Possibility directions. Choice for easy way or hard way.Lyme Disease Protocols: Where To Start

By the time I had been diagnosed with Lyme Disease I had spent years seeing specialists who’d greet me with shrugged shoulders and send me away with more questions than answers. When I was finally diagnosed with Lyme Disease, I was relieved to have a label to my symptoms, terrified about ending up in a wheelchair and overwhelmed by the unknown all at once. First, there was the issue of not knowing much about my own disease. I knew much of my time was about to be spent researching something I’d prefer to know nothing about (even though years later I actually quite love researching infectious diseases). And when I did start looking into my disease, it got confusing really fast. Between the doctors disregarding the existence of Lyme, the dispute between protocols and the conspiracy theories, I was pretty pissed off that of all things, this was my ultimate sentence.

I understand that getting diagnosed with any autoimmune disease is difficult. In another post I will talk more about the mental aspects of getting your diagnosis (i.e. learning to cope mentally with the ways your life changes with a chronic illness is as necessary as finding out which drugs to take). However, when I was first diagnosed, picking a protocol was my biggest concern, so this is the first problem I’d like to address.

Picking A Protocol

This is going to require personalization, so I will not advise for or against specific treatments. I can tell you what my protocol is but I don’t think that would be appropriate, given that I have a different infection than you, my own genetic makeup, live in a different environment and have stressors different than your own. I also have not tried every therapy out there, though I have sure as hell tried a lot. I am going to provide some guidance to help you weigh your options but it is just that – guidance. After you have finished reading this, please do not let your research stop here.

I will say this: your protocol will probably consist of allopathic treatments (things that treat symptoms), holistic treatments (things that treat causes) and variation throughout time. Before you decide on a treatment plan, I think it’s important to weigh your options, be willing to change course, and acknowledge that individualized management is essential over time.

You can weigh your options by doing research, as long as this does not overwhelm you. Research can be as simple as asking your doctor about a drug, to reading case studies involving the same drug, to looking at testimonials online. I think it is important to know the risks involved in treatments. More importantly, I think it is important to know that there is no single step to “fixing” Lyme Disease and that you might not figure out the right treatment plan after one session of research. Keep in mind that some treatments work for some but not all, and that treatments usually cost money. In another post, I will talk about how to be selective about treatments, and how to spot holes in various research methods.

The reality of Lyme Disease is that most people struggle to remain in remission. I have yet to meet anyone who has been in remission for over five years, so I do not like to throw around the “c” word (cure). This is why I say individualized management is essential over time. When I feel like I’m at the peak of remission, bordering the “c” word, my individualized management is as simple as getting adequate nutrition, sleeping 7-8 hours a night, and enjoying life. If I slack on these things and find symptoms subtly returning, I may take a supplement, do a therapy or do blood work to see if my hormones are off (hormone have been a problem area for me personally in the past).

I think the point of starting a treatment protocol is to strengthen your constitution so that you can one day come off of your protocol without relapsing. But that doesn’t mean health management stops when you feel “cured.” Health management is important for everyone, and especially those of us with illnesses like Lyme Disease. Make it a goal to strive for better health every day, even long after you’ve reached remission. It’s a good way to stay in remission longer and stronger.

The Great Antibiotic Debate

This article wouldn’t be complete without a discussion on antibiotics. Deciding whether or not to take them is usually the first major decision a patient makes once they’ve been diagnosed with Lyme Disease. This section will skim the surface of the Great Antibiotic Debate.

I would love to provide statistics for you on how many people are antibiotics to treat Lyme disease, and of those people, how many are on them long-term. Unfortunately, that is a hard stat to come by. Instead of providing you with hard statistics, I will let you know what a few popular Lyme experts have told me. Dr. Chan from the Pangaea Clinic says, “I do not have exact numbers, but the majority of my patients start out with antibiotics if we find evidence clinically from exam, history, or lab reports of a current infection. The range varies widely from a simple 4-week course to many months. Our goal is to get patients off the antibiotics and transition them to herbal antibiotics, and this can usually be done if there is adequate detoxification support, nutritional support, immune dysregulation and anti-inflammatory support, sleep, stress control etc.”

