue, with few objective signs.
Diagnosis of late-stage Lyme disease it is often difficult due to the multi-faceted appearance which can mimic symptoms of many other diseases. For this reason Lyme has often been called the new "great imitator". Lyme disease may be misdiagnosed as Multiple sclerosis, rheumatoid arthritis, fibromyalgia, chronic fatigue syndrome (CFS), or other autoimmune and neurodegenerative diseases.
The serological laboratory tests most widely available and employed are the Western blot and ELISA. A two-tiered protocol is recommended by the CDC: the more sensitive ELISA is performed first, if it is positive or equivocal, the more specific Western blot is run. The reliability of testing in diagnosis remains controversial, however studies show the Western blot IgM has a specificity of 94–96% for patients with clinical symptoms of early Lyme disease.
Erroneous test results have been widely reported in both early and late stages of the disease. These errors can be caused by several factors, including antibody cross-reactions from other infections including Epstein-Barr virus and cytomegalovirus, as well as herpes simplex virus.
Polymerase chain reaction (PCR) tests for Lyme disease have also been developed to detect the genetic material (DNA) of the Lyme disease spirochete. PCR tests are rarely susceptible to false-positive results but can often show false-negative results, and the overall reliability of PCR in this role remains unclear. With the exception of PCR, there is no currently practical means for detection of the presence of the organism, as serologic studies only test for antibodies of Borrelia. High titers of either immunoglobulin G (IgG) or immunoglobulin M (IgM) antibodies to Borrelia antigens indicate disease, but lower titers can be misleading. The IgM antibodies may remain after the initial infection, and IgG antibodies may remain for years.
Western blot, ELISA and PCR can be performed by either blood test via venipuncture or cerebral spinal fluid (CSF) via lumbar puncture. Though lumbar puncture is more definitive of diagnosis, antigen capture in the CSF is much more elusive; reportedly CSF yields positive results in only 10-30% of patients cultured. The diagnosis of neurologic infection by Borrelia should not be excluded solely on the basis of normal routine CSF or negative CSF antibody analyses.
New techniques for clinical evaluation of Borrelia infection are under investigation, including Lymphocyte transformation tests  and focus floating microscopy. New research indicates chemokine CXCL13 may also be a possible marker for neuroborreliosis.
Single photon emission computed tomography (SPECT) imaging has been used to look for cerebral hypoperfusion indicative of Lyme encephalitis in the patient. Although SPECT is not a diagnostic tool itself, it may be a useful method of determining brain function.
In Lyme patients cerebral hypoperfusion of frontal subcortical and cortical structures has been reported. In about 70% of chronic Lyme disease patients with cognitive symptoms, brain SPECT scans typically reveal a pattern of global hypoperfusion in a heterogeneous distribution through the white matter. This pattern is not specific for Lyme disease, as it can also be seen in other central nervous system (CNS) syndromes such as HIV encephalopathy, viral encephalopathy, chronic cocaine use, and vasculitides. However, most of these syndromes can be ruled out easily through standard serologic testing and careful patient history taking.
The presence of global cerebral hypoperfusion deficits on SPECT in the presence of characteristic neuropsychiatric features should dramatically raise suspicion for lyme encephalopathy among patients who inhabit or have traveled to endemic areas, regardless of patient recall of tick bite. Late disease can occur many years after initial infection. The average time from symptom onset to diagnosis in these patients is about 4 years. Because seronegative disease can occur, and because CFS testing is often normal, lyme encephalopathy often becomes a diagnosis of exclusion: once all other possibilities are ruled out, LE becomes ruled in. Although the aberrant SPECT patterns are caused by cerebral vaculitis, a vasculitide, brain biopsy is not commonly performed for these cases as opposed to other types of cerebral vasculitis.
