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Bactrim stomach pain: Causes and prevention

Antibiotics like Bactrim may kill some of the gut’s good bacteria while ridding your infection, causing stomach pain that’s preventable
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By | Feb. 14, 2024 Medically reviewed by Jesse P. Houghton, MD, FACG
Someone holding their stomach: Bactrim stomach pain

Key takeaways

  • Bactrim disrupts the gut microbiome by killing both harmful and beneficial bacteria, leading to side effects like stomach pain, nausea, and vomiting.

  • To prevent stomach pain, Bactrim should be taken exactly as prescribed, with plenty of water, and possibly with food to mitigate nausea.

  • Treatment for Bactrim-induced stomach pain includes staying hydrated, using over-the-counter nausea medications, and incorporating natural remedies or probiotics to restore gut balance.

  • Before taking Bactrim, it’s important to inform healthcare providers about any allergies or medications, and certain populations should consult a doctor due to higher risk of side effects.

In this article:

Bactrim is an antibiotic also known as sulfamethoxazole-trimethoprim. This prescription medication is available as a tablet or liquid that is taken orally. Bactrim is intended for adults and children ages 2 months and older. Bactrim can treat ear infections, respiratory infections, urinary tract infections, and other bacterial infections. Stomach pain, nausea, and vomiting are common side effects when using Bactrim. Learn why Bactrim causes stomach pain, how to prevent or treat Bactrim-related stomach pain, and when to seek medical advice.

Why does Bactrim cause stomach pain?

Bactrim, like many antibiotic medicines, disrupts the balance of the gut microbiome. We all have unique gut microbiomes that evolve with factors like diet, age, and use of antibiotics. The gut microbiome includes trillions of microorganisms; among these are bacteria. 

To kill “bad” infection-causing bacteria, antibiotic medicines clear out bacteria in the gut. But antibiotics like Bactrim often also eliminate some “good” bacteria that keep the digestive system, immune system, and other bodily functions on track. This can temporarily upset the balance in the gut microbiome, leading to unwanted side effects such as stomach pain, nausea, vomiting, and diarrhea.

How to prevent stomach pain from Bactrim

Bactrim should be used only as directed by a healthcare provider. This antibiotic medication should be used for the full recommended treatment time at the prescribed dose, even though it’s common to see improvements after a few days. Bactrim side effects may increase if the medication is not taken as prescribed. 

Bactrim should always be taken with 8 ounces of water. Make sure to drink plenty of water daily while using Bactrim, unless a physician recommends otherwise. Staying hydrated can help prevent side effects such as urinary crystals. Bactrim can be taken with or without food. But food might help mitigate nausea, according to Sarah Lynch, PharmD, BCACP, a clinical associate professor at the Binghamton University School of Pharmacy and Pharmaceutical Sciences.

“Some people may find that Bactrim causes stomach irritation or nausea,” Lynch says. “Taking the medication with a snack or even a glass of milk can help ease the stomach upset.” Registered nurse Lauren Thayer seconds this. “To try to avoid some of the common gastrointestinal symptoms, it is best to take Bactrim with a meal or a snack,” Thayer says.

Probiotic supplements and foods rich in probiotics can also help soothe stomach pain induced by Bactrim—more on that below.

How to treat stomach pain when taking Bactrim

Gastrointestinal symptoms should resolve after completing a course of Bactrim. In the meantime, there are several options to treat Bactrim-related nausea. For those who prefer over-the-counter (OTC) medications, nausea medication such as Pepto Bismol (bismuth subsalicylate) can help. Thayer also suggests ginger, peppermint, or probiotics to soothe an upset stomach. 

While taking Bactrim, probiotics can help ease nausea and rebalance the gut’s microbiome. “Bactrim and other antibiotics can alter the naturally occurring balance of bacteria in your gut,” Thayer says. “You can initiate the use of a probiotic or increase your intake of common probiotic foods . . . Probiotics can help restore the healthy bacteria in your gut that is altered with the use of antibiotics.”

RELATED: Probiotics 101: What are they? And which are the best?

Probiotics are available as OTC supplements, and your healthcare provider can offer medical advice on the right probiotics for your needs. Fermented foods also provide probiotics in varying concentrations. These are some common probiotic foods and drinks:

  • Yogurt
  • Miso soup
  • Cottage cheese
  • Pickles, pickle juice
  • Sauerkraut, kimchi
  • Kombucha
  • Kefir

To help prevent an upset stomach while using Bactrim, Thayer advises avoiding fried, high-fiber, and spicy foods. 

What to avoid when taking Bactrim

Before starting Bactrim, inform your doctor or pharmacist of any allergies and medications you’re taking or have recently taken. Keep these Bactrim contraindications in mind:

  • Bactrim should not be taken concurrently with dofetilide. 
  • Those with a history of drug-induced thrombocytopenia should not take Bactrim. 
  • Those who have had an allergic reaction to sulfamethoxazole, trimethoprim, or any sulfa drugs should not take Bactrim. 
  • Bactrim should not be used during pregnancy or breastfeeding. There are risks of Bactrim affecting an unborn baby, and the medication passes into breast milk. 
  • For more information about drug interactions, direct any questions to your doctor.

Bactrim is a sulfonamide antibiotic. Fatalities associated with sulfonamides such as Bactrim are rare—these cases have involved serious side effects and medical conditions such as Stevens-Johnson Syndrome, Fulminant Hepatic Necrosis, Toxic Epidermal Necrolysis, Aplastic Anemia, Agranulocytosis, and other Blood Dyscrasias. 

Certain populations also face a higher risk of side effects with Bactrim use and should consult a healthcare provider for advice before using the drug: 

  • People ages 65 and older
  • People with impaired kidney function, liver disease, folic acid deficiency, cystic fibrosis, renal dysfunction, severe dehydration, or malnutrition

You should also inform your doctor if you have AIDS or HIV—Bactrim may work differently for you.

Contact your doctor for medical help immediately if you notice any of the following symptoms while using Bactrim, which may indicate serious reactions to the drug: increased coughing, fever, sore throat, pallor, arthralgia, jaundice, purpura, or severe skin reactions such as skin rashes. 

Bottom line 

Bactrim, an antibiotic used to treat bacterial infections, can cause nausea due to its impact on the gut microbiome. To mitigate discomfort from an upset stomach, take Bactrim only as prescribed. Take Bactrim with food and water, and drink plenty of fluids during your Bactrim medical treatment. OTC medications like Pepto Bismol can help alleviate stomach pain caused by Bactrim. Natural remedies like ginger, peppermint, probiotic supplements, and probiotic foods and beverages may also provide relief. Before using Bactrim, it’s crucial to inform your healthcare provider of allergies, current medications, and medical history. If stomach pain persists after the prescribed course of Bactrim, contact a doctor for medical help.

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