Risks, side effects and interaction of antibiotics used in STIs treatment and prevention

Understanding the potential risks and side effects of the usage of antibiotics for post exposure prophylaxis is essential for users seeking effective STI prevention.
April 25, 2024

Given the high efficacy of antibiotics, it's even more important to properly weigh the risks and side effects. While there is a lot of experience in using antibiotics to treat sexually transmitted infections (STIs), the use of antibiotics for post-exposure prophylaxis to prevent STIs is a new tool and should only be used after specific risk events. Let's take a closer look at the drug that can be used as post-exposure prophylaxis against syphilis and chlamydia, its risks and side effects.

“The experience base of antibiotics used in treatment and prevention for syphilis and chlamydia is huge; we have been using the substances in the treatment of humans and animals for over 60 years.”

Overall tolerance and drug interactions

The antibiotic medication that can be used for the prevention of chlamydia and syphilis is known for its general tolerability, with very few negative interactions reported with other prescription drugs. But still interactions can be quite serious in rare cases, therefore we highly recommend to check for interactions with your doctor. Long-term use of such medication has been documented for various medical purposes, such as acne treatment and malaria prophylaxis, but we are still learning about continuous intermittent treatment where we have limited data on development of possible bacterial resistances that could make treatment of STIs or other bacterial infections more difficult. We are also still learning about the effect on the microbiota, which could affect other health conditions. More studies are underway and we will keep you updated as soon as we know more.

Common side effects and minimization strategies

Some individuals may experience side effect when taking an antibiotic for prevention of chlamydia and syphilis, including feelings of nausea, headaches, and gastrointestinal issues. To minimize these risks, it is recommended to take medications with a glass of water, not an empty stomach, and to remain upright for at least 30 minutes after ingestion to prevent reflux. Because of some rare possible side effects concerning the blood and kidney function you should consider some laboratory monitoring at least once a year. Any side effect that leaves you concerned should be evaluated by a doctor.

Interaction with Calcium/Magnesium/Aluminum-rich substances

Avoiding supplements or foods rich in calcium, magnesium, or zinc within 2 hours of taking certain antibiotics for STI post-exposure prophylaxis is crucial, as these substances can weaken the effectiveness of the medication. This includes common items like dairy products, stomach remedies, fitness drinks, and electrolytes. Non-absorbable complexes are formed and neither the drug nor the element reaches the bloodstream.

Increased sensitivity to sunlight

Some antibiotics can increase skin sensitivity to sunlight. Users are advised to wear sunscreen with a sufficient Sun Protection Factor (SPF) when using such antibiotics to minimize the risk of sunburn and other skin-related issues.

“We should never forget that antibiotics are highly effective substances which, even if they are not very noticeable when ingested, should be used with caution. We should always bear in mind their great importance for humanity in many areas.”

Gut microbiome considerations

Antibiotic use, including antibiotics that can be used for post-exposure STI prophylaxis, is associated with potential disruptions to the gut microbiome. While there is currently inconclusive data if and how much which antibiotic influences healthy gut bacteria, users may consider taking proactive steps to preserve gut health. This can include incorporating prebiotics and probiotics into their routine. There are some clinical studies on the way and we expect further gain of knowledge soon.

Antibiotic resistance

The usage of antibiotics for STI prevention raises the questions about antibiotic resistance. We discuss this topic in detail in our article Antibiotic Resistance and STI Prophylaxis.

Potential for yeast infections

The reduction of bacteria in and on the body, a common effect of antibiotic use, can sometimes lead to yeast infections. Individuals using antibiotics for STI post exposure prophylaxis should be aware of this possibility and seek over-the-counter anti-fungal remedies if they experience such infections.

Consultation with healthcare professionals

Individual responses to medications can vary, and it's crucial for users to consult with healthcare professionals if they have concerns or experience any unusual symptoms. Healthcare providers can provide personalized guidance based on an individual's health history and specific circumstances.

Pregnancy and Breastfeeding

If there is a risk of pregnancy, you should not take antibiotics for STI prevention as it can damage the bones and teeth of the unborn child. If you later find out that you were already pregnant while taking such antibiotics, don’t panic. It is unlikely that the usual prescribed antibiotics for STI-Prevention will harm your unborn within the first 3 months of pregnancy. Antibiotics for STI prevention should not be taken while breastfeeding.


Understanding the potential risks and side effects of the usage of antibiotics for post exposure prophylaxis is essential for users seeking effective STI prevention. While the medication is generally well-tolerated, being aware of possible side effects and taking proactive steps to minimize risks ensures a more positive and informed experience. As with any medication, open communication with healthcare professionals enhances the overall safety and effectiveness of its use in maintaining sexual and general health.

Medication can help reduce your risk for bacterial STIs*

* If indicated by a doctor