Abnormal magnetic resonance imaging (MRI) findings are often seen in both early and late Lyme disease. MRI scans of patients with neurologic Lyme disease may demonstrate punctated white matter lesions on T2-weighted images, similar to those seen in demyelinating or inflammatory disorders such as multiple sclerosis, systemic lupus erythematosus (SLE), or cerebrovascular disease. Cerebral atrophy and brainstem neoplasm has been indicated with Lyme infection as well.
Diffuse white matter pathology can disrupt these ubiquitous gray matter connections and could account for deficits in attention, memory, visuospatial ability, complex cognition, and emotional status. White matter disease may have a greater potential for recovery than gray matter disease, perhaps because neuronal loss is less common. Spontaneous remission can occur in multiple sclerosis, and resolution of MRI white matter hyper-intensities, after antibiotic treatment, has been observed in Lyme disease.
The currently recommended prevention practices are to avoid areas where ticks are found, wear clothing that covers the entire body when in a wooded area, use mosquito/tick repellent after exposure to wooded areas, and check all parts of the body (including hair) and clothing for ticks. Attached ticks should be removed promptly.
Protective clothing includes long-sleeve shirts and pants that are tucked into socks or boots. Also, light-colored clothing makes the tick more easily visible before it attaches itself.
A more effective, community wide method of preventing Lyme disease is to reduce in numbers the primary hosts on which the deer tick depends.
Management of host animals
Lyme and all other deer-tick borne diseases can be prevented on a regional level by reducing the deer population that the ticks depend on for reproductive success. This has been effectively demonstrated in the communities of Monhegan, Maine and in Mumford Cove, CT.. The black-legged or deer tick (Ixodes scapularis) depends on the white-tailed deer for successful reproduction.
By reducing the deer population back to healthy levels of 8 to 10 per square mile (from the current levels of 60 or more deer per square mile in the areas of the country with the highest Lyme disease rates) the tick numbers can be brought down to very low levels, too few to spread Lyme and other tick-borne diseases.
A vaccine, called Lymerix, against a North American strain of the spirochetal bacteria was available from 1998 to 2002. It was produced by GlaxoSmithKline (GSK) and was based on the outer surface protein A (Osp-A) of Borrelia. Osp-A causes the human immune system to create antibodies that attack that protein. When taking it off the market, GSK cited poor sales, need for frequent boosters, the high price of the vaccine, and exclusion of children. Some people believe that the actual reason was that the vaccine was neither safe nor effective. A group of patients who took Lymerix developed arthritis, muscle pain and other troubling symptoms after vaccination. Class-action litigation against GSK followed. Cassidy v. SmithKline Beecham, No. 99-10423 (Ct. Common Pleas, PA state court) (common settlement case).
It was later learned that patients with the genetic allele HLA-DR4 were susceptible to T-cell cross-reactivity between epitopes of OspA and lymphocyte function-associated antigen in these patients causing an autoimmune reaction.
Removal of ticks
Many urban legends exist about the proper and effective method to remove a tick. Complete removal of the tick head is important; if the head is not completely removed, local infection of bite location may result. Data has demonstrated that prompt removal of an infected tick, within approximately one day, reduces the risk of transmission to effectively zero percent; however the small size of the tick, especially in nymph stage may make detection difficult.
Antibiotics are the primary treatment for Lyme disease. Penicillin was first demonstrated by researchers to be useful against Borrellia in the 1950s; today the antibiotics of choice are doxycycline, amoxicillin and ceftriaxone. Macrolide antibiotics are also used.
Persons who remove attached ticks should be monitored closely for signs and symptoms of tick-borne diseases for up to 30 days. A three day course of doxycycline therapy may be considered for deer tick bites when the tick has been on the person for at least 12 hours. Patients should report any Erythema migrans over the subsequent two to six weeks. If there should be suspicion of disease, then a course of Doxycycline should be immediately given for ten days without awaiting serology tests which yield positive results only after an interval of one to two months.