I will not condone or condemn antibiotics. My hope is that my research will provide you with a better understanding of the pros and cons of antibiotic treatment so that you can be more confident in your choice to take them (or not). I will discuss the benefits involved in antibiotic usage, however I would like to say that I personally opted against antibiotic usage for myself. To help you understand why, I will also discuss their dangers.

The Consensus

The consensus varies from country to country. In Canada, most doctors are either against long-term antibiotic use, or afraid of losing their licenses if they prescribe them. A 28-day course is typically the maximum dosage Canadians can receive, which is why many of them cross the border to get antibiotics prescribed by American Lyme-literate MDs.

In the United States, LLMDs are prescribing long-term antibiotics to patients – sometimes their patients pulse between antibiotics for years. Dr. Maureen McShane wrote in an email to me:

“A few patients did not have any improvements in symptoms until on antibiotics for 18 months and many really start feeling 40-50% better about that time. IV antibiotics do not seem to be any faster or better than oral for most and it requires several months for some before any significant results are seen. Yet for others IV antibiotics make a great difference. Those with significant neurological issues need an extended time on antibiotics for it to make a difference. Most patients I see will improve and be done within a 2 year time frame if they have not been ill for a long time (4-6 months), otherwise as they say, “it is not a race, it is a marathon. 2 years seems to be a good.”

Meanwhile, in Germany, antibiotics are often used, but rarely without complimentary treatments such as ozone therapy or hyperthermia.

Why Take Long-Term Antibiotics?

As I said earlier, I will not condone or condemn antibiotics. However, before we move past this subject, let’s look at a few possible reasons why they might be a good choice, and why they might not.

Many patients don’t improve on just one month of antibiotic usage. If you are going to “go the antibiotic route,” you may benefit from a longer course of antibiotics. I will propose three reasons:

  1. One reason that long-term antibiotics may help is that Lyme disease has a long life-cycle – an in-vitro replication cycle of about seven days. This is one of the longest life cycles known to bacteria. It means that every spirochete will replicate more than the average bacterium before its death. It also means that short-term antibiotics may not be long enough to take care of reducing the infectious load. Registered Nurse Virginia Savely writes “Antibiotics are most effective during bacterial replication, so the more cycles during a treatment, the better. Since the life cycle of Streptococcus pyogenes (the bacterium that causes strep throat) is about eight hours, antibiotic treatment for a standard 10 days would cover 30 life cycles. To treat Lyme disease for a comparable number of life cycles, treatment would need to last 30 weeks.”[i]
  2. Another reason long-term antibiotics may be administered is because Lyme disease is a particularly tenacious bacterial infection – the spirochetal form of this bacteria is largely responsible for this. Spirochetes, ranging from 3 to 500 micrometers long, are unique bacteria in that their flagella – a tail-like structure that helps them move – allows them to successfully coil through the blood stream and go pretty much where they please. They manifest in the weakest points of the body, and in this way create very personalized symptoms. Once this infection has burrowed into collagen and other tissues outside of the blood stream, it can take a long time for countermeasures to fully reach  and clear out these areas.
  3. Finally, there is potential for Borrelia to take on a cystic form in order to protect itself. Cystic Lyme cannot replicate, however it is impenetrable to some antibiotics and difficult to invade by others. To make matters worse, some cysts may actually form in defense of antibiotics. In other words, when antibiotics are initially introduced into your system, cystic forms start developing, extending the eradication time for the infection just that much longer. Although cysts can form while taking antibiotics, they can also be “busted” by antibiotics – it just takes longer. Allegedly, Plaquenil, Grapefruit seed extract, Flagyl and Tindamax are “cyst busters.”[ii]

Why combine and pulse antibiotics?

A complex treatment plan may be appropriate, because Borrelia can take on quite a few different polymorphic forms. They can live within our host cells, or build their own cell walls and live as spirochetes. They can also take on cystic forms, in which case they are dormant, do not replicate, and are difficult to eradicate. Each form is affected differently by different antibiotics. For example, Macrolide antibiotics like azithromycin’s allegedly attack the spirochetes that camp in our cells. These antibiotics work better on intracellular forms than they do on cystic forms. To make matters more complicated, the intracellular form may morph into another form of the infection to defend itself against the Macrolides. Knowing this, an LLMD will likely advise you to combine or pulse antibiotics.

