Afroditi Kouraki, Christopher Deacon, Jessica Nightingale, Panayiotis Louca, Tony Kelly, Amy Zheng, Alexia Karantana, Noor Kifah Al-Tameemi, Amrita Vijay, Aitor Blanco-Míguez, Davide Bazzani, Mattia Bolzan, Angela Bonadiman, Guendalina Tonidandel, Teresa Vanzo, Suzanne Miller, Benjamin Ollivere, Cristina Menni, Ana M Valdes
Following antibiotics, seven VSGs were increased in rib and five in the frail hip fractures compared to controls (mean Log₂ Fold change: 16.89 and 17.21, respectively). In the frail cohort, 18 ARGs increased, including 14 off-target ARGs (resistance genes for antibiotics not administered; mean Log₂ Fold change >25 compared to controls). Five VSGs correlated with six off-target ARGs in antibiotic-treated patients (Rho = 0.612). Longitudinal analysis of rib fracture patients (n = 10) revealed off-target ARGs increased from discharge to follow-up, paralleling increased VSGs abundances, while on-target ARGs remained mostly stable. In antibiotic-treated compared to controls, phage-related and DNA-repair gene families were enriched, phage gene richness was associated with stress and biofilm formation pathways, and VSGs correlated with opportunistic species (e.g., E. coli). More frail antibiotic-exposed patients (81.5%) carried ARG-containing viral contigs than non-frail patients (41.4%).
INTRODUCTION: Antibiotic prophylaxis alters the gut microbiome, potentially expanding antimicrobial resistance genes (ARGs). The role of bacteriophages in this process remains poorly understood. This study investigates the effects of predominantly flucloxacillin- and gentamicin-based perioperative antibiotic prophylaxis on phage and ARG dynamics in orthopedic trauma patients.
METHODS: Shotgun metagenomic analysis in two orthopedic cohorts: rib fracture fixation (n = 16) and frail hip fracture fixation (n = 22), versus frail (n = 18) and non-frail (n = 95) controls was performed. Phage abundance (viral sequence groups [VSGs] relative abundance) was quantified using MetaPhlAn 4.1, while ARG abundance using ResFinder 7 (v2022) with KMA (v2.3.0). ViroProfiler with CheckV for quality assessment was used to detect ARG-carrying viral contigs in antibiotic-treated patients.
RESULTS: Following antibiotics, seven VSGs were increased in rib and five in the frail hip fractures compared to controls (mean Log₂ Fold change: 16.89 and 17.21, respectively). In the frail cohort, 18 ARGs increased, including 14 off-target ARGs (resistance genes for antibiotics not administered; mean Log₂ Fold change >25 compared to controls). Five VSGs correlated with six off-target ARGs in antibiotic-treated patients (Rho = 0.612). Longitudinal analysis of rib fracture patients (n = 10) revealed off-target ARGs increased from discharge to follow-up, paralleling increased VSGs abundances, while on-target ARGs remained mostly stable. In antibiotic-treated compared to controls, phage-related and DNA-repair gene families were enriched, phage gene richness was associated with stress and biofilm formation pathways, and VSGs correlated with opportunistic species (e.g., E. coli). More frail antibiotic-exposed patients (81.5%) carried ARG-containing viral contigs than non-frail patients (41.4%).
DISCUSSION: Our findings suggest perioperative antibiotics may contribute to phage-associated dissemination of off-target ARGs. Understanding how ARGs spread in the gut microbiome is important for improving antibiotic stewardship and protecting vulnerable patients from difficult to treat infections.