Kills Bartonella: A Brief Guide

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How to kill bartonella in a Lyme disease treatment image from Marty Ross MD

updated 4/18/22

Bartonella Treatment in Lyme Disease - A Lot Has Changed

"The latest laboratory experiments suggest effective Bartonella treatments must do more than kill growing germ forms - they should also kill hibernating persister forms of Bartonella and include agents to remove biofilms and fibrin nests." 

Marty Ross MD

Persisters and Biofilms

Research published in 2019 and early 2020 is changing the approach I take to treat Bartonella. Previous research showed Bartonella has rapidly growing germ forms - thus the antibiotics I recommended in the past treated growing forms only. New research shows that Bartonella also has non-growing forms called persisters. Think of a persister as a hibernating form of the germ that ignores most antibiotics and immune system attacks. This new research also shows that Bartonella forms protective sugar-slime coverings called biofilms. These biofilms can block the immune system and antibiotics from reaching Bartonella. This new research is based on petri dish laboratory experiments.

Bartonella-Fibrin Nests

In addition to these key findings, some with chronic Bartonella may require enzymes to break up nests of Bartonella and the blood clotting protein called fibrin that can form in narrow and small blood vessels. These Bartonella nests limit blood flow to tissues and may block antimicrobials and the immune system from killing these germs. Lumbrokinase, a group of enzymes that come from earthworms, is very effective at breaking up fibrin. Other options include nattokinase or serapeptase, but these enzymes are much weaker than Lumbrokinase.

The Latest Bartonella Research

Growing Bartonella: What Works Best

Ying Zhang, MD and his colleagues at Johns Hopkins show that rifampin and azithromycin are the strongest agents. These are followed closely by doxycycline, methylene blue, oregano oil, clotrimazole and ciprofloxacin. In his experiments he did not study rifabutin, minocycline, clarithromycin, fluconazole or levofloxacin. The following combinations of antibiotics are in the same family: rifabutin and rifampin, minocycline and doxycycline, clarithromycin and azithromycin, clotrimazole and fluconazole or itraconazole, and levofloxacin and ciprofloxacin. If one member in a family works well the other one is likely too - so rifabutin, clarithromycin, minocycline, fluconazole or itraconazole and levofloxacin should work well too.

Note clotrimazole is a topical agent used for vaginal yeast and skin fungus infections. It is not well absorbed in oral forms so is not manufactured in pill form. Fluconazole and itraconazole are oral agents in the same family that is usually used to treat yeast that may work for Bartonella too. In my clinical practice I am finding both of these drugs work well against Bartonella.

In a separate experiment with essential oils, Zhang shows that oregano, cinnamon and clove oils are effective agents to treat growing and persister bartonella. I find these oils in combination work better than oregano oil alone. 

Persister Bartonella: What Works Best

Zhang’s petri-dish research shows methylene blue, oregano oil, and clotrimazole are single agents that work effectively against persister cells. He also shows that the following combinations work very well: azithromycin/methylene blue, rifampin/methylene blue, azithromycin/ciprofloxacin, and rifampin/ciprofloxacin. As I note above, separate work from Zhang shows oregon, cinnamon and clove oils are effective agents for persister bartonella. And the most recent research shows cryptolepis and japanese knotweed can treat persister Bartonella and growing Bartonella too. 

Bartonella Biofilms:

In Zhang’s 2020 study, he showed that the best combinations for persister Bartonella also are the strongest at removing biofilms. These combinations are: azithromycin/methylene blue, rifampin/methylene blue, azithromycin/ciprofloxacin, and rifampin/ciprofloxacin.

In addition to these combinations, I also find that other biofilm busting herbal medicines like oregano oil, cinnamon oil, clove oil, lumbrokinase, the herbs in Biocidin LSF by Biobotanical Research, and BioDisrupt by Researched Nutritionals are helpful. You can read more about these in Biofilms: Lyme Disease Gated Communities.

Effective Bartonella Treatment Steps

In my clinical practice, many different combinations of herbal and prescription antibiotics work to cure Bartonella over four to six months. With these treatments — including steps to boost the immune system and to decrease inflammation — in my experience it is possible to cure Bartonella 95 percent of the time. This means five percent of people may have relapses or require treatments involving a number of the different approaches below.

Step One. Boost the Immune System & Decrease Inflammation

It is critical for Bartonella recovery to take steps that boost the immune system. Boost the immune system following the first ten steps in The Ross Lyme Support Protocol. These steps are designed to:

  • correct sleep,
  • decrease inflammation cytokines,
  • help the immune system adapt to stress,
  • correct hormone imbalances,
  • provide essential micronutrients, and
  • remove yeast overgrowth in the intestines if present.

