Host development shapes resistance, mobility, and virulence networks in the gut microbiome of wild Erinaceus amurensis

Abstract Antimicrobial resistance (AMR) is increasingly recognized as an ecological problem extending beyond clinical and agricultural systems. Wildlife inhabiting human-influenced environments may integrate resistance signals from multiple environmental sources, yet how resistance-related functions are structured across host development remains poorly understood. Here, we used deep metagenomic sequencing to characterize antibiotic resistance genes (ARGs), metal and fungicide resistance genes, mobile genetic elements (MGEs), and virulence factors in the gut microbiota of wild Erinaceus amurensis collected from Northeast China, including male, female, and fetal individuals. We found pronounced developmental stratification of resistance-associated functions. Adult hedgehogs harbored expanded and interconnected networks of ARGs and MGEs, whereas fetal samples exhibited a markedly simplified resistance repertoire and distinct virulence-associated profiles. ARG enrichment in adults was dominated by multidrug, MLS, and β-lactam resistance and strongly co-occurred with transposases, integrases, and insertion sequences, indicating a central role for horizontal gene transfer. In parallel, metal and fungicide resistance genes were enriched in adults, supporting co-selection under long-term environmental chemical exposure. In contrast, fetal microbiomes showed limited resistance diversity but relative enrichment of secretion and adhesion-related virulence factors. Together, these results indicate that resistance, mobility, and virulence functions in wildlife gut microbiomes are not vertically fixed but are progressively shaped by host development and environmental exposure. Our findings highlight wild mammals as ecological integrators of environmental resistomes and underscore the importance of incorporating wildlife into antimicrobial resistance surveillance within a One Health framework.