For many years I've struggled with the choice of when to avoid antibiotics and what situations warrant their use. As a person with chronic lung infections related to cystic fibrosis, antibiotics have saved my life countless times, but in the last few years I've become dependent on them to function normally. Without antibiotics to control my chronic lung infections (MRSA and Pseudomonas), I often feel debilitating fatigue, get a daily fever, and cough lots and lots of mucus. While I've found many natural remedies over the years to reduce my infections, improve my immune system, and strengthen my overall health and digestion, the severity of my infections is such that I cannot avoid antibiotics completely. In general, there are no natural remedies that I know of that match the power of pharmaceutical antibiotics for use in many bacterial infections - and trust me, I've looked!
As a result of my experiences both with conventional pharmaceuticals and natural medicine, my opinions about antibiotics have changed over the years. In the beginning of my healing journey and experimentation with natural medicines, I viewed antibiotics with skepticism and tried to avoid them as often as possible. I made the personal choice to suffer through many months of infection, fatigue, and heavy mucus loads in order to minimize my exposure to this class of drugs. I did this for two major reasons: minimizing the risk of developing antibiotic resistance, and mitigating the impact that excessive use of antibiotics has on the gut microbiome. For about four years, I chose to wait as long as possible between hospitalizations, and do without oral antibiotics for longer and longer periods of time.
Upon reflection, I think avoiding antibiotics as often as I did was a mistake, and I wouldn't recommend people do what I did. I lost lung function during that period and developed some serious and irreversible lung damage. It's not clear whether or not this damage would have developed anyway, even if I had taken more antibiotics. I now believe that the cost-benefit analysis weighs out in favor of using antibiotics when appropriate. In the last year or so I have changed tactics and my health has benefited. Here, I will describe my experiences and review why I made these changes.
I must be absolutely clear: this is not medical advice. I am not advocating for anyone to do what I did and I do not believe my experience is true or applicable to every situation. This is only a reflection on what I have personally experienced. If others can learn from my mistakes in order to benefit themselves, that's great. But ultimately every individual's health is different, and what may be useful for me may not be useful for someone else.
My Old Strategy
For several years I would wait as long as possible between hospitalizations and only go in for a clean out if I really felt horrible. At that time, feeling horrible meant that I was so tired that doing daily errands required an incredible exertion of energy and willpower. I had daily fevers with night sweats, significant mucus production with frequent hemoptysis, and weight loss. I usually admitted myself to the hospital only twice a year, usually after catching a virus that resulted in an exacerbation that I couldn't control with other means, like herbs and essential oils. During this time, I experimented with lots of herbal and natural remedies. Some of these experiments were very successful. I favored experimentation with these new therapies over using antibiotics. I discovered a lot about myself during this period, and did lots of research (much of which I have recorded in this website). So in several ways it was a fruitful period of discovery and personal development.
Then in 2015 I had my first lung collapse. A lung collapse (pneumothorax) in CF is caused by advanced bronchiectasis and severe inflammation stemming from chronic, uncontrolled infection in the lungs. I had a pleuradesis operation, but a few months later I had a smaller collapse again in the same spot. It became clear to me that I was now at a stage in my disease where the lung damage I was experiencing was accumulating and becoming irreversible. I knew in that moment that I had to do everything in my power to preserve the lung capacity that I have left. It caused me to rethink my approach to treating my lung infections and resisting the use of antibiotics. I was beginning to understand that I needed to treat my infections more aggressively and that waiting for excessively long periods of time between antibiotics might have been doing more harm than good. While the gut microbiome can recover somewhat from a disturbance caused by antibiotics, lung scarification from chronic infections cannot be reversed.
A Change in Tactics
Starting last summer, I began to negotiate a little more with my doctors, who had introduced to me the idea of coming in every 3-4 months for a hospitalization regardless of my lung exacerbation status. Previously, I had resisted this idea, as causing overexposure to antibiotics that could disrupt my gut microbiome and make me more susceptible to infections by weakening my immune system, and potentially leading to the development of allergies or fungal overgrowth in the lungs, like Aspergillis. Although these concerns are still forefront in my mind, I now have a better understanding of how to control for them while still using antibiotics strategically and effectively.
