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Diarrhoea After Taking Antibiotics

Also known as: Antibiotic-associated diarrhoea · Clostridioides difficile infection · C. difficile infection

How patients describe the symptoms: Diarrhoea after antibiotics · Watery diarrhoea while taking medicine · Abdominal pain and fever

Antibiotics can change the balance of the bowel microbiota and cause anything from mild antibiotic-associated diarrhoea to C. difficile infection.

A schematic drawing of the condition described on this page.

What is diarrhoea after antibiotics?

Antibiotics are used to eliminate harmful bacteria. But during treatment the balance of the helpful microorganisms that naturally live in the bowel may also change.

As a result, some people develop watery stools and a change in bowel habit while taking an antibiotic or after the course. This is called antibiotic-associated diarrhoea.

Most cases are mild and settle once the antibiotic course is finished.

But in some patients the cause of the diarrhoea is a bacterium called Clostridioides difficile (C. difficile or C. diff). Unlike simple antibiotic-associated diarrhoea, this can produce marked inflammation in the large bowel, that is colitis. C. difficile infection can sometimes be serious and even life-threatening.

Why do antibiotics cause diarrhoea?

A great many different microorganisms live together in our bowels. This community is called the bowel microbiota.

A normal microbiota helps the digestive system to work healthily and helps prevent certain disease-causing microorganisms from multiplying.

When an antibiotic is taken, this natural balance may be upset.

Put simply:

Antibiotic use

A change in the bowel microbiota

Loss of the normal protective balance

A change in bowel function

Diarrhoea

In most patients matters stop at this level and no serious disease develops.

But in some people a different mechanism arises.

How does C. difficile infection develop?

C. difficile is a bacterium that can form spores resistant in the environment.

Some people carry the bacterium in their bowel without it causing any disease. This is called colonisation.

When antibiotics disturb the normal bowel microbiota, conditions may become suitable for C. difficile to multiply.

The toxins the bacterium produces can damage the bowel lining and lead to inflammation and diarrhoea.

The mechanism

Antibiotic use

A fall in the normal bowel bacteria and disturbance of the microbiota

Multiplication of C. difficile

Toxin production

Inflammation in the large bowel (colitis)

Watery diarrhoea + abdominal pain + fever

In severe cases the process may go further and lead to serious complications such as severe colitis → toxic megacolon → sepsis or perforation of the bowel.

Which antibiotics carry more risk?

In fact almost any antibiotic can increase the risk of C. difficile infection.

But the risk is higher with some. These include in particular:

  • Clindamycin,
  • Fluoroquinolones,
  • Third and fourth generation cephalosporins,
  • Carbapenems.

The risk does not depend on the type of antibiotic alone. Taking antibiotics for longer than necessary, or taking more than one, may affect the bowel microbiota more.

For this reason avoiding unnecessary antibiotic use is one of the most important ways of protecting against C. difficile infection.

In whom is the risk of C. difficile higher?

The risk is higher particularly in:

  • People over 65,
  • Those who have recently been in hospital or in a care home,
  • Those who have had C. difficile infection before,
  • Those with a serious chronic illness,
  • People whose immune system is suppressed,
  • Those taking antibiotics for a long time or taking more than one.

But it should not be forgotten that C. difficile can also develop in young people with no other illness.

What are the symptoms?

In mild antibiotic-associated diarrhoea there is usually:

  • Soft or watery stool,
  • An increase in the number of times the bowels are opened,
  • Mild abdominal cramps,
  • Wind and bloating.

In C. difficile infection the diarrhoea may be more marked.

It may be accompanied by:

  • Frequent, watery diarrhoea,
  • Abdominal pain or tenderness,
  • Fever,
  • Loss of appetite,
  • Nausea,
  • Weakness.

Can it appear after the antibiotic has finished?

Yes.

C. difficile infection mostly arises during antibiotic use or in the period following it.

So even if the antibiotic finished a few weeks earlier, when marked new diarrhoea is being assessed recent antibiotic use must be mentioned to the doctor.

Should everyone who takes antibiotics and gets diarrhoea be tested for C. difficile?

No.

This is an important point.

C. difficile can be present in some people’s bowels without causing disease. A positive test in a person with no symptoms may therefore not indicate active infection.

The CDC recommends testing in suitable patients in whom C. difficile is clinically suspected and who have, for example, three or more new watery stools within 24 hours. Other causes that could explain the diarrhoea, such as laxatives, should also be considered.

How is the diagnosis made?

The diagnosis rests on assessing the patient’s symptoms together with stool tests.