There are different ways to combine or pulse antibiotics. Options including cycling between antibiotics and combining multiple strains of antibiotics. A lot of LLMD’s will prescribe bactericidal antibiotics, as these can prove effective at killing Lyme in hard-to-reach tissues. Other antibiotics are bacteriostatic, meaning they manipulate pathogens to stop producing so that our bodies can eliminate what remains. A combination of these antibiotics can cause symptoms to improve quickly.

In Why Can’t I Get Better, LLMD Richard Horowitz claims that the best antibiotics for cell wall formation are:

  1. Penicillins
  2. Cephalosporins
  3. IV Vancomycin
  4. IV Primaxin

For cystic forms he recommends:

  1. Plaquenil
  2. Grapefruit seed extract
  3. Flagyl
  4. Tindamax

And for intracellular forms he recommends:

  1. Macrolides
  2. Quinolones
  3. Tetracyclines

Another way to pulse antibiotics is to take breaks (sometimes day- or week- long) in between antibiotic prescriptions. This approach may trick cystic forms of the infection to come out of hiding so that they are easy to eradicate when it is time for your next round of antibiotics. This also gives your gut and liver a rest from the damage done to them by antibiotics.

Why Avoid Long-Term Antibiotics?

There are two sides to every coin. Here are some reasons why you may choose to avoid the antibiotic route:

  1. It may not be possible to kill 100% of the infection. Unless you have entirely eradicated the infection from every tissue in your body – and that is hard when cystic and potentially biofilm forms exist – you may only reach temporary remission. If even a fraction of your infection remains, it can multiply. Antibiotics can also wreak havoc on both gut and immunity, making your body a perfect spawning ground for infections to multiply. So if your aim is to “cure” yourself of Lyme, you may be on antibiotics for life.
  2. The more you take antibiotics, the more antibiotic-resistant your infection becomes. If 0.01 percent of bacteria remain unkilled, they can multiply and bring you back to ground zero – or worse. A lot of people get stuck in an antibiotic-imposed rut because their infections have become desensitized to antibiotics.
  3. There are billions of casualties when you take antibiotics. It’s well known that we are building resistance to antibiotics, and that there is a desperate need for stronger drugs. But what people don’t talk about is the collateral damage inflicted on the good bacteria living in us that, for millions of years, have served vital functions and contributed to our survival. A round of antibiotics, especially broad spectrum antibiotics, can wipe out billions of these guys like a fire spreading through a tropical rainforest. Germs live all over us. On our skin, in our mouth and in our gut, they do more than defend us against bacterial invaders. They make our immune systems stronger against our environment. They help us digest vitamins. They are also good for our brains, because many of our neurotransmitters are created in the gut by neuroendocrine cells that communicate with your microbiota.
  4. When good bacteria are killed, populations of resistant bacterial invaders can flourish. Martin Blaser, author of Missing Microbes emphasizes the significance of resistant bacteria; “In a population of a million pneumococci, there might be one with a small genetic variation – an outlier – that arose by chance and that is resistant to amoxicillin.” (Click HERE to buy the 23andme genetic test now available on Amazon.) It’s true the other 999,999 are killed, but the single anomaly that multiplies will have a very empty home to decorate, with no defenders to stop it! It’s ironic and tragic that in our attempts to kill one bug, we eliminate our defense squad and let other bugs grow out of control. In extreme cases, people die from antibiotic-associated colitis, C. difficile.
  5. Antibiotic usage is linked to gluten sensitivity. Bacteria in your gut help you digest your food, as their primary function. A Swedish study by Drs. Karl Marlid and Jonas Ludvigsson on people with celiac disease, witnessed that people with recently developed celiac were 40 percent more likely than others to have been on antibiotics within the few months before their diagnoses.
  6. It is easy to mistake adverse antibiotic drug reactions for Lyme disease. Some people may blame their symptoms on Lyme disease when in reality, their symptoms are related to something else – like weakness due to accumulating liver damage from taking too many antibiotics. It is easy to mistake adverse drug reactions to antibiotics for Lyme disease.
  7. IV pic lines can get infected and cause blood clots.
  8. Immunity goes down with antibiotics. We are more ‘allergic’ or sensitive to our environment today than ever in history. Allergies occur when the immune system overreacts to anything that makes contact with your body that is not you. Blaser calls our microbiome our “coast guard” bacteria, which, when depleted, turn our city of coast guards into a much smaller village. The smaller your ecosystem, the more prone you are to endemics wiping it out. Studies with mice, and stats on humans indicate that we are far more likely to get sick following a round of antibiotics. In labs, “germ free” mice were unable to fight off artificially introduced bacterial invaders that didn’t even faze the “normal” mice.
  9. Antibiotics don’t get filtered out of our bodies. CYP3A4 enzymes are hematic and intestinal phase I enzymes that metabolize drugs. Antibiotics are CYP3A4 inhibitors, so they are toxic because they inhibit your detox enzymes, thus allowing the meds to build up in your body. If antibiotics, already unnecessary for your infection, are killing your good bacteria and weakening your immunity, the last thing you need is more toxins added to an already toxic body. Toxic side effects may result in nerve damage or organ failure. Histamines are also produced in the body to get rid of the drug, which often cause inflammation and allergic reactions.
  10. Antibiotics cause nutrient depletions. James B. LaValle, R.Ph., C.C.N., N.D., writes in Cracking The Metabolic Code of the nutrient depletions that follow courses of antibiotics. For example, Penicillins, Cephalosporins, Fluoroquinolones, Macrolides, and Aminoglycosidescan deplete Biotin, Inositol, Lactobacillus acidophilus, Bifidobacteria bifidum, B1, B2, B3, B6, B12 and Vitamin K. Meanwhile, Tetracyclines and Sulfonamides can deplete all of these as well as Calcium, Iron, and Magnesium.

