Metagenomic changes in response to antibiotic treatment in severe orthopedic trauma patients

We investigated changes in microbiome composition and abundance of antimicrobial resistance (AMR) genes post-antibiotic treatment in severe trauma patients. Shotgun sequencing revealed beta diversity (Bray-Curtis) differences between 16 hospitalized multiple rib fractures patients and 10 age- and sex-matched controls (<i>p</i> = 0.043), and between antibiotic-treated and untreated patients (<i>p</i> = 0.015). Antibiotic-treated patients had lower alpha diversity (Shannon) at discharge (<i>p</i> = 0.003) and 12-week post-discharge (<i>p</i> = 0.007). At 12 weeks, they also exhibited a 5.50-fold (95% confidence interval [CI]: 2.86-8.15) increase in <i>Escherichia coli</i> (<i>p</i> = 0.0004) compared to controls. Differential analysis identified nine AMRs that increased in antibiotic-treated compared to untreated patients between hospital discharge and 6 and 12 weeks follow-up (false discovery rate [FDR] < 0.20). Two aminoglycoside genes and a beta-lactamase gene were directly related to antibiotics administered, while five were unrelated. In trauma patients, lower alpha diversity, higher abundance of pathobionts, and increases in AMRs persisted for 12 weeks post-discharge, suggesting prolonged microbiome disruption. Probiotic or symbiotic therapies may offer future treatment avenues.