Plant Developmental Stage Separates Lettuce Molecular Sensitivity from Donor-Cell and RP4-Associated Marker Abundances After Antibiotic-Resistant Escherichia coli Exposure

Plant developmental state may alter crop-associated antibiotic-resistant bacterium-plasmid systems and host responses, but these processes are rarely resolved together. Independent lettuce cohorts at seedling, rapid-growth and harvest stages were root-drenched with dual-labelled, RP4-bearing antibiotic-resistant Escherichia coli. At 15 days after inoculation, donor-cell mCherry and RP4-associated gfp abundance, culture recovery, transcriptomes and metabolomes were examined in roots and leaves. The markers concentrated in seedling roots and harvest leaves and correlated strongly (Pearson r = 0.961, p = 2.5 × 10−10), whereas their association disappeared after stage × tissue adjustment (r = −0.209, p = 0.493), indicating that pooled marker concordance was largely structured by developmental context. Seedling roots mounted the strongest response, characterized by cross-omics phenylalanine-metabolism enrichment and signatures of transport, membrane and cell-wall remodeling, and specialized carbon metabolism. Harvest leaves retained donor- and RP4-associated markers and frequently yielded donor-marker-positive colonies under triple-antibiotic selection despite moderate reprogramming with a narrower hormone-rebalancing signature. After adjustment for developmental context and measured donor-cell mCherry abundance, residual variation in the RP4-associated gfp marker was associated with 30 genes but no metabolites after FDR correction; 22 genes converged on seedling-root gfp-associated/mCherry-subthreshold features. Together, the contrasting endpoints provide a stage-resolved framework linking host-response analysis with donor- and RP4-associated marker monitoring, informing One Health research on antimicrobial resistance in leafy vegetables.