Antibiotics are important in some cases. However, they can also have side effects. They range from diarrhea and stomach upset to depression, anxiety, sore tendons, and a generally weakened immune system. We present the most important side effects of antibiotics.

What side effects do antibiotics have?

Antibiotics are still widely used. Treating a patient with antibiotics is called antibiosis. Antibiotics can have numerous side effects.

Although there are many different antibiotic medications, which can of course have different side effects, the package insert (using the example of amoxicillin, which belongs to the penicillins) usually lists the following:

• Gastrointestinal complaints such as nausea, vomiting, diarrhea, loose stools, flatulence, abdominal pain, taste disturbances
• Inflammation of the oral mucosa
• Discoloration of the tooth surface, which is temporary and can be avoided by good oral hygiene
• Hypersensitivity reactions of the skin, such as itching, rash (which can also be severe if a skin fungus develops at the same time or has developed in the first place thanks to antibiotics), hives
• Increase in liver values
• Infections with other bacteria or yeasts (e.g., vaginal yeast infections, as antibiotics weaken the immune system and eliminate beneficial bacteria (not only those of the intestinal flora, but also those of the vaginal flora), allowing fungi and harmful bacteria to prevail
• Allergic reactions up to anaphylactic shock or hypersensitivity reactions (drug fever)

Unfortunately, the package insert does not list other side effects that may only occur several weeks, months, or even years after antibiotic treatment. We present some of them below.

When should antibiotics not be prescribed?

Despite the long list of side effects, antibiotics are still prescribed too often, and often for the wrong indications. You’re probably familiar with this: You go to the doctor—for a sore throat, a cold, a cough, a simple urinary tract infection, or whatever—and come out with a prescription for antibiotics.

However, especially for the aforementioned symptoms, antibiotics are not always advisable, at most in 10 percent of sore throat patients, namely when certain bacteria (streptococci) are involved in the infection. Nevertheless, antibiotics are prescribed in 60 percent of all cases for sore throats alone (1) – according to a 2014 US study.

Even in Australia, antibiotics are still prescribed far too often for colds. One in four (25 percent) receives an antibiotic for a cough, runny nose, or hoarseness – fortunately, the trend is declining. A few years ago, just under 40 percent of cold sufferers left their family doctor’s office with a prescription for an antibiotic.

Do antibiotics also work against viruses?

Antibiotics can be effective in treating bacterial diseases (e.g., urinary tract infections or ear infections) and can often be life-saving, for example, in cases of bacterial pneumonia or severe bacterial diarrhea.

However, since antibiotics can ALWAYS have unwanted side effects, they should only be used if a helpful effect can be expected, which is rarely the case with colds with a sore throat, runny nose and cough, since 90 percent of these symptoms are caused by viruses – and most antibiotics simply do not help against viruses (an exception is, for example, the macrolide azithromycin with a broad spectrum of activity against bacteria AND viruses).

In some respiratory infections, bacteria can also join in after a few days (superinfection), which can then worsen symptoms or lead to complications such as sinusitis, ear infections, or pneumonia. In these cases, an antibiotic can naturally be effective and provide relief.

How do I know I’m taking the right antibiotic?

Furthermore, the wrong antibiotic is often prescribed. Not only are antibiotics mistakenly prescribed for viral infections, but even for bacterial infections, the wrong medication is often chosen. Because not all antibiotics are created equal.

A so-called antibiogram prior to administration would help here. This involves taking a urine sample (for urinary tract infections) or a swab, for example, of the throat mucosa. A laboratory test is then conducted to determine which antibiotic would be most suitable for the specific infection, i.e., which would be most effective.

According to a 2016 health insurance study, it was shown that doctors almost always (in 95 percent of cases) prescribe an antibiotic on suspicion, i.e. without first clarifying its effectiveness.

In this study, it was found that even for urinary tract infections, a corresponding test is only ordered in one in four cases. In internal medicine, physicians ordered only 30 antibiograms for 119,000 cases of infection, and among general practitioners – auditors found only 15 antibiograms among more than 350,000 infections treated with antibiotics.

The doctors interviewed justified this behavior by saying that patients expected a medication quickly (but the results were only available after 48 hours), that a corresponding sample also took a lot of time, and that they had concerns about costs for all of this.

Multi-resistant germs are developing

If an antibiotic is prescribed too often or unnecessarily, or if the wrong antibiotic is given for the infection in question, this practice promotes the dangerous development of resistance in bacteria, so that multi-resistant pathogens can develop, against which no antibiotic is then effective in the case of really serious health problems.

The side effects of antibiotics

Since antibiotics do not specifically target harmful, disease-causing bacteria, but also eliminate beneficial bacteria, such as the bacteria in the oral flora, vaginal flora, and intestinal flora, antibiotics often result in unwanted side effects, with digestive problems being at the top of the list.

Diarrhea during and after antibiotics

Diarrhea is one of the most common side effects of antibiotics, along with flatulence and abdominal cramps, due to the intestinal flora disturbance caused by antibiotics.