Step Two. Use Continuous Antibiotics

Research suggests Bartonella replicates and creates new germs every 24 hours. This means during any period off of antibiotics, Bartonella grows back. Some physicians pulse antibiotics when treating Bartonella. Such regimens can include two weeks taking antibiotics followed by two weeks off. In my practice, I do not find these treatments to work. This is likely due to Bartonella growing back during the period that someone is off of the antibiotics.

Step Three. Use Combination Antibiotics & Biofilm Breakers to Cure Bartonella

Bartonella can be difficult to treat when a person has a Borrelia (Lyme) infection. To prevent relapse, it is best to use three antibiotic combinations. There are two tiers of treatments I recommend. Tier One includes prescription and herbal antibiotics - Tier Two is an herbal antimicrobial combination for the person who cannot tolerate prescription antibiotics or when the prescriptions do not work. Tier One combinations appear to work 85 to 90 percent of the time. Tier Two seems to work 70 to 75 percent of the time or less.

As I noted above, there is no useful clinical science to guide treatment decisions for Bartonella in someone who has Lyme. What follows is based on my experience treating Bartonella in Lyme disease. In general, if a treatment is working, the symptoms of Bartonella should start to improve in one to two months. If they do not start to improve, then change to a different regimen. Read more about Bartonella symptoms in How to Diagnose Bartonella in Chronic Lyme Disease (

Tier One Bartonella Treatment Approaches

Here are some combinations that treat growing and persister Bartonella and target biofilms. In these combinations, I find using three agents work best. I include methylene blue and a combination essential oil product of cinnamon, clove and oregano to treat persister forms, remove biofilms, and to treat growing forms. I list the combinations in order of effectiveness. The strongest treatments are at the top. Note, all of these can be effective depending on the person.

  • fluconazole plus (azithromycin or clarithromycin) plus cinnamon, clove and oregano oil combination product
  • fluconazole plus (doxycycline or minocycline) plus cinnamon, clove and oregano oil combination product
  • (rifampin or rifabutin) plus (azithromycin or clarithromycin) plus (methylene blue or cinnamon, clove and oregano oil combination product)
  • (rifampin or rifabutin) plus (doxycycline or minocycline) plus (methylene blue or cinnamon, clove and oregano oil combination product)
  • (azithromycin or clarithromycin) plus (doxycycline or minocycline) plus (methylene blue or cinnamon, clove and oregano oil combination product)
  • (rifampin or rifabutin) plus Bactrim DS plus (methylene blue or cinnamon, clove and oregano oil combination product)
  • (azithromycin or clarithromycin) plus (Bactrim DS) plus (methylene blue or cinnamon, clove and oregano oil combination product)

Here is how to dose the various prescriptions and the oregano supplement in these combinations:

  • fluconazole 200 mg 1 pill 1 time a day
  • methylene blue 50 mg 1 pill 2 times a day (this has to be made by a compounding pharmacy)
  • liposomal cinnamon, clove and oregano capsules 1 pill 2 times a day (each capsule should include 75 mg of oregano)
  • rifampin 300 mg 2 to 4 pills 1 or 2 times a day
  • rifabutin 150 mg 2 to 4 pills 1 or 2 times a day
  • azithromycin 500 mg 1 pill 1 time a day
  • clarithromycin 500 mg 1 pill 2 times a day can be substituted for azithromycin, but rifampin also decreases clarithromycin blood levels.
  • minocycline 100 mg 1 pill 2 times a day,
  • doxycycline 100 mg 1 pill 2 times a day can be substituted for the minocycline, but rifampin decreases doxycycline levels in the blood.
  • Bactrim DS 1 pill 2 times a day

About Fluoroquinolone-based Treatments

Fluoroquinolones are a class of antibiotics that include a number of members like levofloxacin (Levaquin) and ciprofloxacin (Cipro). I no longer use these treatments due to the risk of permanent tendon pain or even breakage.

Tier Two Bartonella Treatment Approach

  • Houttuynia plus Sida Acuta plus Cinnamon, Clove and Oregano Oil Combination

I started using the houttuynia and sida acuta together in the summer of 2015. Based on Zhang’s research I now include cinnamon, clove and oregano oil to treat persisters and biofilms. This combination effectively supports a Bartonella treatment about 70 to 75 percent of the time.

