When you’re managing inflammatory bowel disease (IBD) with immunosuppressive medications like biologics or immunomodulators, getting sick can feel overwhelming. Should you continue your medication during a respiratory infection? When is it safe to restart your biologic after a bout of food poisoning? These questions keep many people with IBD awake at night, and for good reason—the decisions you make about medication management during illness can significantly impact both your infection recovery and IBD control.

This comprehensive guide is specifically designed for people with IBD who are taking immunosuppressive therapies and need clear, actionable guidance on managing their medications during various types of infections. Whether you’re on adalimumab, infliximab, azathioprine, or combination therapy, you’ll learn how to make informed decisions about medication timing, coordinate care between specialists, and safely navigate the complex balance between infection management and IBD maintenance.

By the end of this guide, you’ll have practical decision-making frameworks, specific protocols for different infection types, and the confidence to work effectively with your healthcare team during illness episodes.

Understanding the Immunosuppression Challenge in IBD

The medications that help control IBD inflammation—biologics like anti-TNF agents, integrin inhibitors, and IL-12/23 inhibitors, along with immunomodulators like methotrexate and azathioprine—work by suppressing your immune system. This creates a delicate balancing act: while these medications effectively reduce intestinal inflammation, they also make you more susceptible to infections and can potentially slow your recovery from illness.

Research shows that people with IBD on immunosuppressive therapy have a 1.5 to 3-fold increased risk of serious infections compared to those not on these medications. However, the absolute risk remains relatively low, and the benefits of maintaining IBD remission typically outweigh the infection risks. The key challenge lies in knowing when and how to temporarily modify your medication regimen during active infections.

Many people with IBD face common misconceptions about medication management during illness. Some believe they should automatically stop all IBD medications at the first sign of any infection, while others worry that missing even a single dose will trigger a severe flare. The reality is more nuanced—different infections require different approaches, and the decision to hold or continue medications depends on multiple factors including infection severity, medication type, and your individual IBD history.

Decision Framework: When to Hold IBD Medications During Infections

The decision to temporarily discontinue immunosuppressive IBD medications during infections isn’t one-size-fits-all. Here’s a structured approach to help you and your healthcare team make these critical decisions:

Severe Infections: Automatic Hold Considerations

Certain infections typically warrant holding immunosuppressive medications immediately:

• Hospitalization-requiring infections: Pneumonia requiring inpatient treatment, severe cellulitis, sepsis, or any infection requiring IV antibiotics
• Opportunistic infections: Tuberculosis, histoplasmosis, or other fungal infections that take advantage of immunosuppression
• Live vaccine-associated infections: Though rare, any infection potentially related to live vaccines
• Hepatitis B reactivation: Requires immediate cessation and antiviral therapy

Moderate Infections: Case-by-Case Assessment

These infections require careful evaluation with your gastroenterologist:

• Bacterial gastroenteritis with systemic symptoms: Fever, dehydration, or bloody stools may warrant holding medications
• Respiratory infections with fever: Bronchitis or upper respiratory infections with high fever (>101°F/38.3°C) lasting more than 48 hours
• Urinary tract infections: Complicated UTIs or those with systemic symptoms
• Skin and soft tissue infections: Cellulitis or abscesses requiring antibiotic treatment

Minor Infections: Usually Continue Medications

These typically don’t require medication changes:

• Common cold or mild upper respiratory symptoms without fever
• Viral gastroenteritis that’s mild and resolving within 24-48 hours
• Minor skin infections responding well to topical treatments
• Uncomplicated cystitis in women

Medication-Specific Holding Protocols

Different IBD medications require different approaches when infections occur. Understanding these nuances is crucial for safe medication management.

Anti-TNF Biologics (Adalimumab, Infliximab, Golimumab, Certolizumab)

Anti-TNF medications have the longest track record and most established protocols for infection management:

• Holding duration: Typically hold until infection completely resolves plus 1-2 weeks
• Special considerations: Higher risk for tuberculosis reactivation and invasive fungal infections
• Restart criteria: Complete symptom resolution, normal inflammatory markers (if elevated), and completion of antibiotic course

Integrin Inhibitors (Vedolizumab, Natalizumab)

These gut-selective medications generally have lower systemic infection risk:

• Holding approach: May continue during minor to moderate infections
• Exception: Hold for severe infections requiring hospitalization
• PML consideration: Natalizumab requires monitoring for progressive multifocal leukoencephalopathy

IL-12/23 and IL-23 Inhibitors (Ustekinumab, Risankizumab, Mirikizumab)

Newer biologics with potentially lower infection risk profiles:

• Infection risk: Generally lower than anti-TNF agents
• Holding approach: Similar to anti-TNF for severe infections, more flexible for moderate infections
• Monitoring: Watch for unusual infections due to IL-23’s role in immune defense

Immunomodulators (Azathioprine, 6-Mercaptopurine, Methotrexate)

These medications require careful consideration due to their broad immunosuppressive effects:

• Azathioprine/6-MP: Hold for moderate to severe infections; monitor white blood cell counts
• Methotrexate: Often held for any infection requiring antibiotics; restart when infection resolves
• Combination therapy: May need to hold both biologic and immunomodulator for severe infections

Coordinating Care: Building Your Infection Management Team

Effective infection management while on IBD medications requires seamless coordination between multiple healthcare providers. Here’s how to build and maintain these crucial relationships:

Your Primary Care Team

Your primary care physician or urgent care provider is often your first point of contact during infections. Ensure they understand:

• Your complete IBD medication regimen, including dosing and timing
• Your IBD history and current disease activity
• When to consult with your gastroenterologist before prescribing treatments
• Signs that warrant immediate specialist consultation