In many patients, diarrhea subsides after stopping the medication, and the intestines and intestinal flora recover on their own – at least, this is how it seems at first, since antibiotic-induced damage to the intestinal flora can lead to chronic intestinal problems or completely different health problems in the long term.

However, in some patients, “normal” antibiotic-induced diarrhea develops into life-threatening diarrhea immediately during or after antibiotic treatment.

This is mostly caused by Clostridioides difficile (formerly: Clostridium difficile) – a bacterium that is normally also present in the intestinal flora of healthy people – but only in small numbers because it is kept in check by the beneficial intestinal bacteria.

However, if the beneficial intestinal flora is severely suppressed by an antibiotic, C. difficile can easily spread. Its toxic secretions trigger severe, sometimes life-threatening diarrhea. This condition is known as pseudomembranous colitis. C. difficile is one of the most common hospital pathogens because it is resistant to numerous disinfectants and even some antibiotics.

Stomach problems caused by antibiotics

Stomach problems such as nausea, abdominal pain, vomiting, and heartburn can also occur or be aggravated by antibiotics.

They irritate the mucous membranes in the mouth, throat, and stomach. At the same time, they can eliminate the stomach bacteria Helicobacter pylori, which, according to some experts, can often protect healthy people from symptoms such as reflux and heartburn—a sign that even bacteria with a bad reputation aren’t always bad, but can also offer health benefits (2).

Chronic inflammatory bowel diseases caused by antibiotics

If antibiotics primarily affect the intestines, it is obvious that these drugs may also cause or promote chronic inflammatory bowel diseases such as Crohn’s disease and ulcerative colitis.

A 2011 study using data from 2,234 patients with inflammatory bowel disease found that they were more likely to have been prescribed an antibiotic than over 22,300 healthy controls (2 to 5 years before the onset of the disease) (3).

Those who had taken antibiotics at least once or twice were more likely to develop Crohn’s disease, while those who had been prescribed antibiotics three or more times were more likely to develop ulcerative colitis. Antibiotics are therefore considered a possible cause of chronic inflammatory bowel disease.

Irritable bowel syndrome due to antibiotics

Irritable bowel syndrome can also develop as a long-term consequence of antibiotic treatment, which represents a particularly vicious cycle, since antibiotics are prescribed for irritable bowel syndrome when other measures fail. This is because irritable bowel syndrome is associated with a massive disturbance of the intestinal flora, and antibiotics are used to try to reduce this unfavorable intestinal flora (4).

Symptoms (bloating, stomach ache, etc.) usually improve immediately. However, after stopping the antibiotic—10 to 14 days later—the symptoms often recur, so the medication is taken a second time or even long-term. In this case, it’s better to look for the underlying causes of irritable bowel syndrome, which can often be alleviated with holistic measures.

Vaginal yeast infection caused by antibiotics

In women, antibiotic therapy often leads to vaginal yeast infections (5). As explained above, antibiotics not only alter the intestinal flora, but also the vaginal flora. The protective lactic acid bacteria are reduced in number, which allows yeast infections to spread and cause itching, discharge, vaginal dryness, etc. Find naturopathic treatments for vaginal yeast infections.

Obesity due to antibiotics

A study published in the International Journal of Obesity in 2015 found that antibiotics in childhood can promote the development of obesity – not only in childhood but also years later (6).

Diabetes caused by antibiotics

Another study – published in October 2015 in the Journal of Clinical Endocrinology and Metabolism – showed that antibiotics may be linked to type 2 diabetes.

Danish researchers examined data from more than 1.5 million people and found that those who had taken antibiotics two to four times in the years before their diagnosis had a 23 percent higher risk of developing diabetes compared to people who had never taken an antibiotic. Those who had to take antibiotics five or more times had a 53 percent increased risk of diabetes (7).

Of course, in these relationships there is always the possibility of a simple correlation without causality, for example that people with a tendency to diabetes are generally more susceptible to infections and therefore take antibiotics more often.

Depression and anxiety caused by antibiotics

You may have heard of the gut-brain axis, which describes the mutual influence of the gut and brain.

So if the intestines suffer as a result of antibiotics, this can also have a negative impact on the psyche.

For example, a study published in the Journal of Clinical Psychology in November 2015 showed that just one dose of antibiotics is enough to increase the risk of depression and anxiety (8).

The more often you have to take antibiotics, the more the risk increases, until it is finally increased by 50 percent after five courses of antibiotic therapy.

Sick tendons and psychoses caused by antibiotics

Antibiotics from the fluoroquinolone group, also known as gyrase inhibitors (e.g., norfloxacin, ciprofloxacin, moxifloxacin, and levofloxacin), can have particularly severe side effects. They can damage tendons and nerves, leading to tendon ruptures and nerve pain.

The corresponding symptoms of nerve damage include tingling, numbness, and muscle pain. Fluoroquinolones can also trigger panic attacks, hallucinations, suicidal thoughts, and liver damage.

Unfortunately, these side effects do not necessarily disappear after discontinuing the antibiotic, but can persist for many months or even permanently.

Some of the tingling sensations in the face and hands appear on the package insert under “rare side effects.” In reality, however, as entries in the EU side effect databases show, tens of thousands of patients are already affected.