  • houttuynia 5 drops 2 times a day and increase daily by 1 drop per dose till at 30 drops 2 times a day.
  • sida acuta 1/4 tsp 3 times a day and after 1 week if tolerating it increase to 1/2 tsp 3 times a day.
  • liposomal cinnamon, clove and oregano capsules 1 pill 2 times a day (each capsule should include 75 mg of oregano)

If someone cannot tolerate the cinnamon, clove and oregano capsules, then for persisters (and growing Bartonella) I substitute either cryptolepis or Japanese knotweed.

  • cryptolepis 5 ml 3 times a day OR
  • Japanese knotweed 30 drops 2 times a day

I am not impressed with other herbal options. For instance, I have tried a formula called A-BART by Byron White, which are herbs that seem to help less than 50 percent of the time. Likewise, houttuynia by itself only works 50 percent of the time. And I have not had any success using the Beyond Balance herbal products.

Step Four - Remove Bartonella-Fibrin Nests

At two months into a Bartonella treatment, add lumbrokinase to break apart Bartonella-fibrin nests if there is not significant improvement in Bartonella symptoms supporting the immune system and using combination antimicrobials. I also attack the Bartonella-fibrin nests in any person who has a Bartonella relapse. In this situation, I add lumbrokinase as I restart Bartonella antimicrobials.

  • Lumbrokinase 16 mg to 20 mg 1 pill 2 times a day. If there is not a significant Bartonella herxheimer reaction, consider increasing the lumbrokinase to 2 pills 2 times a day after 1 month. Lumbrokinase must be taken on an empty stomach. This means a person should stop all medicines, supplements, and food 1 hour before taking the Lumbrokinase through 1 hour after taking Lumbrokinase. It is OK to take the lumbrokinase with water.

Treatment Course

For most of the combinations described above, treatment requires four to six months. Treat until most of the Bartonella symptoms go away. Fortunately, 95 percent of people recover from Bartonella using the immune supports, Tier One or Two approaches, and possibly lumbrokinase. The remaining five percent may have relapses or require continuous antibiotics to keep Bartonella under control. If a person relapses, three or four antibiotic combinations work well.


The ideas and recommendations on this website and in this article are for informational purposes only. For more information about this, see the sitewide Terms & Conditions.


View Citations

  1. Buhner SH. Healing Lyme Disease Coinfections: Complementary and Holistic Treatments for Bartonella and Mycoplasma. Rochester, VT: Healing Arts Press; 2013.
  2. Biswas S, Rolain JM. Bartonella infection: treatment and drug resistance. Future Microbiol. 2010;5(11):1719-1731. doi:10.2217/fmb.10.133 (View)
  3. Zheng X, Ma X, Li T, Shi W, Zhang Y. Effect of different drugs and drug combinations on killing stationary phase and biofilms recovered cells of Bartonella henselae in vitro. BMC Microbiol. 2020;20(1):87. Published 2020 Apr 10. doi:10.1186/s12866-020-01777-9 (View)
  4. Li T, Feng J, Xiao S, Shi W, Sullivan D, Zhang Y. Identification of FDA-Approved Drugs with Activity against Stationary Phase Bartonella henselaeAntibiotics (Basel). 2019;8(2):50. Published 2019 Apr 29. doi:10.3390/antibiotics8020050 (View)
  5. Ma X, Shi W, Zhang Y. Essential Oils with High Activity against Stationary Phase Bartonella henselaeAntibiotics (Basel). 2019;8(4):246. Published 2019 Nov 30. doi:10.3390/antibiotics8040246 (View)
  6. Ma X, Leone J, Schweig S, Zhang Y. Botanical Medicines with Activity Against Stationary Phase Bartonella henselae, Infectious Microbes & Diseases: August 2, 2021 - Volume - Issue - doi: 10.1097/IM9.0000000000000069 (View)
  7. Lindner H. Chronic Babesiosis Caused by Babesia odocoilei: Pathophysiology, Diagnosis and Treatment. Lecture presented at The International Lyme and Associated Diseases Annual Conference; October 2021; Orlando.
  8. Mozayeni R. Bartonella Update. Lecture presented at The International Lyme and Associated Diseases Annual Conference; October 2021; Orlando.
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About the Author

Marty Ross, MD is a passionate Lyme disease educator and clinical expert. He helps Lyme sufferers and their physicians see what really works based on his review of the science and extensive real-world experience. Dr. Ross is licensed to practice medicine in Washington State (License: MD00033296) where he has treated thousands of Lyme disease patients in his Seattle practice. 

Marty Ross, MD is a graduate of Indiana University School of Medicine and Georgetown University Family Medicine Residency. He is a member of the International Lyme and Associated Disease Society (ILADS) and The Institute for Functional Medicine.

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