In later stages, the bacteria disseminate throughout the body and may cross the blood-brain barrier, making the infection more difficult to treat. Late diagnosed Lyme is treated with oral or IV antibiotics, frequently ceftriaxone, 2 grams per day, for a minimum of four weeks. Minocycline is also indicated for neuroborreliosis for its ability to cross the blood-brain barrier.
Antibiotic treatment controversy
With little research conducted specifically on treatment for late/chronic Lyme disease, particularly Lyme encephalopathy, treatment remains controversial. Currently there are two sets of peer-reviewed published guidelines in the United States; the International Lyme and Associated Diseases Society (ILADS) advocates extended courses of antibiotics for chronic Lyme patients in light of evidence of persistent infection, while the Infectious Diseases Society of America does not recognize chronic infection and recommends no treatment for persistent symptoms. Double-blind, placebo-controlled trials of long-term antibiotics for chronic Lyme have produced mixed results.
A controversial new guideline developed by the American Academy of Neurology, finds conventionally recommended courses of antibiotics are highly effective for treating nervous system Lyme disease. They find no compelling evidence that prolonged treatment with antibiotics has any benefit in treating symptoms that persist following standard therapy. The guideline is endorsed by the Infectious Diseases Society of America (IDSA). However, these guidelines refer mostly to early acute lyme neuroborreliosis, as there is a paucity of studies on late lyme encephalopathy and parenchymal CNS disease. The guideline leader was John J. Halperin and was co-written by Gary Worsmer and Eugene Shapiro, neither of whom are neurologists. Halperin, Worsmer and Shapiro were all co-authors of the IDSA Lyme guidelines released in 2006 by the Journal of Clinical Infectious Diseases. There is significant disagreement with this guideline (www.ilads.org).
The latest double blind, randomized, placebo-controlled multicenter clinical study, done in Finland, results indicated that oral adjunct antibiotics were not justified in the treatment of patients with disseminated Lyme borreliosis who initially received intravenous antibiotics for 3 weeks. The researchers noted the clinical outcome of said patients should not be evaluated at the completion of intravenous antibiotic treatment but rather 6-12 months afterwards. In patients with chronic post-treatment symptoms, persistent positive levels of antibodies did not seem to provide any useful information for further care of the patient.
Antibiotic treatment is the central pillar in the management of Lyme disease. In the late stages of borreliosis, symptoms may persist despite extensive and repeated antibiotic treatment. Lyme arthritis which is antibiotic resistant may be treated with hydroxychloroquine or methotrexate. Experimental data are consensual on the deleterious consequences of systemic corticosteroid therapy. Corticosteroids are not indicated in Lyme disease.
Antibiotic refractory patients with neuropathic pain responded well to gabapentin monotherapy with residual pain after intravenous ceftriaxone treatment in a pilot study. The immunomodulating, neuroprotective and anti-inflammatory potential of minocycline may be helpful in late/chronic Lyme disease with neurological or other inflammatory manifestations. Minocycline is used in other neurodegenerative and inflammatory disorders such as multiple sclerosis, Parkinsons, Huntingtons disease, rheumatoid arthritis (RA) and ALS.
A number of other alternative therapies have been suggested, though clinical trials have not been conducted. For example, the use of hyperbaric oxygen therapy (which is used conventionally to treat a number of other conditions), as an adjunct to antibiotics for Lyme has been discussed. Though there are no published data from clinical trials to support its use, preliminary results using a mouse model suggest its effectiveness against B. burgdorferi both in vitro and in vivo. Anecdotal clinical research has shown potential for the antifungal azole medications such as diflucan in the treatment of Lyme, but has yet to be repeated in a controlled study or postulated a developed hypothetical model for its use.
Alternative medicine approaches include bee venom because it contains the peptide melittin, which has been shown to exert inhibitory effects on Lyme bacteria in vitro; no clinical trials of this treatment have been carried out, however.
