Comparative Effectiveness Randomized Clinical Trial Using Next-generation Microbial Sequencing to Direct Prophylactic...

Area of Science:

• Urology
• Infectious Diseases
• Microbiology

Background:

• Next-generation sequencing (NGS) offers enhanced sensitivity for detecting urinary pathogens.
• Standard urine cultures may miss low-level or fastidious organisms.

Purpose of the Study:

• To evaluate if NGS microbial profiling can guide antibiotic prophylaxis and reduce infections compared to the standard of care.
• To assess the impact of NGS on antibiotic selection and patient outcomes in urologic stone interventions.

Main Methods:

• A prospective randomized controlled trial involving patients undergoing urologic stone interventions.
• Urine samples were analyzed using both standard culture and NGS diagnostics.
• Infectious disease pharmacists recommended prophylactic antimicrobial regimens based on NGS findings.

Main Results:

• NGS-guided prophylaxis significantly reduced postsurgical urinary infection risk (7.1% reduction in mITT analysis, p=0.045).
• NGS altered antibiotic distribution (p=0.025), with poor adherence to NGS findings linked to increased infection odds (OR=5.9, p=0.046).
• Women had higher infection odds (OR=10, p=0.03) and distinct microbial profiles (p<0.001).

Conclusions:

• Urinary microbial NGS-guided antibiotic prophylaxis improves antibiotic selection and reduces healthcare-associated urinary infections before urologic stone lithotripsy.
• Treatment efficacy may depend on adherence to the recommended NGS-guided protocol.
• NGS holds potential for individualized antibiotic use in urologic procedures.