How to get rid of antibiotic-resistant bacteria?

Hello! Please note that all links on this blog leading to Amazon are affiliate links. This allows us to maintain an independent opinion when reviewing brands while earning commission when you shop. Please support us and go on a shopping spree with Amazon :)

Intimate prebiotic wash

Promote healthy vaginal flora with prebiotics.

As early as in 2016 American Center for Disease Control and Prevention (CDC) has awarded more than $14 mullion to fund new approaches to combat antibiotic resistance, with a focus on the human microbiome and how microorganisms that live on and in our bodies could help prevent infections caused by multi-drug resistant organisms (MDR).

“Understanding the role the microbiome plays in antibiotic-resistant infections is necessary to protect the public’s health,” said CDC Director Tom Frieden, M.D., M.P.H., “We think it is key to innovative approaches to combat antibiotic resistance, protect patients, and improve antibiotic use.”

Since then, multiple studies came out on the topic of antibiotic-resistant bacteria, the role antibiotics play in our susceptibility to these organisms, and multiple hypotheses on how to prevent diseases caused by organisms resistant to popular first-line treatment antibiotics.

What’s a microbiome?

First of all, let’s start with the basics.

You might not realize, but your body contains nearly 2-3 pounds of bacterial cells which constitutes almost 50% of your total DNA-composition. You are, in fact, 50% bacterial. Bacteria live in and on you and most of them are beneficial.

They are responsible for or participate in many vital processes in our bodies.

The combination of all bacteria in your body is called the microbiome. Bacteria distinctively present in certain body areas (gut, vagina, mouth, etc) are identified as a microbiome of that particular organ or body part.

You are born with a small subset of bacteria that resembles your mother’s body microbiome. For the first decade of your life, your body is busy not only replicating you human cells but also acquiring more and more bacterial colonies through environmental exposures, diet, and lifestyle. Furthermore, the bacterial composition is ever-changing and is never final.

Bacteria as we now know, are roughly divided into three classes: beneficial, opportunistic (could be good or bad) and harmful.

The healthy microbiome is the one that is in the state of balance. This means there are plenty of different types of bacteria and none of them can grow out of proportion because (simply put) all of them compete for the same nutrients. And in some cases, the bi-product of one bacterial community acts as a natural anti-bacterial suppressing the growth of another bacterial community. Ideally, every bacterial colony minds their bacterial business and co-exists peacefully with the rest. Even notorious E.coli could be busy producing vitamin K and participating in other healthy processes if they are restrained from overgrowing.

However, “opportunistic” bacteria are called so due to their ability to grow fast at any opportunity that presents itself. When they get out of control, bad things happen (urinary tract infection, for example). Most often this happens when the good bacteria are depleted and they can no longer suppress the growth of opportunistic bacteria.

What’s unfortunate, opportunistic bacteria tend to grow much faster than the beneficial ones.

Everyone has antibiotic-resistant bacteria

A little known fact: “The human gut microbiota has been established as a significant reservoir of antibiotic resistance”. In simple words: antibiotic-resistant bacteria are already in your gut, as well as in every human’s gut, including newborns and isolated human populations, and uncontacted tribes that have never been administered antibiotics.

While you certainly can acquire additional strains of MDR bacteria from hospital settings or from eating farm-grown animals or even fish, the bacterial species that resist antibiotics are already in you and have always been.

You don’t suddenly “become” antibiotic-resistant, that’s the dysbiosis of your own gut microbiome allows for the MDR bacteria to overgrow.

As one researcher states: “Antibiotics are ancient molecules that have played roles in microbial sensing and signaling. Not surprisingly, antimicrobial resistance is also ancient and has been a part of the human microbiome from its earliest evolutionary origins”.

Just to clarify: antibiotics (penicillin) were isolated and used for the first time in 1928 but the mechanism of action that disrupts bacterial growth is ancient.  The scientist learned from nature and emphasized the effect of natural antibiotics when developing new drugs. The main principles though remain the same.

Additional exposure to MDR bacteria

The more antibiotic-resistant types of bacteria you have, the higher your chances to let one of those colonies flourish and cause an infection.

Where else one can acquire a multi-drug resistant bacteria?

Hospitals are notorious breeding grounds for bacteria since there are so many people who are treated with antibiotics. A hospital is an epicenter of the battle between bacteria and humans.

Hospitalization: “Many studies have demonstrated that the gloves or gowns of healthcare workers can be colonized with MDR pathogens, such as MRSA or VRE”. Study Link.