The Alternative medicine philosophy includes building up the immune system so the body can defeat Lyme disease.
For early cases, prompt treatment is usually curative. However, the severity and treatment of Lyme disease may be complicated due to late diagnosis, failure of antibiotic treatment, simultaneous infection with other tick-borne diseases including ehrlichiosis, babesiosis, and bartonella, and immune suppression in the patient.
A meta-analysis published in 2005 found that some patients with Lyme disease have fatigue, joint and/or muscle pain, and neurocognitive symptoms persisting for years despite antibiotic treatment. Patients with late stage Lyme disease have been shown to experience a level of physical disability equivalent to that seen in congestive heart failure.
Urbanization and other anthropogenic factors can be implicated in the spread of the Lyme disease into the human population. In many areas, expansion of suburban neighborhoods has led to the gradual deforestation of surrounding wooded areas and increasing "border" contact between humans and tick-dense areas. Human expansion has also resulted in a gradual reduction of the predators that normally hunt deer as well as mice, chipmunks and other small rodents -- the primary reservoirs for Lyme disease. As a consequence of increased human contact with host and vector, the likelihood of transmission to Lyme residents has greatly increased. Researchers are also investigating possible links between global warming and the spread of vector-borne diseases including Lyme disease.
The deer tick (Ixodes scapularis, the primary vector in the northeastern U.S.) has a two-year life cycle, first progressing from larva to nymph, and then from nymph to adult. The tick feeds only once at each stage. In the fall, large acorn forests attract deer as well as mice, chipmunks and other small rodents infected with B. burgdorferi. During the following spring, the ticks lay their eggs. The rodent population then "booms." Tick eggs hatch into larvae, which feed on the rodents; thus the larvae acquire infection from the rodents. (Note: At this stage, it is proposed that tick infestation may be controlled using acaricides (miticide).
Adult ticks may also transmit disease to humans. After feeding, female adult ticks lay their eggs on the ground, and the cycle is complete. On the west coast, Lyme disease is spread by the western black-legged tick (Ixodes pacificus), which has a different life cycle.
The risk of acquiring Lyme disease does not depend on the existence of a local deer population, as is commonly assumed. New research suggests that eliminating deer from smaller areas (less than 2.5 ha or 6.2 acres) may in fact lead to an increase in tick density and the rise of "tick-borne disease hotspots".
Lyme disease is the most common tick-borne disease in North America and Europe, and one of the fastest-growing infectious diseases in the United States. Of cases reported to the United States Center for Disease Control (CDC), the ratio of Lyme disease infection is 7.9 cases for every 100,000 persons. In the ten states where Lyme disease is most common, the average was 31.6 cases for every 100,000 persons for the year 2005.
Although Lyme disease has now been reported in 49 of 50 states in the U.S, about 99% of all reported cases are confined to just five geographic areas (New England, Mid-Atlantic, East-North Central, South Atlantic, and West North-Central). Charts and tables for Lyme disease statistics in the U.S. can be found at the CDC website.
The number of reported cases of the disease have been increasing, as are endemic regions in North America. For example, it had previously been thought that B. burgdorferi sensu lato couldn't be maintained in an enzootic cycle in California because it was assumed the large lizard population would dilute the prevalence of B. burgdorferi in local tick populations, but this has since been proven false as lizards are now known carriers of ticks in North America, Europe and North Africa. Indeed, the DNA of Borrelia has been detected in lizards, indicating that they can be infected.
While B. burgdorferi is most associated with deer tick and the white tailed mouse, Borrelia afzelii is most frequently detected in rodent-feeding vector ticks, Borrelia garinii and Borrelia valaisiana appear to be associated with birds. Both rodents and birds are competent reservoir hosts for B. burgdorferi sensu stricto. The resistance of a genospecies of Lyme disease spirochetes to the bacteriolytic activities of the alternative complement pathway of various host species may determine its reservoir host association.