Gastroenterologist Communication Protocol

Establish clear communication channels with your IBD specialist:

• Contact preferences: Know whether to call, message through patient portal, or go to emergency protocols
• After-hours coverage: Understand who covers IBD-related questions when your doctor isn’t available
• Decision authority: Clarify who makes final decisions about holding medications during infections
• Documentation: Keep records of previous infection episodes and medication decisions

Specialist Coordination

When infections require specialist care, ensure all providers are informed:

• Infectious disease specialists: May be needed for complex or recurrent infections
• Emergency department: Provide wallet card with current medications and emergency contacts
• Pharmacists: Can help identify drug interactions and provide medication counseling

Post-Infection Restart Protocols: Safely Resuming Treatment

Knowing when and how to restart your IBD medications after an infection is just as important as knowing when to stop them. Premature restart can lead to infection recurrence, while delayed restart risks IBD flare.

General Restart Criteria

Before restarting any immunosuppressive IBD medication after infection, ensure:

• Complete symptom resolution: No fever, pain, or other infection symptoms for at least 48-72 hours
• Antibiotic completion: Finish entire prescribed antibiotic course
• Normal inflammatory markers: If initially elevated, C-reactive protein and white blood cell count should normalize
• Adequate hydration and nutrition: Especially important after gastrointestinal infections

Medication-Specific Restart Timelines

Biologics: Typically restart 1-2 weeks after infection resolution. For severe infections, may wait 2-4 weeks with close monitoring for IBD symptoms.

Immunomodulators: Can often restart sooner (within 1 week) for minor infections, but may require longer delays for severe infections with neutropenia risk.

Combination therapy: May restart medications sequentially rather than simultaneously, beginning with the medication most critical for IBD control.

Monitoring During Restart Phase

The first few weeks after restarting immunosuppressive therapy require vigilant monitoring:

• Infection recurrence signs: Return of fever, worsening symptoms, or new infections
• IBD symptom monitoring: Watch for signs of disease flare during the medication gap
• Laboratory monitoring: May need repeat blood work to ensure stable white blood cell counts
• Gradual activity increase: Don’t immediately return to full activities; allow immune system recovery time

Resources and Tools for Infection Management

Essential Mobile Apps and Tools

• MyIBD by AbbVie: Track symptoms and medication timing during illness episodes
• IBD Passport: Digital wallet card with medication information for emergency situations
• Medisafe: Medication reminder app that can be adjusted during infection periods
• Temperature tracking apps: Monitor fever patterns to share with healthcare providers

Professional Organizations and Resources

• Crohn’s & Colitis Foundation: Medication guides and infection prevention resources
• American Gastroenterological Association: Clinical practice guidelines for IBD medication management
• International Organization for IBD (IOIBD): Global consensus statements on medication safety
• IBD Nurse Network: Specialized nursing support for medication questions

Questions to Ask Your Healthcare Team

Prepare these specific questions for your next appointment:

• “What specific signs should prompt me to hold my IBD medications during an infection?”
• “Who should I contact first when I develop an infection—you or my primary care doctor?”
• “How long should I wait to restart my medications after different types of infections?”
• “What emergency situations require immediate medication cessation?”
• “How do we balance infection risk with IBD flare risk for my specific case?”
• “Should I receive any additional vaccines or preventive treatments given my medications?”

Common Mistakes to Avoid

Stopping Medications Too Quickly

Many people with IBD panic at the first sign of illness and immediately stop all medications. This can lead to unnecessary IBD flares, especially for minor infections that don’t require medication changes. Always consult your healthcare team before making medication decisions, even if symptoms seem concerning.

Restarting Medications Too Soon

The pressure to resume normal medication schedules can lead to premature restart, risking infection recurrence or prolongation. Follow established restart criteria and don’t rush the process, even if you’re worried about IBD symptoms returning.

Poor Communication Between Providers

Failing to keep all healthcare providers informed about medication changes during infections can lead to dangerous drug interactions, inappropriate treatments, or conflicting medical advice. Always ensure your gastroenterologist knows about infections and your primary care doctor knows about IBD medication changes.

Ignoring Preventive Measures

Focusing only on infection management while neglecting prevention is a missed opportunity. People on immunosuppressive therapy should prioritize hand hygiene, appropriate vaccinations, and avoiding known infection sources. Prevention is always preferable to treatment.

Not Documenting Infection Episodes

Failing to keep detailed records of infections, medication holds, and outcomes makes it difficult to establish patterns and make informed decisions about future episodes. Maintain a simple log of infection dates, types, treatments, and medication management decisions.

Moving Forward: Your Action Plan for Confident Infection Management

Managing IBD medications during infections doesn’t have to be a source of constant anxiety. With proper preparation, clear communication protocols, and evidence-based decision-making frameworks, you can navigate these challenges confidently while maintaining both your health and IBD control.

Your immediate next steps should include creating a personalized infection management plan with your healthcare team, establishing clear communication protocols, and gathering the resources and tools that will support you during future illness episodes. Remember that every infection episode is a learning opportunity that can help refine your approach and improve outcomes.

Most importantly, remember that you’re not alone in this journey. The IBD community understands these challenges, and your healthcare team is there to support you through every decision. By staying informed, prepared, and connected, you can manage infections effectively while keeping your IBD under control.

Medical Disclaimer: This guide provides educational information and should not replace personalized medical advice from your healthcare providers. Always consult your gastroenterologist and other healthcare team members before making decisions about medication management during infections. Individual circumstances vary, and treatment decisions should always be made in consultation with qualified medical professionals who understand your specific health history and current condition.