The tests used include:

Toxin tests, the GDH antigen test and NAAT/PCR tests that look for the genes by which the bacterium forms toxin.

In some centres these are used together or in stepwise algorithms.

PCR is a highly sensitive method. But it has one disadvantage:

A positive PCR does not always mean active C. difficile disease.

It may also be positive in people carrying the bacterium without disease. It is therefore important that the test result is interpreted together with the characteristics of the patient’s diarrhoea.

Is a colonoscopy needed?

In most patients a colonoscopy is not needed to diagnose C. difficile.

The diagnosis is generally made from the clinical findings and stool tests.

But endoscopic assessment may be needed in particular situations where the diagnosis is uncertain or another bowel disease is suspected.

In severe C. difficile colitis, the characteristic yellow-white plaques called pseudomembranes may be seen on the bowel wall.

How is it treated?

Whether the antibiotic that may have caused the diarrhoea is still needed is assessed first.

The patient should not stop the antibiotic on their own initiative. The decision to stop or change the drug should be made by the doctor managing the treatment.

Mild antibiotic-associated diarrhoea that is not due to C. difficile usually settles with supportive treatment and replacement of the fluid lost.

If C. difficile infection is found, specific antibiotic treatment directed at the bacterium is needed.

The main drugs in use today include fidaxomicin and oral vancomycin. Treatment is chosen according to the severity of the illness, whether C. difficile has occurred before, and the patient’s own circumstances. The CDC’s current clinical information likewise names these two among the main options.

Can anti-diarrhoeal medicines be used?

In diarrhoea that develops after antibiotics, and where C. difficile is a possibility in particular, it is not right to take anti-diarrhoeal medicine without medical assessment.

The cause and severity of the diarrhoea should be established first.

Are probiotics needed?

This is a rather more complicated matter.

There is no general rule that “everyone taking antibiotics must take a probiotic”.

The effect of probiotics varies with the species and even the strain of microorganism used. Although the AGA states that certain specific probiotic preparations may be considered for preventing C. difficile infection in people taking antibiotics, it stresses in particular that not all probiotics have the same effect.

Probiotics also do not take the place of standard treatment for active C. difficile infection.

So rather than a general recommendation to “take a probiotic”, it is more accurate to say that the benefit of probiotics may vary with the product and the patient.

Does C. difficile recur?

Yes.

In some patients the diarrhoea may return after successful treatment.

In recurrent infection, different antibiotic regimens and, in suitable patients, other treatments may be considered.

In recurrent C. difficile infection in particular, faecal microbiota-based treatments are now among the important options. The AGA supports the use of faecal microbiota-based treatments in suitable adults with recurrent C. difficile infection after standard antibiotic treatment has been completed.

Is a repeat stool test needed after treatment?

In patients whose symptoms have settled completely, a routine test to ask “has the C. difficile been cleared?” is not recommended.

This is because the test may remain positive for a while even after the person has recovered.

So unlike H. pylori, no routine “eradication test” is done for C. difficile.

This distinction is particularly useful in explaining things to patients.

Is it contagious?

C. difficile can be transmitted.

The bacterium forms spores that spread into the environment in the stool and can survive for a long time. They can be carried to other people by the lavatory, by surfaces and by contaminated objects.

It is important in particular that a person with C. difficile infection washes their hands thoroughly with soap and water after using the lavatory.

Cleaning the lavatory and frequently touched surfaces properly at home also helps reduce the risk of transmission.

When should a doctor be consulted?

If marked and continuing watery diarrhoea develops while taking antibiotics or shortly after a course, a doctor should be consulted.

Assessment should not be delayed particularly where there is:

  • Opening the bowels many times a day with watery stool,
  • Fever,
  • Severe or increasing abdominal pain,
  • Marked swelling of the abdomen,
  • Bloody stools,
  • Serious weakness,
  • Signs of fluid loss such as a dry mouth or reduced urine.

Marked abdominal swelling, high fever, low blood pressure, a change in consciousness or a serious deterioration in general condition require emergency assessment.

What is the outlook?

The great majority of diarrhoea associated with antibiotic use is mild and temporary.

C. difficile infection is different. With early diagnosis and suitable treatment the great majority of patients recover; but in some the infection may recur.

Rarely, serious complications such as severe colitis, toxic megacolon, perforation of the bowel and sepsis may develop.

Sources

  1. Prof. Ali Tüzün İnce, MD — 2026 revision

Prof. Ali Tüzün İnce, MD — https://www.alituzunince.com/en/conditions/diarrhoea-after-antibiotics/