Injectable antibiotics reprogram the gut microbiota-immune-resistome axis in ducks before detectable changes in growth performance.

The widespread use of injectable antibiotics in intensive poultry production disrupts gut microbial balance and host immune function, potentially affecting nutrient utilization and promoting antimicrobial resistance. To assess the effects of injectable antibiotics on the gut microbiota, host immunity, tissue accumulation, and antimicrobial resistance in ducks, we systematically evaluated six commonly used injectable antibiotics-gentamicin sulfate, oxytetracycline, florfenicol, tylosin tartrate, lincomycin hydrochloride, and enrofloxacin. Although no statistically significant differences were observed in the feed conversion ratio and organ indices over the 28-day trial, antibiotic exposure disrupted microbiota-organ associations, suggesting subclinical effects despite the absence of detectable phenotypic differences. Enzyme-linked immunosorbent assay results showed a clear class-dependent accumulation of antibiotics in muscle tissues, with tylosin tartrate and enrofloxacin persisting through day 28. Single-molecule real-time full-length 16S rRNA sequencing revealed a significant decline in Escherichia coli abundance and an enrichment of several Gram-positive taxa, indicating a marked restructuring of the gut microbiota following antibiotic exposure. Antibiotic residues in tissues were associated with drug-specific enrichment patterns of antibiotic resistance genes (ARGs) and altered host innate immune-related transcriptional profiles, including changes in inflammatory cytokine expression (IL-6, IL-10, and TNF-α). Furthermore, an integrative microbiota-immunity-residue-ARG network was constructed, revealing a conserved association framework centered on TLR2, NF-κB1, TLR4, and IL-6 as network hubs. Collectively, these findings indicate that injectable antibiotics are associated with coordinated alterations in host-microbiota-resistance interactions before measurable growth changes occur. These results provide an integrative framework for evaluating antibiotic-associated risks in poultry production.