Age is a risk factor since the relative abundance of antibiotic-resistant bacterial genes increases when you get older. “We found that antibiotic resistance genes were prevalent in the human gut, and older people harbored more complex and more diverse antibiotic resistance genes than younger individuals, which could potentially be explained by gradual exposure to different antibiotics”. Study Link.

Cattle, poultry, and fish. “Cattle and poultry often get infected due to crowded conditions and are routinely treated with antibiotics. Although some antibiotics are designed exclusively for veterinary use, most of the antibiotics being used in veterinary medicine belong to the same antimicrobial classes as those being used for human diseases. Surprisingly, until recently, about 70% of the antibiotics administered to food animals were for non-therapeutic purposes, such as growth promotion. Such usage is generally performed through feeding at very low concentrations over long periods (a very dangerous practice which could enrich resistant bacterial populations).
As global production of aquatic species (fish, shellfish, shrimp, and mollusks) has been growing rapidly in the last decade, the use of antibiotics in aquaculture also increased. Many MDR (Multidrug-resistant) fish pathogenic bacteria were found in fish farmsStudy Link.

How antibiotics contribute to the problem

Microbiome dysbiosis

Right after an antibiotic treatment, there are massive shifts and changes in your native bacterial population. Unfortunately, the effect of antibiotics on gut microbiota is both short and long-term. Especially lasting effect antibiotics have on kid’s gut microbiome even if the mother is treated during the pregnancy.

Antibiotics kill all types of bacteria: the beneficial ones, the opportunistic, and the harmful ones. Now, remember that opportunistic bacteria throw themselves at any opportunity like an eager intern. Once there are less beneficial bacteria, the opportunistic ones start multiplying out of control. Now they get all the food they had to share with the good guys before.

In one study, a five-day course of Cipro produced immediate changes in the gut microbiome leading to up to 50% less of certain beneficial strains. “And while after the first treatment the microbiome took a couple of weeks to recover, However, a second five-day course of ciprofloxacin given six months after the first led to a new shift in the microbiota of all subjects that persisted for at least two months after this second exposure”, highlights the study.

As a result, the microbiota imbalances caused by antibiotics can negatively affect health in numerous manners and for long periods of time.

Further antibiotic resistance

Think of antibiotic treatment as an “America’s got talent” audition. Those who survived an antibiotic attack, pass on to the next round. When the colonies re-grow (after antibiotics are out of the system), the survivors are going to be leading the herd. This is an evolution on steroids.

Strategies to overcome antibiotic resistance

While the problem might seem scary, remember that your body once was able to successfully solve it. You were born with antibiotic-resistant bacteria and have been suppressing them for a very long time. They just got out of control and you need to work on putting them back in their place.

Killing is not an option. Suppression is the only way to go.

Here are the main pillars of the suppression strategy that are available for you today:

  • Diet
  • Improving gut function & health
  • Natural antimicrobials
  • Prebiotics
  • Probiotics
  • Hormones

There are also less realistic options such as a fecal microbiome transplant (FMT) that we wrote about earlier. Or use of synthetic microbial communities (advanced probiotics) which is not yet commercially available.

Diet & Prebiotics

The easiest, and yet the most difficult change you have to make.

“The host’s diet profoundly affects the composition of the microbiota, with repercussions for the physiology, immunity, and susceptibility to infectious diseases of the host. Dietary choices have been shown to affect colonization by enterohaemorrhagic Escherichia coli (EHEC) serotype O157:H7 and the severity and length of its resulting disease.”. Basically, this study (performed on mice) confirms that your mother was right: eat your veggies.

Briefly: include a variety of fiber, veggies, whole grains. Exclude sugars and processed carbohydrates.

For more information read these three posts:

If you need any further convincing, here is a clinical study published in Nature that demonstrated that dietary changes in less than 90 days eliminated 48 antibiotic-resistant strains and reduces the abundance of more than 77% of the rest of antibiotic-resistant bacteria in the research participants. The right diet, full of non-digestible carbohydrates provides plenty of prebiotics to support the growth of beneficial bacteria.

Improving gut function & health

Aging is not fun. If you are over thirty, your body starts to slack on many fronts. Some of these biological changes affect how you digest your food. With age often comes reduced amounts of gastric, pancreatic and other digestive system secretions.

Things you should do:

  • With your doctor’s permission stop anti-acid medicine. In short: it doesn’t solve the issue, only covers the symptom and has potential side-effects you do not need.
  • Instead, start taking digestive enzymes.

