Fecal microbiota transplantation accelerates clearance of carbapenemase-producing Enterobacterales intestinal carriage: influence of recipient gut microbiome ecology.

BACKGROUND

Persistent intestinal carbapenemase-producing Enterobacterales (CPE) carriage challenges infection prevention and antimicrobial stewardship. We evaluated fecal microbiota transplantation (FMT) for decolonization and response-associated recipient microbiome features.

METHODS

This prospective cohort study assessed intestinal CPE clearance in 131 adult carriers (68 receiving FMT; 63 under observation). Responders achieved clearance, defined as three consecutive negative rectal surveillance cultures for CPE, obtained at 3-day intervals within 1 month after FMT. Following least absolute shrinkage and selection operator (LASSO)-based covariate selection, Cox proportional hazards models estimated associations between FMT and time to successful decolonization within prespecified 0-30-day and 0-90-day windows. A longitudinal metagenomic subcohort of 21 FMT recipients (102 fecal samples) underwent shotgun sequencing to characterize taxonomic composition, microbial network organization, functional pathways, antimicrobial resistance genes (ARGs), and donor engraftment.

RESULTS

After LASSO-based covariate selection, FMT was associated with faster CPE clearance than observation at 1 month (hazard ratio, 4.02; 95% confidence interval, 1.84-8.79), with effects sustained at 3 months. Responders showed relatively preserved baseline microbial network organization and enrichment of taxa annotated with arginine-related pathway features, suggesting metabolic relevance to microbial niche competition. After FMT, responders had greater engraftment of donor-associated taxa and donor-like ecological reassembly, with reduced Klebsiella pneumoniae dominance and ARG abundance.

CONCLUSIONS

FMT may accelerate intestinal decolonization in CPE carriers; response variability was associated with recipient gut-microbiome ecology, suggesting microbiome-guided patient selection could optimize microbiota-based strategies.