Pre-HCT Microbiome State Predicts ESBL Gene Accumulation in Pediatric Transplant Recipients

Background Infections are the leading cause of non-relapse mortality among pediatric hematopoietic cell transplant (HCT) recipients, and up to 90% of bacteremia events in these patients can be traced to gut-colonizing organisms. Despite receiving intense antibiotics early after transplant, how antibiotic resistance genes (ARGs) evolve in the gut microbiome is poorly understood. Methods We conducted a prospective multi-center study of the gut microbiomes of pediatric HCT patients to investigate how antibiotic exposures impact selection for extended spectrum beta-lactamase (ESBL) genes. Stool from 142 participants across 5 centers were collected from children, median age 8.4, who mainly underwent HCT for Acute Myeloid Leukemia (38%) or other malignancies (49.4%). All participants received an allogeneic transplant, most commonly from a matched related (45.8%) donor. They received multiple antibiotic doses (median 42 daily doses) for fever and neutropenia and infection treatment. Participants at St. Jude also received daily antibiotic prophylaxis (trimethoprim-sulfamethoxazole, fluoroquinolones). DNA extracted from stool underwent Illumina metagenome sequencing (depth 25 million reads/sample). ARGs were identified using MEGARes and changes over time were compared based on antibiotic exposure using linear mixed models. Results The proportion of participants colonized with ESBLs increased in the European cohort and decreased in the St. Jude cohort withing the study period. This trends with the average daily doses of beta-lactam antibiotics administered in the 30 days post HCT (15.3 versus 6.8 daily doses). However, exposures to beta-lactams, cephalosporins, antibiotics with B. fragilis coverage (a proxy for anaerobic activity), or total daily doses of antibiotics did not correlate with ESBL gene selection between HCT and neutrophil engraftment (table1). Instead, we compared composition of ARGs in the gut microbiome and found that the resistomes of participants were highly distinct from the resistomes of healthy children (Fig1). The distance between a participant’s sample at HCT and the centroid of the healthy cohort was the strongest predictor of ESBL accumulation for both cohorts (table1). Conclusion The resistome at HCT, rather than antibiotic exposures during early transplant, determines ESBL gene dynamics in pediatric HCT patients, underscoring the importance of antibiotic stewardship before HCT for these vulnerable patients.