Environmental microbiome, resistome and plasmidome in agricultural areas with intensive poultry litter use: A metagenomic multicompartmental analysis of antimicrobial resistance gene dissemination

• ARGs disperse from poultry litter to soil, rhizosphere, water, and sediment. • Plasmids carrying clinically critical ARGs disperse into farm environments. • tet(L) and tet(X4) genes detected on plasmids from poultry production sites. • Plasmid pER24y-8ksm in chayote rhizosphere carried tet(X4) resistance gene. • Evidence of environmental transmission routes for AMR within agroecosystems. Antimicrobial resistance (AMR) represents an escalating global public health threat, largely driven by the intensive use of antimicrobials in animal production. This study investigated the dissemination of antimicrobial resistance genes (ARGs) from poultry litter into adjacent environmental compartments—fertilized soil, the rhizosphere of Sechium edule (chayote), irrigation pond water and its surface sediment—across poultry-producing areas. The samples were collected in triplicate and subjected to DNA extraction and shotgun metagenomic analysis. The bioinformatic workflow included quality control procedures, contig assembly, gene prediction, functional profiling, plasmid detection, and ARG screening. KEGG Orthology annotation revealed that ∼1% of the genes were associated with AMR. Poultry litter presented the greatest ARG diversity (117, of which 97 were unique). Genes such as sul2, mtrA , and rbpA were more abundant in the soil, rhizosphere, and water, indicating dispersal from poultry litter. Putative plasmid-like contigs related to the mobilizable Bacillus cereus plasmid pBC16 and carrying tet(L) were detected in poultry litter, soil, and rhizosphere samples, whereas contigs similar to the Escherichia coli plasmid pER24y-8ksm and harboring tet(X4) —which confers resistance to tigecycline, a last-resort tetracycline—was identified in the rhizosphere. Therefore, clinically critical ARGs associated with plasmid-like contigs were detected across multiple agricultural environmental compartments, providing clear evidence of a dissemination route driven by poultry litter. These results indicate that poultry litter functions as a hotspot for ARGs and mobile genetic elements and contributes to their spread across agricultural ecosystems, reinforcing the need for improved waste management strategies under a One Health framework.