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Lyme Disease and Co-infections: Testing and Treatment




Lyme disease causing tick

Dr. Sarah Myhill MB BS

March 2016


There is no doubt that Lyme Disease and other such co-infections exist as real clinical entities. In the short term they present with all the symptoms of an acute ‘flu like illness. In the longer term, and given the ‘right’ set of stresses on the body’s system, they can present with a chronic fatigue syndrome. Not everyone who is exposed to Lyme microbes suffers active or chronic infection – much of the reason for this varied response has to do with individual susceptibility. Therefore, there must be a two pronged approach: improve the defences and attack the attackers. Indeed these general principles hold good for the treatment of any chronic infection from the fermenting gut to tuberculosis!


Improve the Defences - Summary

Put into place all those interventions that supply the immune system with the necessary energy and raw materials to put up an effective fight by:

Implementing fully my “Basic Package” of treatments. This is a treatment package that we should all be doing, all the time, in order to optimise health and is the starting point to treat all disease. 

Put into place the “Bolt on Extras” to improve energy delivery mechanisms. These bolt on extras will vary from patient to patient as described in my book but for a summary of some of the potential interventions, please see below.


Attack the Attackers - Summary

Demonstrate the presence of microbes from Lyme and other co-infections by appropriate tests.

Reduce the numbers of microbes, and the body’s inappropriate immune reactions, with appropriate antimicrobial interventions which may be nutritional, herbal and/or prescription medication.


Improve the Defences - Detail

The Basic Package – what we should all be doing all the time:

  • Stone-age diet (staple foods: meat, fish, eggs, vegetables, nuts seeds, salad, berries. Occasional treats: dairy, grains, fruit) this is a diet which we all should follow.
  • Multivitamins, minerals, essential fatty acids etc.
  • Sleep – Sleep is vital for good health.
  • Exercise
  • Sunshine and Light – Vitamin D produced in response to sunlight exposure protects against cancer, heart and bone disease.
  • Reduce the Chemical Burden – do a good chemical clean-up (detox): chemicals make you fat and fatigued!
  • Sufficient physical and mental security to satisfy our universal need to love and care, and be loved and cared for.
  • Avoid infections and treat aggressively.

The Bolt on Extras to improve energy delivery mechanisms - address these:

  • Poor mitochondrial function – the engines that make energy.
  • Thyroid function – the accelerator pedal.
  • Adrenal function – the gear box.
  • Circadian rhythms – timing is vital.


Attack the Attackers - Where are They?

With Lyme and co-infections the microbes do not exist in one form - they exist in a “cell wall” form but once established in the body they cycle between “cell wall” forms and “cystic” forms. It may be that they clump together and hide behind “biofilms”. Biofilm is a barrier which microbes throw up to hide themselves away from the body's natural defenses. Biofilm on teeth we call dental plaque. Dr Alan MacDonald has shown that borrelia conceal themselves in amyloid. Amyloid has been known about for years and is associated with many chronic diseases - -see Wikipedia Article on Amyloid - but its reason for existing is unknown. However if amyloid is indeed the shield under which microbes hide then this opens up very interesting avenues for treatment of any disease associated with amyloid! That is to say it may be a marker for a chronic inflammation driven by infection, Note the term amyloid is a misnomer - it is not a starch but a tough protein with some sugars bound within.

This means that chronic Lyme is more difficult to treat than acute Lyme because the passage of time has meant that biofilms have been “fully” formed and so all these aspects need assailing in order to achieve a clinical result. So, first we need to determine how best to test for Lyme Disease and only then can we put into place the required treatment regimes. Please see the next section for a discussion of the various tests that are available and then afterwards for sections on treatment regimes for Acute and Chronic Lyme Disease.