The best way to choose enzymes is based on your stool analysis done in a naturopathic clinic. They can tell you if you are having problems digesting certain types of nutrients and suggest a blend based on the results.

Alternatively, you could try an enzyme blend and see if it makes a difference in how you feel. Since your situation is unique as well as your diet, there really is no one “right” or “best” enzyme formula for everyone.

If you feel bloated and just starting to include veggies and beans, Beano enzyme could be a great option. For the rest, choose from any available options on Amazon. Make sure to read the descriptions, warnings, and reviews to find a combination that better suits your case.

Natural antimicrobials

While we wrote extensively on this topic, here are some products that deserve a call-out and should be included in your diet if you can tolerate them safely. You should aim to include at least one of the following in your daily diet:


This amazing ingredient falls into several categories: it is a prebiotic, a natural antibacterial, an anti-inflammatory, and an immunostimulating protein. Lactoferrin is naturally present in many bodily fluids, but the highest concentration is in colostrum. Interestingly enough, the concentration of lactoferrin in the vagina naturally varies depending on the time of the cycle and remains quite low all the time if you are taking oral contraceptives.

There are hundreds of research papers on a variety of ways lactoferrin is used in medicine, here is one of the quotes: “Lactoferrin has antimicrobial, immunostimulating, anti-inflammatory, and antitumor properties. The ability to bind iron allows lactoferrin to prevent bacteria from using free iron. The first step in bacterial pathogenesis is the binding of the pathogen to the host cell surface. Lactoferrin can inhibit the pathogen from binding to the host by binding to the lipopolysaccharide of the bacterial wall, ultimately resulting in bacterial cell lysis. Lactoferrin promotes the growth of beneficial bacteria with low iron requirements, such as Lactobacillus and Bifidobacterium. Lactoferrin also has antiviral activity against viruses such as cytomegalovirus, herpes simplex virus, HIV, human hepatitis C, and human hepatitis B“.

There is also an interesting study in cows, where rectally administered lactoferrin in just 10 days eliminated rectal colonization of the cows by a viral strain of E. coli (E. coli O157:H7). “However, when lactoferrin was administered orally, no clearance could be observed. This could indicate that orally administered lactoferrin might not reach the recto-anal junction in a sufficient way”, concluded the study.

Another study found that administering lactoferrin with probiotics increased the colonization of the vagina with desirable strains.

If you are a woman, your UTI-causing bacteria ascend towards urethra with a stop in your vagina. The vagina is your last chance to prevent an infection. For a long time, we have been advocating for vaginal probiotics (with your doctor’s approval) and now you can also ask if it’s okay to mix you probiotics with lactoferrin and using this mixture orally, vaginally, and/or rectally.

This Intimate SERUM with Lactoferrin also contains Xylitol and prebiotics. The formulation promotes good bacteria, inhibits opportunistic ones, and acidifies the perineal skin with a pH of 4.3. It is unisex and is applied topically on the genitals.


Check out our post on how to choose the right probiotics for your vagina and consider including probiotics that target your gut health, especially during antibiotic treatment (in that case take probiotics at least 4 hours after an antibiotic pill).

Strains to look for? Bacillus subtilis.

There is only one product that I found to solely contain this strain (LMK if you find any others). Available on Amazon.

A study that looked at 101 stool samples found that samples that contained Bacillus did not feature S. aureus and vice versa. Moreover, this bacterium capable of inhibiting the growth of many S. aureus strains, “including USA300 MRSA, the potent superbug that is responsible for most of the threatening S. aureus community-associated infections in the U.S.”.

The Plan

Here is my suggestion for you if your UTI-causing bacteria have been identified as an antibiotic-resistant type (with permission of your doctor since your GI, vaginal and overall health have to be taken into account) try the following:

  • Make sure to include at least 10 different fiber-rich products per day. Include at least one natural antimicrobial per meal. Stop eating anything made with flour, sugar, and take it easy with sweet fruits.
  • Take digestive enzymes if you are older than 30.
  • Add probiotics, especially if you are taking antibiotics or finished an antibiotic cycle in the past 6 months.
  • Use lactoferrin orally, vaginally, rectally. Combine with coconut oil or another carrier to make your own suppositories. (Ask your MD first).

Try this for 90 days, then see if they can check your stool or urine for the earlier identified MDRs.

Good luck!

Microbiome-friendly personal care

Prebiotic wash
Scroll to Top