In Europe, cases of B. burgdorferi sensu lato infected ticks are found predominantly in Norway, Netherlands, Germany, France, Italy, Slovenia and Poland, but have been isolated in almost every country on the continent. Lyme disease statistics for Europe can be found at Eurosurveillance website.
In South America tick-borne disease recognition and occurrence is rising. Ticks carrying B. burgdorferi sensu lato, as well as canine and human tick-borne disease, have been reported widely in Brazil, but the subspecies of Borrelia has not yet been defined. The first reported case of Lyme disease in Brazil was made in 1993 in Sao Paulo. B. burgdorferi sensu stricto antigens in patients have been identified in Colombia and in Bolivia.
In Western and sub-Saharan Africa, tick-borne relapsing fever was first identified by the British physicians Joseph Dutton and John Todd in 1905. Borrelia in the manifestation of Lyme disease in this region is presently unknown but evidence indicates that Lyme disease may occur in humans in sub-Saharan Africa. The abundance of hosts and tick vectors would favor the establishment of Lyme infection in Africa. In East Africa, two cases of Lyme disease have been reported in Kenya.
In Australia there is no definitive evidence for the existence of B. burgdorferi or for any other tick-borne spirochete that may be responsible for a local syndrome being reported as Lyme disease. Cases of neuroborreliosis have been documented in Australia but are often ascribed to travel to other continents. The existence of Lyme disease in Australia is controversial.
Most clinicians agree on the treatment of early Lyme disease infections. There is, however, considerable disagreement regarding prevalence of the disease, diagnostic criteria, treatment of late-stage Lyme disease, and the likelihood of chronic, antibiotic-resistant infections. Some authorities contend that Lyme disease is relatively rare, easily diagnosed with available blood tests, and most often easily treated with two to four weeks of antibiotics, while others propose that the disease is under-diagnosed, available blood tests are unreliable, and that extended antibiotic treatment is often necessary.
The majority of public health agencies such as the U.S. Centers for Disease Control maintain the former position. While this narrower position is sometimes described as the "mainstream" view of Lyme disease, published studies involving non-randomized surveys of physicians in endemic areas found physicians evenly split in their views, with the majority recognizing seronegative Lyme disease, and roughly half prescribing extended courses of antibiotics for chronic Lyme disease.
In recent years prominent American Lyme researchers of the camp that denies, or belittles the importance of, Lyme as a chronic neurological infectious disease have received substantial federal government funding for biowarfare research. For example, Alan Barbour, credited with first culturing the Lyme bacteria, and whose B31 strain became the basis of all subsequent diagnostic tests for the disease, was recently placed in charge of the multi-million dollar new biowarfare research center at UCI.  Similarly, Jorge Benach, whose team collected the batch of ticks from which Barbour's strain was isolated, was chosen in 2004 as recipient for a $3 million bioterrorism research grant.  And Mark Klempner, author of a famous study contending that persisting symptoms in Lyme patients treated with antibiotics were unlikely due to chronic infection, was recently placed in charge of the 1.6 billion-dollar biowarfare mega-complex at Boston University.
The selection of leading Lyme researchers for such senior posts in bioweapons research, coupled with the fact that many of them have a long history of such work, which pre-dates the expansion of this field after the 2001 anthrax attacks, has fuelled accusations that Lyme disease is intimately connected with biological warfare science, and that military objectives have influenced these scientists to obfuscate the facts surrounding this disease, to the detriment of patients.
The unearthing, in recent years, of a number of documents referring to the study of Lyme disease in BSL-4 (Biosafety Level 4) labs, the very highest level of biocontainment which is generally reserved for airborne biowarfare organisms such as weaponised anthrax, has only served to stoke suspicion further. (An example of one such piece of evidence is the section on biocontainment in a 2003 letter from the director of a California Health Department concerning a bid for a biowarfare grant.
