Clostridioides difficile (C. diff) in children with IBD: Understanding the Firestarter

C. diff in children with IBD is something many families never expect to come across, yet it’s surprisingly common. C. difficile can live quietly in the gut for years in its dormant spore form. You wouldn’t feel it, you wouldn’t know it’s there. Problems only begin when the gut environment shifts and those spores “switch on”, multiply, and start releasing toxins that irritate the gut lining.

This is especially relevant for children with Crohn’s or ulcerative colitis. C. diff infections are more common in IBD, often more active, and can lead to hospitalisations more easily. In more severe cases, they may increase the longer-term risk of colon surgery. Early recognition really does help.

Dormant vs Active C. diff in Children with IBD

C. diff exists in two forms:

Dormant spores: inactive, harmless, unnoticed.

Active bacteria: awake, multiplying, and releasing toxins A and B.

A healthy, diverse microbiome helps keep C. diff dormant. Protective bacteria create natural competition, support mucus production, and maintain an environment that signals “no vacancy”. When these signals weaken, C. diff is more likely to activate.

What Wakes C. diff Up in Children with IBD

C. diff becomes active more easily when the gut environment is disrupted. Common triggers include:

• antibiotics

• a thinner or disrupted mucus layer

• low levels of Akkermansia, Faecalibacterium, and Bifidobacteria

• high inflammation

• reduced microbial diversity

• temporary dips in gut immune function

Once active, C. diff produces toxins that inflame the gut lining and can cause pain, diarrhoea, mucus, or blood.

Why C. diff Matters in IBD Flares

In IBD, the gut barrier is already more fragile. Protective microbes are often lower. This means C. diff in children with IBD can activate more easily and cause a stronger inflammatory reaction.

Active infection can:

• thin the mucus layer

• increase gut permeability

• heighten immune sensitivity

• intensify an existing flare

Because symptoms overlap so closely, C. diff can look identical to an IBD flare and can even trigger one. If symptoms change quickly, stool testing is crucial.

Supporting Recovery After C. diff in Children with IBD

Once treated, most children improve quickly, but the microbiome takes time to rebuild. This recovery phase is essential for preventing recurrence.

Helpful strategies include:

• gentle fibres like oats, lentils, cooked then cooled potatoes or rice, ripe bananas

• polyphenol-rich foods such as berries, apples, herbs, colourful vegetables

• nutrients that support mucus repair

• reducing processed foods to create space for beneficial microbes

• practitioner-guided Saccharomyces boulardii, which may help reduce recurrence

  
  

Practical note: C. diff spores are not killed by alcohol hand gel. Washing with soap and water is the only reliable way to prevent reinfection.

When symptoms are high

If your child is in a flare or highly symptomatic, softer, easier-to-digest foods are usually best. Think mashed potatoes, soups, smoothies, ripe bananas, and well-cooked meals. Fibre can be added back as symptoms settle.

In Short: Keeping C. diff Dormant in IBD

C. diff in children with IBD is often harmless when kept dormant by a strong, diverse microbiome. But when the gut is fragile, C. diff is more likely to activate and mimic or trigger a flare. Treatment is essential, and rebuilding the microbiome afterwards is what helps keep it dormant long term.

For more on the gut microbiome check out the microbiome hub