Treatment Does Not Stop At Antibiotics

With all the research I’ve done, and all the patients and experts I’ve talked to, I honestly cannot tell you if antibiotics are an appropriate option or not. What I can tell you, however, is that we need to detox toxins and medications, feed the right bugs, starve the wrong ones without starving ourselves in the process, and keep our immune systems strong. Taking antibiotics means there is just that much more detoxification needed during or afterwards, so be prepared to do more than simply pop your prescription antibiotics. If you do opt for antibiotics, use them prudently and not just for marginal benefits.

Natural Antibiotics

Herbal antibiotics are becoming a popular alternative for treating Lyme. I think this is because people are aware that Lyme Disease is a long-term illness. Some people take antibiotics for a few months and then switch to herbals. Others take both in conjunction. Whether or not you take prescription or herbal antibiotics, I still think the goal is to be strong enough to come off of them (and stay off them) one day.

Stephen Buhner, a popular herbalist in the Lyme world, believes herbs are a better option than antibiotics. In the article, Herbal Antibiotics: An Effective Defense Against Drug-Resistant ‘Superbugs’ he says, “As soon as a bacterium develops a method for countering an antibiotic, it systematically begins to pass the knowledge on to other bacteria at an extremely rapid rate. In fact, bacteria are now communicating across bacterial species lines — something they were never known to do before the advent of commercial antibiotics. They transfer a significant amount of resistance information by releasing it into the environment to be taken up by other bacteria.” Bacteria quickly learn how to survive – they always have.

Plants, on the other hand, have responded to life in the bacterial-infested dirt by becoming complex anti-bacterial herbs. Some contain many if not hundreds of strains (ahem, marijuana) that can be antibacterial, as opposed to single compound antibiotics that are far easier for the bugs to become resistant towards. These multiple-compound antibiotics can also be free, as opposed to pharmaceutical antibiotics, which can cost thousands of dollars (despite being made cheaply, with sketchy additives because the people who make them care more about profit than about you).

I think herbs are a great option, even though they are not as potent as pharmaceutical antibiotics. I think they helped get my infection down, while I worked on my immunity, gut, detoxification pathways, liver and kidney health, and hormonal and adrenal balance. Antibiotics are a “quick fix” – sometimes. Sometimes we are just too weak to fight and we are indeed desperate for the help they provide. After treating thousands of patients, Dr. McShane has come to believe that antibiotics and antimicrobials are more effective when taken together.

