Cause and effect? A review of the impact of antibiotics on the gut microbiome in patients undergoing hematopoietic stem cell transplantation.

Introduction: Patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) are at high risk of infection due to immunosuppression, prompting routine use of prophylactic and broad-spectrum antibiotics for treatment. However, emerging evidence suggests that gut microbiome disruption (dysbiosis), partly caused by antibiotic use, is associated with poorer transplant outcomes, including graft-versus-host disease (GVHD), infection, and mortality.

Areas covered: This narrative review discusses antibiotic use to prevent and treat febrile neutropenia in allo-HSCT recipients, including effectiveness, impacts on microbiome and GVHD, antimicrobial resistance and Clostridioides difficile infection (CDI). It also reviews available strategies to reduce unnecessary antibiotic use and proposes potential future interventions. A comprehensive PubMed search was conducted through 2024 using terms related to HSCT, antimicrobials, microbiome, resistance, and CDI.

Expert opinion: Improving outcomes while minimizing emergence of antibiotic resistance and CDI requires personalized, risk-adaptive antimicrobial stewardship (AMS). Tailored AMS approaches, including patient risk stratification and early de-escalation, could limit unnecessary antibiotic use and mitigate adverse effects. In the future, microbiome preservation and restoration may reduce transplant complications by maintaining colonization resistance and immune balance. Integrating these strategies into allo-HSCT care is essential for optimizing both clinical and microbiological outcomes.