Mark Klempner, Alan Barbour, Allen Steere, David Dennis, Edward McSweegan, Philip Baker, Captain Paul Mead and many others who have had a profound influence on Lyme disease diagnostic and treatment policy have a history of association with bioweapons research in the past, and/or with the Epidemic Intelligence Service, founded in the 1950's as an elite biowarfare think tank.
The denial, by the United Kingdom government during a parliamentary debate, that research into Lyme disease had taken place during a time when the UK's top biowarfare facility Porton Down was indeed studying it, further stoked this controversy. The work at Porton Down has since been confirmed, being noted for example, by the British delegation to an international conference on bioterrorism 
In October 2006, further controversy erupted with the release of updated diagnosis and treatment guidelines from the Infectious Diseases Society of America (IDSA). The new IDSA recommendations are more restrictive than prior IDSA treatment guidelines for Lyme, and now require either an EM rash or positive laboratory tests for diagnosis; seronegative Lyme disease is no longer acknowledged (except incidentally in early Lyme disease). The authors of the guidelines maintain that chronic Lyme disease does not result from persistent infection, and therefore treatment beyond 2-4 weeks is not recommended, even in late stage cases. An opposing viewpoint has been expressed by the International Lyme and Associated Disease Society (ILADS), which proposes extended antibiotic treatment beyond four weeks for both early and late Lyme disease.
Advancing immunology research
The role of T cells concomitant to Borrelia infection was first made in 1984, and long term persistence of T cell lymphocyte responses to B. burgdorferi as an "immunological scar syndrome" was hypothesized in 1990. The role of Th1 and interferon-gamma (IFN-gamma) in borrelia was first described in 1995. The cytokine pattern of Lyme disease, and the role of Th1 with down regulation of interleukin-10 (IL-10) was first proposed in 1997.
Recent studies in both acute and antibiotic refractory, or chronic, Lyme disease have shown a distinct pro-inflammatory immune process. This pro-inflammatory process is a cell-mediated immunity and results in Th1 upregulation. These studies have shown a significant decrease in cytokine output of (IL-10), an upregulation of Interleukin-6 (IL-6), Interleukin-12 (IL-12) and IFN-gamma and disregulation in TNF-alpha predominantly.
These studies suggest that the host immune response to infection results in increased levels of IFN-gamma in the serum and lesions of Lyme disease patients that correlate with greater severity of disease. IFN-gamma alters gene expression by endothelia exposed to B. burgdorferi in a manner that promotes recruitment of T cells and suppresses that of neutrophils.
Studies also suggest suppressors of cytokine signaling (SOCS) proteins are induced by cytokines, and T cell receptor can down-regulate cytokine and T cell signaling in macrophages. It is hypothesized that SOCS are induced by IL-10 and B. burgdorferi and its lipoproteins in macrophages, and that SOCS may mediate the inhibition of IL-10 by concomitantly elicited cytokines. IL-10 is generally regarded as an anti-inflammatory cytokine, since it acts on a variety of cell types to suppress production of proinflammatory mediators.
Researchers are also beginning to identify microglia as a previously unappreciated source of inflammatory mediator production following infection with B. burgdorferi. Such production may play an important role during the development of cognitive disorders in Lyme neuroborreliosis. This effect is associated with induction of nuclear factor-kappa B (NF-KB) by Borrelia.
Disregulated production of pro-inflammatory cytokines such as IL-6 and TNF-alpha can lead to neuronal damage in Borrelia infected patients. IL-6 and TNF-Alpha cytokines produce fatigue and malaise, two of the more prominent symptoms experienced by patients with chronic Lyme disease.IL-6 is also significantly indicated in cognitive impairment.