Litigation in Lyme Disease

Ed: Before the extraordinarily knowledgable and wise Dr. Myhill continues. Have you ever thought about litigation in Lyme disease? Without condoning 'Blame Culture' - there is certainly a question to be answered here! Thise excellent Guide by helps visitors with information about liability in various situations and insurance. The website was launched to provide clarity regarding liability in The Netherlands. It effortlessly breaks down whether General Practitioners (GPs) - a Uk / EU term for the US 'Family Doctor' - or more likely employers, or others responsible for your well-being, may be to blame for loss earnings, doctors fees, suffering etc. Included are even cases of litigation against employer's for Lyme disease in The Netherlands. 

Whether a patient yourself, or have a loved one with Lyme, we at EiR genuinely feel this is a high quality resoucre that you should be reading right now about litigation in Lyme disease: (Article in Dutch. But modern web browsers will all prompt for simple one-click translation to English)

Considering the above and you may suffer from a different Environmental or Invisible Illness (or likely illnesses) - the same factors would likely apply. Now is the time to take years or decades of medical dismissal and loss of earnings to the courts for we, the surviviors of invisible illness, plus those not so "lucky." Please do your own litigation research and consider both individual and 'class action' law suits in your own countries!    

Testing for Chronic Lyme Disease

No test is perfect either because it lacks “sensitivity” (i.e. the test does not “see” the microbe if it is present only in low numbers) or perhaps because it does not display “specificity” (i.e. the test “sees” other microbes which do not represent a clinical problem). There are various tests available. 

  • Polymerase Chain Reaction (PCR). This is highly specific for Lyme and co-infections but is not very sensitive. If this test is positive then that is likely to be a true result. However if this test is negative then that does not exclude Lyme and co-infections.
  • Borrelia Burgdorferi Antibodies - this is the only test available on the NHS but it lacks sensitivity. There will be many false negatives ie a negative result does not exclude the diagnosis of Lyme. I have only ever seen 2 patients with a positive antibody test. This test is unreliable.
  • Enzyme-linked Immunosorbent Spot Assay (Elispot - LTT). This is a promising test which has been tested clinically showing specificity of 96.7%. Importantly after these Lyme patients had been treated, 90.7% showed negative or greatly reduced lymphocyte reactivity and, more importantly, this negative or reduced reactivity correlated well with clinical improvement. It looks like this will be the most helpful test for diagnosing Lyme and monitoring response to treatment. Indeed this test, called Elispot-LTT has received FDA and CDC approval. Further information about the technique used in this test can be found at Elispot.

Elispot is available from Academy of Nutritional Medicine - AONM to diagnose and monitor the following infections:

  • Borrelia Burgdorferi
  • Chlamydia pneumoniae
  • Chlamydia trachomatis
  • Ehrlichia/Anaplasma
  • Yersinia species
  • Epstein Barr Viruss (EBV)
  • Cytomegalo Virus (CMV)

AONM are the UK distributors for Armin Labs.

The test requires special blood tubes which are easily posted, with results back 5 days after they have been received by the lab. I think that the best way forward is for the patient, once they have been recommended to have the test by me, to go ahead and order and pay for the test direct from the laboratory. Then, once the results have come back, I can interpret and advise the patient accordingly. The costs of these tests can be seen in the Academy of Nutritional Medicine - AONM test order form which you can access below.


Treatment for Acute Lyme - Antimicrobials

Treating acute infections aggressively is so important and is indeed the most efficient way to treat Lyme. The best course of action, sadly not often possible, is to diagnose and treat Lyme during the acute phase before it becomes entrenched. However this relies on a high index of suspicion – and this is almost always lacking. The following recommendations come for Dr Richard Horowitz’s book “Solving the mystery of Lyme and other chronic diseases”:

If there is any clinical suspicion of acute Lyme, with or without positive blood tests, then the recommended treatment would be:

  • With tick bite and bull’s eye rash/erythema migrans only: all of the Basic Package (but rest not exercise!) plus doxycycline 100mgs twice daily for 3 weeks.
  • With above rash and additional systemic symptoms such as fever (immune system fighting), headache and stiff neck (inflammation in central nervous system), tingling (inflammation in peripheral nervous system), treat as follows:

Month 1: 
--Doxycycline 200mgs twice daily 
--Serrapeptidase or other enzymes (to breakdown “bio-films”)
--Plaquenil 200mgs daily (immune modulator – needs an eye check with optician once a month)
--Antifungals such as nystatin (presumably to prevent yeast fermentation in the gut – but this will be also addressed by a low carb Stone Age diet)

Month 2 Treatment is the same as month 1 but swap doxycycline for another antibiotic to tackle any cell wall forms that may have survived doxycycline. So, the treatment package for Month 2 becomes:
--No more doxycycline
--Metronidazole up to 400mgs three times daily 3 days a week (to tackle cystic forms) Monday Tuesday Wednesday
--Co-amoxyclav 500/125 two capsules taken three times daily 4 days a week Thursday Friday Saturday Sunday (to tackle “cell wall” forms)
--Serrapeptidase 500mgs 2 capsules 3 times daily or other enzymes (to breakdown bio-films)
--Plaquenil 200mgs daily (immune modulator – needs an eye check with optician once a month)
--Antifungals such as nystatin (presumably to prevent yeast fermentation in the gut – but this will be addressed by a low carb Stone Age diet)


Treatment for Chronic Lyme

This is much more difficult because the organism has overcome the body’s natural defences and made itself comfortably at home in the body. Lyme and co-infection are not like infectious diseases that doctors currently recognise. They are much more difficult to diagnose and eradicate and I think this is for several possible reasons.

  • Lyme and co-infection subvert the body’s immune system and energy delivery systems to put them in such a state so as to make the environment favourable to these microbes. This idea was flagged up by Paul Cheney and there is an article about this at Chronic infections in CFS. Essentially these microbes impact on mitochondria and the immune system to create an environment that is comfortable for these co-infections to live in. As Pasteur famously said on his death bed “the microbe is nothing the environment is everything”.
  • Bio-films – the idea here is that biofilms are thrown up by microbes as part of their defence against attack. This is a further facet of the Arms Race! In the gut these biofilms are layers of mucopolysaccharide which should be susceptible to attack by enzymes that digest starch and sugars (part of pancreatic enzymes). A further possibility in other areas of the body could be fibrin clots around areas of inflammation.

I suspect the above two issues, and possibly others, explain why Lyme and co-infections are so different from other infections and so difficult to get rid of. However, more importantly, the above ideas give us clear practical implications for treating chronic Lyme Disease.

The big question, of course, is how to diagnose Lyme, distinguish it from other infectious disease triggered CFSs and treat it effectively. This is where the Eli-spot test will be very useful.

So the rules of the game for treating Lyme is that we have to:

I - Make the environment as uncomfortable for Lyme as possible by:

A - Putting in place everything to address mitochondrial dysfunction.

B - Putting in place everything to address the inflammation/free radical problem. Dr. Cheney in particular has flagged up the potential of artesunate for dealing with this.

But other well recognised tools of the trade to damp down the pro-inflammatory biochemical fire of the NO/ON/OO cycle include the following 6 possibilities:

Correct poor anti-oxidant status - simply taking the basic package of nutritional supplements of vitamins and minerals will go a long way towards correcting poor antioxidant status. However I routinely measure levels of antioxidants and deficiencies are common. I would use, in response to the following deficiencies:

-- Superoxide dismutase – copper 1mgs at breakfast, manganese 3mgs midday, zinc 30mgs at night - these timings reflect the time of day these nutrients are best absorbed. -
-- Glutathione peroxidase – glutathione 250-500mgs, selenium 200-500mcgms at night
-- Co-enzyme Q 10 – co Q 10 250-500mgs daily Other important antioxidants such as vitamins A, C, D, E are part of the Basic Package. There are many natural anti-oxidants within our diet which are additionally helpful. These are found in vegetables, nuts, seeds and berries.