I realized that in my years of dogmatic avoidance of antibiotics, there were no significant developments in the two major fears I had (developing antibiotic resistance and degrading my gut microbiome), at least not in a way that was directly attributable to my use of antibiotics. My digestion had improved significantly during that period, but that could be attributed to many things including a major shift in my diet, better exercise, and the regular use of digestive herbs, prebiotics, and probiotics. There were no major changes to my sputum cultures during that time other than a slight improvement in antibiotic sensitivites, but those also could have been due to the use of herbs that inhibit bacterial resistance to antibiotics (like thyme, goldenseal, or rosemary). So while there were some fairly clear drawbacks to my avoidance of antibiotics in terms of lengthy periods of uncontrolled infection and permanent lung damage (I lost about 5% of lung function during that time), there were no measurable benefits to the lungs. I did, however, learn a lot, and in experimenting with antibiotic alternatives I discovered many things that have helped other people in very real ways.
So now I have developed a new routine of antibiotic use, one that rotates antibiotics to minimize developing resistance, but never going for lengthy periods without having some type of antibiotic on board. This is tailored specifically to my colonizing bacteria and my symptoms. Throughout the years I have gotten to know my bugs very well and their patterns are very predictable. My major bug is MRSA, and if I go too long without antibiotics (more than 2-3 weeks) I get fevers, fatigue, and excessive mucus production. So my new regimen goes like this: I do 4-5 days in the hospital with ceftazidime (covering Pseudomonas) and vancomycin (covering MRSA), then continue for 10 more days of IVs at home. After finishing this course of IVs I usually have about 3-4 weeks with no fevers (this period has lengthened since improving my adrenal resilience with adaptogenic herbs, using testosterone, and supplementing with my herbal antimicrobial tincture formula - thyme, usnea, barberry, elecampane - as needed). Then I start a month of inhaled vancomycin, and for the last 2 weeks of that month I use oral minocycline (because I usually start to develop a fever at that point). Then I wait another two weeks (usually using my antimicrobial lung tincture and/or nebulizing colloidal silver) and then go on two weeks of Sivextro (tedizolid). Sivextro is a newer cousin to Zyvox (linezolid). Zyvox is a very effective anti-MRSA drug with very intense and very serious side effects that I cannot tolerate, but Sivextro is as effective but has far fewer side effects (none for me), although it is extremely expensive. Luckily, I have great health insurance (Medicare + Medicaid) that covers Sivextro with minimal whining. Then I wait another two weeks until I develop a fever, and start the whole cycle over again. So I end up going into the hospital about every three months.
Since starting this regimen I have more energy and feel sick and fatigued much less often, which allows me to exercise more, improving my airway clearance and overall strength, as well as my quality of life. I think that's a big point I want to make: my new routine improves my quality of life so that I am happier and more active, which improves my overall health. I am still very focused on maintaining a strong and diverse microbiome, so I supplement daily with probiotics and eat a diet high in prebiotic plant fibers and fermented foods.
Things to Note
I must admit though that there is a big variable in here that has contributed to the overall improvement in my health in addition to this new antibiotic routine: supplementing with testosterone. Since I am a transgender person identifying as trans-masculine, I have been supplementing with testosterone for about a year and a half. Alongside top surgery, testosterone has radically improved my life in more ways than I can express. This has to do both with finally getting the treatment I've needed my whole life, improving my mental state and reducing gender dysphoria, giving me more energy, and helping to remediate the negative effects that estrogen has on cystic fibrosis.
You will also notice that I do not inhale any anti-Pseudomonal antibiotics. This is because I noticed that for me personally, they have no effect on either my symptoms or my sputum cultures. Furthermore, I recently listened to an excellent lecture by Dr. Richard Moss from Stanford, put on by CFRI, on the growing problem of Aspergillus colonization and Aspergillosis in CFers. One of the major causes of increased Aspergillus colonization in CF lungs is the constant use of inhaled antibiotics, specifically anti-Pseudomonals like Tobi/tobramycin and Cayston. Using these inhaled antibiotics with no breaks makes overgrowth of fungus in the lungs more likely because it disrupts the lung microbiome; remember that antibiotics are antibacterial but not antifungal.