A developing hypothesis is that the chronic secretion of stress hormones as a result of Borrelia infection may reduce the effect of neurotransmitters, or other receptors in the brain by cell-mediated pro-inflammatory pathways, thereby leading to the dysregulation of neurohormones, specifically glucocorticoids and catecholamines, the major stress hormones. This process is mediated via the Hypothalamic-pituitary-adrenal axis. Additionally Tryptophan, a precursor to serotonin appears to be reduced within the CNS in a number of infectious diseases that affect the brain, including Lyme. Researchers are investigating if this neurohormone secretion is the cause of neuro-psychiatric disorders developing in some patients with borreliosis.
Antidepressants acting on serotonin, norepinephrine and dopamine receptors have been shown to be immunomodulatory and anti-inflammatory against pro-inflammatory cytokine processes, specifically on the regulation of IFN-gamma and IL-10, as well as TNF-alpha and IL-6 through a psycho-neuroimmunological process. Antidepressants have also been shown to suppress Th1 upregulation.These studies warrant investigation for antidepressants for use in a psycho-neuroimmunological approach for optimal pharmacotherapy of antibiotic refractory Lyme patients.
New research has also found that chronic Lyme patients have higher amounts of Borrelia-specific forkhead box P3 (FoxP3) than healthy controls, indicating that regulatory T cells might also play a role, by immunosuppression, in the development of chronic Lyme disease. FoxP3 are a specific marker of regulatory T cells. The signaling pathway P38 mitogen-activated protein kinases (p38 MAP kinase) has also been identified as promoting expression of pro-inflammatory cytokines from Borrelia.
The culmination of these new and ongoing immunological studies suggest this cell-mediated immune disruption in the Lyme patient amplifies the inflammatory process, often rendering it chronic and self-perpetuating, regardless of whether the Borrelia bacterium is still present in the host, or in the absence of the inciting pathogen in an autoimmune pattern.
Researchers hope that this new developing understanding of the biomolecular basis and pathology of cell-mediated signaling events caused by B. burgdorferi infection will lead to a greater understanding of immune response and inflammation caused by Lyme disease and, hopefully, new treatment strategies for chronic antibiotic-resistant disease.
Lyme funding and treatment controversy
Many of the scientists involved in formulating what have become controversial Lyme diagnostic tests and treatment guidelines have been heavily involved in both bioweapons research and commercial vaccine and diagnostic test development, which the Lyme patient community views as a conflict of interest.  In response to these and other concerns expressed by the expanding national community of patients, Richard Blumenthal, the Attorney General of Connecticut has launched an investigation exploring possible corruption.
To date, federal research aimed at developing treatments for chronic Lyme disease is roughly $30 million, as contrasted to a $22 billion budget for military biodefense. Scientists setting Lyme treatment and diagnostic testing policy in the United States have a well publicised history in the biodefense field, and many have recently received lucrative biodefense grants for BSL-3 and BSL-4 Labs where, critics contend, Lyme treatment research lacks transparency, accountability and focus on treatment research, though, it should be pointed out, that labs obtaining such grants are required to make their research findings publicly available via publication and focus their studies on issues pertinent to human health . Most, including scientist, contend that the new grants and centers stimulate research by bringing together experts in the field and providing a stable source of funding.
In 2003, Lyme researcher Dr. Mark Klempner was appointed head of the new $1.6 billion biodefense top-security facility at Boston University. In 2004, Lyme researcher Dr. Jorge Benach, was reportedly chosen as a recipient for a $3 million biodefense research grant, and in 2005, Lyme researcher Dr. Alan Barbour was reportedly placed in charge of a $40 million dollar new biodefense complex based at UC Irvine. 
Former NIH Lyme disease program officer, Edward McSweegan has published numerous articles and letters to editorial pages relating to biowarfare topics ranging from anthrax to plague. Curiously, Mr. McSweegan's novel, Deliberate Release, is biowarfare thriller that describes the deliberate release of a germ weapon. 