  • Vitamin D – vitamin D evolved in response to the skin being exposed to sunshine. It is an anti-inflammatory and protects the skin from pro-oxidant stress caused by ultraviolet light. It then diffuses through the body where it has generalised anti-inflammatory actions. It is protective against infection and improves muscular strength. It protects against allergy, auto-immunity, metabolic syndrome, osteoporosis and cancer. The incidences of all these conditions increase the further away from the Equator you live. It is important to measure blood levels in anyone with any of these conditions since absorption can be variable. I like to see levels between 75 and 200nmol/l. To achieve this requires up to 10,000 IU daily.
  • Vitamin B12 by mouth and by injection – this provides instant anti-oxidant cover and protection whilst the other antioxidants are being corrected by supplements.
  • Alkalinisation – the use of bicarbonates and carbonates has been long recognised as a way to switch off allergy reactions, especially to foods. I suggest magnesium carbonate 500mg-2,000mgs last thing at night, or at least away from mealtimes. We need a window of time, at least 90mins after food, to achieve an acid stomach to allow normal gut function. Magnesium carbonate may be additionally useful if acid supplements are being used to treat hypochlorhydria.
  • Low dose naltrexone (LDN) – naltrexone is an opiate blocker. Typically, it is used, in high doses such as 50mg, to reverse the effects of poisoning by opiates such as morphine. However, LDN can used in tiny doses such as 1-4mgs at night. The idea is to slightly block the action of the body’s own endogenous opiates (endorphins) which then results in an increase in endogenous production. Endorphins are natural anti-inflammatories and so, in this way, LDN has an anti-inflammatory action. This property gives LDN wide clinical applications from the treatment of cancer, auto-immunity and neurodegenerative disorders. See Low Dose Naltrexone Org for detailed information.
  • Exercise, music, singing, love and laughter – if there is energy to do these things! All are addictive because they increase endorphins with anti-inflammatory actions arising downstream. Some addictions are useful!

It may be for some patients that the above package is sufficient to get rid of chronic Lyme. I say this because many of my patients recover well with these regimes and many must have had Lyme since this disease appears to be such a common problem. However some will ADDITIONALLY need the following:

II - Kill the microbes with anti-microbials 
First one has to expose the microbes to the antimicrobials by breaking down biofilms. If indeed this additionally has to do with protective layers within the gut and mucous, then restoring normal gut function with respect to stomach acid, pancreatic enzymes, bile salts and so on may be very helpful – i.e. all my usual package used to treat the upper fermenting gut. See Fermentation in the gut and CFS.

Again it is notable in my readings about Lyme disease that enzymes, such as serrapeptidase 80,000iu tablets (2 capsules taken three times daily), are often used to break down the biofilm and my guess is that they are impacting with respect to gut function and possibly fibrin clots.

Having got all the above in place one then has to consider antimicrobials to kill these co-infections. In dealing with them we have to take a 'tuberculosis like' approach i.e. it is combinations of antibiotics that will get the result and these have to be taken over months, not weeks.

Again these recommendations I have taken from Dr Horowitz’s book. He often uses intravenous antibiotics – I have not included those regimes simply because they are almost always impossible to put in place in the UK. However I hope, and believe, that by putting in the above regimes to improve the defences, this will make the oral regimes as effective as the intravenous ones. It is important to combine antimicrobials for “cell wall” and “cystic” forms of Lyme together with those to get at intracellular microbes. The oral regimes of antibiotics he recommends are as follows:

  • Cell wall forms: co-amoxyclav 500/125 two capsules taken three times daily.
  • Cystic forms: metronidazole 400mgs three times daily.
  • Intracellular location: doxycycline 100mgs twice daily Other oral antibiotics that can be used in the same durations as above if there is intolerance to medications or poor clinical response to treatment:
    -- Cell wall forms - cefuroxime 500mgs twice daily
    -- Cystic forms – tinidazole 400mgs three times daily
    -- Intracellular location – azithromycin 500mgs once daily, ciproxin 500mgs twice daily

Duration of Treatment

Dr Horovitz recommends that treatment should be given for at least 2 months, and continued for 2 months after the patient is symptom free. This may be possible at a lower rate of dosing.

Response to Treatment

This can be monitored clinically (how do you feel?) and also with Eli-spot blood tests to show (hopefully!) that the white cells are reacting less against the microbes as the numbers (of microbes) come down.


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