I wrote a short paper on the subject and posted it over at the Lyme Enigma, but I'll post it here, too, just in case you are interested:
Lyme disease has been, and currently is, defined in numerous ways, depending on who is doing the defining. The Infectious Diseases Society of America (IDSA) contends that Lyme is relatively easy to diagnose, and that 21-28 days of antibiotic therapy is effective against most cases , while the International Lyme and Associated Diseases Society (ILADS) argues that Lyme disease can be very difficult to diagnose and can require years of antibiotic therapy in many cases, especially in cases that are not treated early in the course of the disease .
When one reads both guidelines side by side, it seems apparent that there exists a lot of conflicting data. I would be willing to argue, however, that there is a way that much of the data collected on both sides, as conflicting as it all first appears to be, might still be valid. In my reading, I have found that countless people who have fallen ill after a known tick bite have presented with countless manifestations of disease, although similarities do also exist between these individuals. I have also found that a disease is sometimes only considered rare as long as doctors aren’t looking for it in their patients. So where am I going with this?
I propose that the medical community redefine “Lyme” … or, more specifically, drop this problematic name altogether and work together to delineate what we now define as “Lyme” into three separate categories:
1. Borreliosis – caused by Borrelia burgdorferi and other Borrelia similar enough to cause a positive Bb titer
2. Borreliosis – caused by one or more other Borrelia species, such as B. hermsii, that may or may not show up on tests specifically made to detect Borrelia burgdorferi
3. Complex Borreliosis – caused by any number of Borrelia, combined with one or more commonly known and/or unsuspected co-infections, which can make proper treatment more complicated
All other cases must be considered caused by one or more other, unrelated illnesses, autoimmune illness, and/or hypochondriasis.
It is apparent that several factors are likely involved in chronic cases. While treatment failure may sometimes be the result of numerous proposed defensive mechanisms employed by the spirochete, it is also very likely that often the wrong treatment is simply being administered. Different Borrelia species require different antibiotics, just like different co-infections require very different, sometimes very specific treatments. Many of these diseases cause similar symptoms and can cross-react weakly in antibody assays, therefore making an accurate and complete clinical diagnose difficult if not impossible [3,4].
The Right Drug for the Right Bug
It is interesting to consider the vast contrast between the numerous studies concluding that a month or less of certain antibiotics can eradicate most cases of “Lyme” borreliosis against the numerous legitimately ill patients who are believed either to have had Lyme, and now live with sequelae, or appear to suffer chronic treatment failure. It very well may be the case that findings by both the IDSA and ILADS on this matter may be completely founded, however the interpretation of their collective data simply fell victim to the wide chasm that currently exists between the two camps.
Consider, for example:
How many physicians, IDSA and ILADS alike, take the time to rule out this particular form, or any other known forms, of the Borrelia strain(s) that cause tick-borne relapsing fever? How many people suffering from relapsing fever or a similar disease might be diagnosed clinically as having Lyme, based on the above symptoms? Is there a possibility that other strains of Borrelia have the ability to leave behind neurological and/or rheumatological sequelae?In the United States, TBRF [tick-borne relapsing fever] usually occurs west of the Mississippi River, particularly in the mountainous West and the high deserts and plains of the Southwest. In the mountains of California, Utah, Arizona, New Mexico, Colorado, Oregon, Washington, infections are usually caused by Borrelia hermsii and are often acquired in cabins in forests. It is possible that the risk now extends into the southeastern United States….
+ Sudden onset of high fever
+ Headache; neck stiffnes
+ Muscle aches (myalgia)
+ Joint aches (arthralgia)
+ Unsteady gait
+ Facial droop
+ Facial droop
+ Myocarditis -- may lead to arrhythmias
+ Liver dysfunction
+ Widespread bleeding
+ Deadly reaction to antibiotics (Jarisch - Herxheimer's reaction) 
Consider, now, the following abstract:
This particular Borrelia strain, which is not named in the abstract, could be more common than science has had the time, insight, or interest to measure. Moreover, it is always possible that many cases of atypical or seronegative borreliosis are caused by other similar, yet-to-be-discovered strains. This could be significant in that different Borrelia need to be treated with different antibiotics, and thus even early treatment or long-term antibiotic treatment might ultimately result in treatment failure if the wrong antibiotic or combination of antibiotics is administered. A doctor might assume the antibiotic course is sufficient and discount continuing symptoms, while the patient might truly still continue to suffer from active infection, convinced the “Lyme” is still present. On the opposite end of the pole, a doctor might treat a chronically ill patient with the same antibiotics for two years, and still fail to reach the target infection.A new Borrelia species isolated from patients with relapsing fever in Spain.
BACKGROUND: Lyme disease and tick-borne relapsing fever are worldwide systemic borrelioses caused by several Borrelia species transmitted by hard ticks (family Ixodidae) and soft ticks (family Argasidae), respectively. A previous seroepidemiological study of Lyme borreliosis showed several serologically reactive patients with clinically atypical presentations, and this discovery led to the hypothesis that some of the cases of Lyme borreliosis had been caused by another borrelia organism. METHODS: Blood from patients in southern Spain who had suspected Lyme disease or relapsing-fever borreliosis was cultured before treatment began. Isolates of Borrelia spp were inoculated into several strains of mice of different ages. The 16S rRNA and flagellin in genes of Borrelia spp were sequenced by PCR and assessed by phylogenetic analyses. FINDINGS: We isolated a species of Borrelia from three patients with relapsing fever and from Ornithodorus spp ticks in southern Spain. This organism (refractory to in-vitro cultivation) caused a relapsing spirochaetaemia with multiple organ involvement in laboratory mice that recreated the human disease. Phylogenetic analysis showed that this organism is a previously unrecognised species. INTERPRETATION: We have discovered a new borrelia pathogen that is closely related to the other tick-borne agents of relapsing fever in Europe and Africa, and which causes a relapsing systemic disease with serological similarities to Lyme borreliosis  9emphasis mine).
