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

Kouraki, Afroditi; Zheng, Amy S.; Miller, Suzanne; Kelly, Anthony; Ashraf, Waheed; Bazzani, Davide; Bonadiman, Angela; Tonidandel, Guendalina; Bolzan, Mattia; Vijay, Amrita; Nightingale, Jessica; Menni, Cristina; Ollivere, Benjamin J.; Valdes, Ana M.

Abstract

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 (p = 0.043), and between antibiotic-treated and untreated patients (p = 0.015). Antibiotic-treated patients had lower alpha diversity (Shannon) at discharge (p = 0.003) and 12-week post-discharge (p = 0.007). At 12 weeks, they also exhibited a 5.50-fold (95% confidence interval [CI]: 2.86–8.15) increase in Escherichia coli (p = 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.

Citation

Kouraki, A., Zheng, A. S., Miller, S., Kelly, A., Ashraf, W., Bazzani, D., Bonadiman, A., Tonidandel, G., Bolzan, M., Vijay, A., Nightingale, J., Menni, C., Ollivere, B. J., & Valdes, A. M. (2024). Metagenomic changes in response to antibiotic treatment in severe orthopedic trauma patients. iScience, 27(9), Article 110783. https://doi.org/10.1016/j.isci.2024.110783

• Journal Article Type: Article
• Acceptance Date: Aug 19, 2024
• Online Publication Date: Aug 22, 2024
• Publication Date: Sep 20, 2024
• Deposit Date: Sep 26, 2024
• Publicly Available Date: Sep 27, 2024
• Journal: iScience
• Electronic ISSN: 2589-0042
• Publisher: Cell Press
• Peer Reviewed: Peer Reviewed
• Volume: 27
• Issue: 9
• Article Number: 110783
• DOI: https://doi.org/10.1016/j.isci.2024.110783
• Keywords: Trauma, Genomics, Microbiome
• Public URL: https://nottingham-repository.worktribe.com/output/39994683
• Publisher URL: https://www.cell.com/iscience/fulltext/S2589-0042(24)02008-X?_return