If inhaled anti-Pseudomonal drugs are effective for you, that's excellent. But I worry about constant use for the above reason. That also goes for constant use of antibiotics of any sort - oral or IV. Thus, I think taking breaks in between antibiotic courses and also including regular use of antifungal herbs are good ideas. Certain essential oils are antifungal (such as thyme, lemongrass, or tea tree oil) and can be used in a diffusor, steamed, nebulized, applied topically, or put in rectal suppositories. Other herbs can be taken in tincture or tea form like thyme, usnea, barberry, calendula, and many others.
Rigid Ideologies and Misunderstandings
An important issue I wish to mention is the shame we might feel if we have a rigid anti-pharmacetuical belief system but our health declines to the point where we require antibiotics or other drugs, even when we've done everything else "right". This is really difficult - I've experienced this shame many times and blamed myself for "not doing enough" healthy things. Don't get trapped in this blame-shame game! It's not true! I see many problematic messages out there on the internet blaming sick people for their illness, saying "you caused it and you're not doing enough. If you only did X,Y,Z you would be healthier..." This is part of capitalist, post-Puritanical conditioning; it's deeply harmful and untrue. Some of us will get sick no matter what we do - that's the nature of CF and other chronic illnesses. Although natural heathcare can often improve our health, it's usually neither miraculous nor a cure-all... neither is conventional medicine for that matter! We are mortal, thus we cannot always be healed, and it's not our fault!
In addition, I have come accross multiple people in the CF community who have rigid ideological beliefs concerning germ theory versus terrain theory. I have seen some individuals in the CF community, usually those without much medical knowledge, offer their opinions trying to "debunk" germ theory (i.e. that germs and pathogens - bacteria, viruses, fungi - cause disease) and espousing the idea that disease is cause only by unhealthy tissue terrain which can be improved by a healthy diet. While I agree that conventional medicine often over-emphasizes the role that germs play in disease and deny the importance of human colonization by healthy bacteria, germs do indeed cause disease in a lot of cases and using antibiotics can help clear up infections. AND, unhealthy tissue terrain can make us more vulnerable to these infections. Both sides are true. But it is extremist and inacurate to believe that only one side of that equation is true and each of those extremes leads us to make poor medical choices. There is much more to say on this point (and it would involve a review of the last two hundred years of medical history) but I'll leave it at that for now.
I still believe that antibiotics need to used only when absolutely necessary and with very careful planning and study of all potential repercussions. People in the U.S. (and most people with access to Western medicine) uses antibiotics too frequently and often inappropriately. There are many consequences to the overuse of antibiotics that I have outlined elsewhere in this website including disturbance of the gut microbiome, digestive diseases, allergies, autoimmunity, antibiotic resistance, reduced immunity, and increased risk of fungal infections. However, they are literally lifesaving when properly used, and in CF we need them in many situations.
So my views on antiobiotics have changed significantly in many ways. I have let go of many dogmatic beliefs and take a more practical, balanced approach now. It's also possible that my tactics may change again with updated information - that's what a good scientist does! I still use herbal remedies in a complementary way with antibiotics because many herbs make antibiotics work better (e.g. rosemary, thyme, barberry). I know for sure that using antibiotics has saved my life many times and their continued use will lengthen my life by decades. But they will only continue to help me if I use them judiciously and in conjunction with other therapies.
UPDATE: January 2022
Since starting Trikafta in November 2019, my lung function has improved over 10% and I no longer need to take antibiotics regularly. In fact, the last time I used antibiotics was in May 2020 when I was recovering from a severe and life-threatening pneumonia. This drug (Trikafta) has been a miracle for me, and I will probably live decades longer. My quality of life is much improved. Now that my cells function more normally, I no longer need antibiotics, and my herbal antimicrobial tinctures (elecampane, barberry root, thyme) work better than before if I feel like I need help clearing mucus or if I might be coming down with a respiratory infection. Ironically, my improvement from Trikafta proves the validity of terrain theory - when you improve the tissue terrain, the germs are less likely to take hold. And, at the same time, if I needed antibiotics at any point in the future I wouldn't hesitate to take them, under the right circumstances.
Mica (they/he) is a clinical herbalist, nutritionist, ecologist, and writer living in Abenaki territory (Vermont).
The archive of the old version of this blog (2013-2021) is available here.
Disclaimer: The content of this website and blog is for educational purposes only and should not be considered medical advice. The information provided here is not intended to replace medical care.