Complex Borreliosis and Borreliosis Imitators
Just as various strains of Borrelia likely add to its diagnostic pitfalls, other non-related micro-organisms, which may or may not be contracted from a tick bite, likely complicate numerous difficult-to-treat cases. These diseases, when combined with borreliosis, may present with more severe presentations, affect more systems and/or organs, and potentially impact more severely the failure of one’s immune response, when compared to simple borreliosis. Compare the following diseases, both “common” and “uncommon,” to “Lyme” borreliosis:
Babesia:Patients with ehrlichiosis usually present with severe headache, myalgias, and fever. Shaking chills often are present. Nausea, vomiting, and abdominal pain are uncommon and mild….
Ehrlichiosis is a difficult infectious disease to diagnose because it presents as an acute undifferentiated febrile RMSF-like illness with few/no physical findings. The majority of patients previously diagnosed with RMSF without rash, in fact, probably had ehrlichiosis .
Q fever:Initial symptoms begin gradually and are nonspecific. Common symptoms include the following:
+ Shaking chills
+ Fever (Fever may be sustained or intermittent, and temperatures may reach levels of 40ºC.)
+ Abdominal pain
+ Depression and emotional lability
+ Dark urine
+ Photophobia, conjunctival injection, sore throat, cough (less common symptoms) .
Brucelosis:* Patients initially present with influenzalike symptoms.
* Respiratory symptoms appear 4-5 days after initial onset of illness (most prominently a dry nonproductive cough and pleuritic chest pain).
* Symptoms include the following:
+ Severe headache
+ Pleuritic chest pain
+ Nausea and Vomiting (rare) 
According to the above authors, brucellosis can also progress to cause severe neurological problems and chronic fatigue.Physical examination findings in brucellosis, like history, often are nonspecific.
Focal infection of bones, joints, or the genitourinary system may present with localized abnormal physical findings in the affected areas. Arthritis, joint effusions, urethritis, or, in patients with severe cases, costovertebral angle tenderness may be observed. Epididymo-orchitis has been described in association with brucellosis. Focal osteomyelitis of the vertebrae, tibia, and especially knee has also been associated with brucellosis infection, even in the absence of other significant systemic symptoms.
+ Some patients may present with hepatosplenomegaly, 10-30% with hepatomegaly, and 10-70% with splenomegaly. Right upper quadrant pain and jaundice may indicate hepatic abscess.
+ In chronic infection (>3-6 mo), weight loss may be apparent.
+ Infection of the nervous system may present with focal findings (abscesses) or nuchal rigidity (leptomeningitis). Of note, nuchal rigidity was present in fewer than half of patients with brucella leptomeningitis. Typical focal findings may steer toward an abscess. Global depression of cognition may occur. At least one case of spondylitis with resulting spinal cord compression has been documented.
+ Dermal manifestations may include cutaneous ulcerations, petechiae, purpura, and erythema nodosum. Brucella may be cultured from these skin lesions.
+ Endocarditis may present with murmurs, and mycotic aneurysms of ventricles, brain, and aorta have been observed .
When comparing these diseases, and then considering the fact that numerous other pathogens can cause similar sets of symptoms, it becomes clear just how little value a clinical diagnosis holds without other clear diagnostic tools. A patient with Q fever, presenting with fever, severe headaches, myalgias, anorexia, cough, pleuritic chest pain, sweats, chills, nausea, and vomiting, for example, might be diagnosed clinically with chronic Lyme disease because numerous antibiotic treatments have failed and blood tests have been interpreted rashly. Unfortunately that patient will not recover, and might eventually go on to develop endocarditis, which will require a specific combination of doxycycline and hydrocychloroquine for up to three years in order to treat completely .
There are likely numerous cases in which patients have also clearly presented with borreliosis, their diagnoses backed with positive blood tests, but undiagnosed co-infections with any number of these similarly presenting diseases have caused apparent chronic treatment failure when, in actuality, the borrelia treatment itself was a success. This may explain why some patients describe a changing or waning of some symptoms, but the persistence of others, during and following various antibiotic treatments.
With all of the problems that exist with the current two-tiered system in testing for Lyme disease, with various other methods that can be used to detect borrelia and other infections, one must wonder why more is not being done to diagnose these different diseases more accurately. For example, dark-field microscopy can detect Ehrlichia and Borrelia , and dark-field microscopy is commonly used to diagnose relapsing fever .
Why isn’t this technology being used more often? Why, when patients are presenting with “atypical Lyme,” “seronegative disease,” and “chronic infection” isn’t more being done to determine, without a doubt, just what other disease or diseases might be causing or exacerbating these persistent, often disabling cases?
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Human Granulocytic Anaplasmosis, and Babesiosis: Clinical Practice Guidelines by the Infectious
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2. Cameron, Daniel, et al. ILADS Guidelines for Lyme Disease, 2004. http://www.ilads.org/files/ILADS_Guidelines.pdf.
3. Lynne Strasfeld et al. Correspondance: False-Positive Serological Test Results for Lyme Disease
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http://www.nlm.nih.gov/medlineplus/ency ... 001350.htm.
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Ixodes ticks in the Baltic regions of Russia. 2001. PubMed abstract: http://www.ncbi.nlm.nih.gov/sites/entre ... ew&indexed
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