The first record of a condition associated with Lyme disease dates to 1883 in Breslau (formerly in Germany) where physician Alfred Buchwald described a degenerative skin disorder now known as acrodermatitis chronica atrophicans. In 1909, Arvid Afzelius presented research about an expanding, ring-like lesion he had observed. Afzelius published his work 12 years later and speculated that the rash came from the bite of an Ixodes tick, and that meningitic symptoms and signs occur in a number of cases; this rash is now known as erythema migrans (EM), the skin rash found in early stage Lyme disease. In 1911, parasitologist Andrew Balfour of the Wellcome Research Laboratory in Khartoum identified "infective granules" or spore-type "cysts" as the cause of persistence of spirochetal infection in the Sudanese Fowl.
In the 1920s, French physicians Garin and Bujadoux described a patient with meningoencephalitis, painful sensory radiculitis, and erythema migrans following a tick bite, and they postulated the symptoms were due to a spirochetal infection. In the 1940s, German neurologist Alfred Bannwarth described several cases of chronic lymphocytic meningitis and polyradiculoneuritis, some of which were accompanied by erythematous skin lesions.
In 1948 spirochete-like structures were observed in skin specimens by Swedish dermatologist Carl Lennhoff. In the 1950s, relations between tick bite, lymphocytoma, EM and Bannwarth's syndrome are seen throughout Europe leading to the use of penicillin for treatment.
In 1970 a physician in Wisconsin named Rudolph Scrimenti reports the first case of EM in U.S. and treats it with penicillin based on European literature.
The full syndrome now known as Lyme disease was not recognized until a cluster of cases originally thought to be juvenile rheumatoid arthritis was identified in three towns in southeastern Connecticut in 1975, including the towns Lyme and Old Lyme, which gave the disease its popular name. This was investigated by Dr. David Snydman and Dr. Allen Steere of the Epidemic Intelligence Service, and by others from Yale University. The recognition that the patients in the United States had EM led to the recognition that "Lyme arthritis" was one manifestation of the same tick-borne condition known in Europe.
Before 1976, elements of B. burgdorferi sensu lato infection were called or known as tickborne meningopolyneuritis, Garin-Bujadoux syndrome, Bannworth syndrome, Afzelius syndrome, Montauk Knee or sheep tick fever. Since 1976 the disease is most often referred to as Lyme disease, Lyme borreliosis or simply borreliosis.
In 1976, Jay Sanford, a former physician at the Walter Reed Army Institute of Research, published a chapter in the book The Biology of Parasitic Spirochetes. In it, Dr. Sanford stated: "the ability of borrelia, especially tick-borne strains, to persist in the brain and in the eye during remission after treatment with arsenic or with penicillin or even after apparent cure, is well known.”  Although the notion of persistent neurological infection was identified early on by military researchers such as Dr. Sanford, later Lyme researchers curiously denied the possibility of persistent Borrelia infection in the brain, with many researchers ignoring evidence of persistent infection.
In 1980 Steere, et al, began to test antibiotic regimens in adult patients with Lyme disease In 1982 a novel spirochete was cultured from the mid-gut of Ixodes ticks in Shelter Island, New York, and subsequently from patients with Lyme disease. The infecting agent was then identified by Jorge Benach at the State University of New York at Stony Brook, and soon after isolated by Willy Burgdorfer, a researcher at the National Institutes of Health, who specialized in the study of spirochete microorganisms such as Borrelia and Rickettsia. The spirochete was named Borrelia burgdorferi in his honor. Burgdorfer was the partner in the successful effort to culture the spirochete, along with Alan Barbour.
After identification B. burgdorferi as the causative agent of Lyme disease, antibiotics were selected for testing, guided by in vitro antibiotic sensitivities, including tetracycline antibiotics, amoxicillin, cefuroxime axetil, intravenous and intramuscular penicillin and intravenous ceftriaxone. The mechanism of tick transmission was also the subject of much discussion. B. burgdorferi spirochetes were identified in tick saliva in 1987, confirming the hypothesis that transmission occurred via tick salivary glands.
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