 “I do think it is important to use herbals with antibiotics as patients seem to get better faster,” she says, continuing, “Herbal detox during the treatment also significantly decreases herxes. Almost all new patients with a history of antibiotic treatment failure have babesia symptoms and if that is not treated all symptoms are going to remain. Most patients have babesia symptoms and many also have bartonella symptoms. From my perspective, if the co-infections are not treated antibiotics will fail.” 

Ultimately, what I want you to get out of this is that fighting Lyme Disease is a marathon, not a sprint. Taking antibiotics is not a quicker route – there will be side effects to deal with and antibiotics don’t guarantee remission. Taking antibiotics is a serious decision, and it comes with just as much work – if not more – as taking a more natural approach. Taking a combination of herbs and antibiotics can help, according to some of the biggest names in Lyme Disease. I know people in remission who have taken antibiotics, and who, like myself, have opted against them. Each route has its own obstacles.

There Are Other Options

Your options go beyond antibiotics and herbal antimicrobials. There are ozone treatments (ozonating your blood to change the molecular structure of your infection), rife treatments (killing the infection with audio frequencies), hyperthermia treatments (heating your body to 107 degrees to kill the infection) and other options. I have heard success and failure stories related to each of these options as well as others.

[i] http://www.clinicaladvisor.com/features/controversy-continues-to-fuel-the-lyme-war/article/117160/

[ii] Why Can’t I get better



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3 thoughts on “Lyme Disease Protocols: Where To Start”

  1. Another great post! This is really an informative blog!

    After a tick bite/attachment, I removed the tick and sent it to LabCorp for testing. It was positive for Borrelia Burgdorferi. (Unfortunately, at the time, I didn’t know about other labs that might have offered more advanced testing.)

    I went through 10 days of Doxycycline, as my “regular” Doctor said that’s all I would need, since the tick was attached for “only” 12 hours or so. Fortunately, I consulted an “alternative” provider, and, although I had a two week lapse, I took another 15 days of Doxycycline. Later, I went through several rounds of high-dose (50 grams) of Intravenous Vitamin C.

    Things seemed okay for about four months. Then, I had a return — and worsening — of many Lyme-ish (and Chronic Fatigue-ish, and Fibromyalgia-ish, and insert-other-similar-condition-here-ish) symptoms that had plagued me for the year prior to the tick bite.

    After going round-and-round with several providers, I requested to be referred to the local Infectious Disease Doctors. For reasons still unknown, the Infectious Disease Doctors declined to see me. I called and asked why, but was only told they would speak to my Doctor. My Doctor was never given a reason for the declined referral, and, after reading online, I found this was not at all uncommon. So, I counted myself lucky and told my Doctor to stop pursuing them for an answer.

    Anyway, eventually, I found the website Vital Plan . com and started their “Restore” program. It was about three months into the program that I started feeling much, much better. So, I decided to stop the plan (it’s not cheap) and see how I felt. Well, in less than a week, I went from being able to do some moderate walking to feeling terrible. So bad, in fact, that I went back on the medical hamster wheel to look for some expedited help. I didn’t feel I could wait a few months to load my system with the “Restore” program.

    I ended-up with another “alternative” provider that works part time and one of the Lyme clinics. I had many (additional) tests ran and found some things like:

    – Low manganese
    – High zinc
    – Low testosterone
    – High IgG and IgM values for Chlamydia Pneumonia
    – High IgG values for Mycoplasma Pneumonia
    – High IgG values for HHV 6
    – Slightly elevated liver enzymes
    – Two “Present Abnormal” IgG bands for Lyme (via Western Blot)
    – One “Present Abnormal” IgM band for Lyme (via Western Blot)

    (Among other things. This one test was seven pages of stuff. I have stacks of other tests, too, from the past two years.)

    The suggestion was for me to go on a pulsed rotation of four antibiotics:

    Week 1:
    Monday, Wednesday, and Friday
    – Omnicef 300mg / 1 to 2 am & pm
    – Azithromycin 500mg / am & pm
    – Minocin 100mg / am & pm

    Week 2:
    – Same as Week 1
    – Thursday and Friday, add Flagyl 500mg / am & pm

    Week 3:
    – Off all week

    Week 4:
    – Repeat cycle

    Another suggestion was to consider low dose naltrexone.