Fluoroquinolones are now considered reserve antibiotics, meaning they should only be given when there are no other options – and certainly not for trivial infections such as bacterial sinusitis, chronic bronchitis or uncomplicated urinary tract infections, because the risk of serious side effects clearly outweighs the benefits.

Organ damage caused by antibiotics

Issue 4/2016 of the journal Medication Therapies lists the toxic effects of various antibiotics on organs. For example, some cause damage to the central nervous system, which can manifest itself in seizures. Others damage the kidneys, which can lead to renal failure, and still others damage the striated muscles, which can result in myopathy.

Antibiotics in the macrolide group can damage the heart, which can lead to cardiac arrhythmias, and antibiotics in the oxazolidinones group can even affect the bone marrow, which manifests itself in blood formation disorders and can lead to thrombocytopenia (too few platelets), which in turn can cause internal bleeding.

Antibiotics weaken the lungs’ defenses against influenza viruses

In a study on mice in the summer of 2019, London scientists found that antibiotics—if taken shortly before a flu infection (e.g., for a urinary tract infection)—can adversely affect the course of the flu (9). The underlying mechanism is as follows:

Antibiotics damage the intestinal flora. However, the intestinal flora can activate the lung epithelial cells via messenger substances, allowing them to better protect themselves against viruses. Especially in the first two days of an infection, the body’s immune cells are not yet ready for the antiviral fight. During this time, however, the virus can multiply rapidly if the lung cells do not protect themselves. If the intestinal flora is damaged by antibiotics, this self-protection no longer functions.

If the immune cells are finally ready after two days, the infection is already very advanced, so that complications and a significantly more severe course can occur.

Side effects of antibiotics during pregnancy

Pregnant women are said to be advised to avoid antibiotics in the first trimester of pregnancy. However, a 2015 study shows that antibiotics can also be problematic later in pregnancy. It found that antibiotics taken in the third trimester can increase the risk of respiratory diseases in the child (10).

Antibiotics can cause miscarriages

If pregnant women take an antibiotic in the first trimester (within the first three months of pregnancy), the risk of miscarriage increases (11) – according to a Canadian study in which antibiotics from the groups macrolides, quinolones, tetracyclines, sulfonamides, etc. were examined.

Antibiotics can cause birth defects

Another study (August 2017) based on 139,938 births showed that antibiotics—if prescribed in the first trimester— can lead to birth defects in the child (12). The following antibiotics were cited: clindamycin, doxycycline, quinolones, macrolides, and phenoxymethylpenicillin.

Side effects that nobody thinks about

Doctors, however, consider antibiotics to be medications with few side effects. This is why they are so readily prescribed, so often, and so carelessly. After all, a little diarrhea isn’t a big deal. It will pass. Most doctors fail to recognize that diarrhea is just the tip of the iceberg and a symptom of an often long-term and serious intestinal flora disorder.

But how often do patients say: I had a bladder infection, was given an antibiotic, and from that point onward, I suffered from allergies, food intolerances, irritable bowel syndrome, chronic back pain, or an autoimmune disease? Doctors don’t see any connection. It’s all just a coincidence, they like to say. So remain skeptical if you’re prescribed an antibiotic!

What should you pay attention to when taking an antibiotic?

If your doctor prescribes antibiotics, ask the following questions:

1. Is an antibiotic even appropriate for my symptoms? Or could it be that my illness is a viral infection? Could it be that antibiotics would only shorten my symptoms by a day or two, meaning that the illness would take only slightly longer to heal on its own without antibiotics, but I have to live with the risk of side effects?
2. Are there alternatives? Naturopathic remedies or simple home remedies? Read at the end of this page: CBD as an alternative to antibiotics and CBD oil for pain.
3. Was the right antibiotic chosen for my symptoms? Was an antibiogram performed?
4. Were my pre-existing medical conditions taken into account? These include organ damage, chronic conditions, or mental health issues.
5. Has it been taken into account that I need to take other medications? Could there be interactions between my medications and the antibiotic? How long should I wait between the medications?
6. How often per day should I take the antibiotic? With food or on an empty stomach? How often should I take it after meals?
7. Do I have to take the prescribed number of tablets, even if the symptoms subside sooner? (We now know that in many cases, antibiotics can be discontinued earlier, so this does not lead to increased resistance, as once assumed.)

How can you prevent the side effects of antibiotics?

If an antibiotic cannot be avoided, make sure you do everything you can to prevent side effects:

Eat the best possible diet (alkaline, rich in vital substances, wholesome, plant-based) so that your body is not weakened by an unhealthy diet, but is optimally supplied with all vital substances.

Choose the right supplements for you, such as vitamins, minerals, and antioxidants, to support the body’s healing process.

And most importantly

Take a high-quality probiotic, such as P3 Probiotic and Super-Pro alongside your antibiotics and for four to twelve weeks afterward.

Probiotics protect the intestinal flora and help it regenerate quickly, preventing many side effects (such as diarrhea) from occurring. Read our article here: How to take probiotics correctly.