    I ended-up taking another 10 days of Doxycycline, hopefully to address the Chlamydia Pneumonia. (This was my fifth antibiotic in the past two years.) It did seem to offer me a little relief. As soon as I finished them, however, I started back on the “Restore” program from Vital Plan . com. I’m hoping I can use this non-pharmaceutical route to help me, rather than trying the “Scorched Earth” policy with the four antibiotics.

    The person that started Vital Plan (Bill Rawls, MD) had been diagnosed with Fibromyalgia. Later, with Lyme Disease. He, like many of us that are chronically sick, tired of not getting help, and obsessed with finding an answer, did his own investigation — including the work of Stephen Buhner — and slowly started to get better. Later, he formulated his own supplements to help naturally suppress microbes. He’s not generally a fan of antibiotic therapy, it seems, for conditions like Lyme. He has a nice blog with some good information.

    NOTE: Aside from paying for a couple of consultations with Dr. Rawls and purchasing his products, I have no affiliation (financial or otherwise) with him, his company, or his products. I simply wish I had found the products sooner. Of course, the products may not be for everyone or for every condition. I’m hoping they work for me again — if it was even them that helped me the first time.

    Good luck to everyone!


    1. Aaron, I’m glad you enjoy the blog. I’ve never heard the term “medical hamster wheel” but I will add that to my vocab.

      I just looked at VitalPlan.com and, actually, I do like some of these formulas! If it works for you – and you can afford the blow to your bank account – keep at it. I do like that he INCLUDES the ingredients so that you can re-create his formulas if you wants (unlike Cowden and so many of these Lyme monopoly men).

      What I, myself, would recommend for most people is to take a few ingredients at a time – in case of an adverse reaction to something. The last thing any Lymie needs is to pay for more inflammation. I also prefer to buy my herbs seperately. Is this cheaper? Hmm, if I use them all throughout the year, then probably. Is it better? Hard to say. I do think that if you are feel poorly when coming off everything, then there is something else that has to be addressed. Have you addressed your low managanese and testosterone? When you come off VitalPlan do you feel okay or FRAKKIN GREAT. It takes a ton of energy to fight, and you can get that energy when your hormones/nutrient ratios are in balance, when your toxic load is low enough and you immune system is strong enough to do its job, and when your adrenals, thyroid and metabolism are in gear.

      1. ha ha – thanks. Initially, I wrote “medical mill.” But, since I feel like a hamster that’s endlessly pedaling and not making much progress, I improvised. Maybe we can make that a household term.

        As for your recommendations, I agree 100%. Starting slow is always advisable. I’ve tended to be sensitive to most medications and even some supplements, for most of my life.

        Additionally, I believe you’re also right that buying the ingredients separately is probably cheaper. Supplement protocols are similar to food items, when it comes to preparation and cost. The more preparation that’s done, the more expensive it will be. It’s paying for convenience. But, it’s also more costly and we have less control over the ingredients. There’s always that trade-off.

        As you likely know better than anyone, these “mysterious,” chronic conditions are rarely just one thing. My issues really started about 12 years ago, regarding fatigue, anxiety, palpitations, muscle pain/weakness, dizziness, and so on. But, I didn’t understand what was happening. I was lucky that I slowly got better, over time. But, over the years, I’ve relapsed several times. Each one worse than the prior and requiring more time to recover. I now realize why I’m having problems again — because I never found or resolved the root cause. I was always focusing on the smoke, rather than the fire.

        I’m trying to address the nutrients and hormones, too. In all the money I’ve spent, I had a NutrEval Plasma test that also showed me to be waaay low in B1 and Magnesium. I was borderline low in several other nutrients and amino acids. I also pair for a Gastrogram study and was found to have low stomach acid. So, I’m now taking HCL with Pepsin before meals and a digestive enzyme at the end of the meal.

        Lately, my sleep has been terrible. I’ve tried a couple of non-pharmaceutical supplements with inconsistent and marginal results. I have prescriptions for some medicines that will supposedly help. (Trazodone is one.) I don’t really want to go that route, but I also realize that sleep is mandatory.


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