Disseminação de genes de resistência a antimicrobianos em ambientes agrícolas com uso intensivo de cama de aviário como fertilizante orgânico

Abstract

Antimicrobial resistance (AMR) is one of the leading threats to global public health and is exacerbated by the intensive and indiscriminate use of antimicrobials in animal production. Agroecosystems, particularly poultry farming systems and agricultural areas that utilize organic residues as fertilizers, are recognized as reservoirs and sources of antimicrobial resistance genes. This thesis investigated, in an integrated manner and under the One Health perspective, the persistence, mobilization, and dissemination of resistance genes from poultry litter to different environmental compartments: agricultural soil, the rhizosphere of Sechium edule (chayote), water, and the sediment of irrigation ponds. Sampling of these environmental compartments was carried out in multiple agricultural areas of São José do Vale do Rio Preto (Rio de Janeiro, Brazil) during the dry and rainy seasons. Multiple analyses were performed using the collected samples, including the isolation of bacterial strains under antimicrobial selective pressure, molecular characterization of resistance determinants, 16S rRNA gene sequencing, and shotgun metagenomics. Microbiome analyses, based on 16S rRNA sequencing, revealed that the environmental compartment was the primary determinant of bacterial richness and diversity, surpassing the influence of seasonal and geographic factors. A similar pattern was observed in the functional diversity of microbial communities, as assessed through metagenomics. Poultry litter showed the highest abundance and diversity of resistance genes and plasmids, with mobilization to soils and ponds more evident during periods of higher rainfall, suggesting the influence of surface runoff. Clinically relevant resistance genes, including blaTEM and blaGES (β-lactams), sul1 and sul2 (sulfonamides), intI1 (class 1 integron integrases), mtrA (macrolides and penicillins), rbpA (rifampicin), and tet(X4) (resistance to broad-spectrum tetracyclines), were widely detected across different environmental compartments, farming areas, and seasonal periods. The blaGES gene, rarely reported in natural environments, was detected in genera such as Stenotrophomonas and Brevundimonas, isolated from soil. In addition, higher abundances of genes such as sul2, mtrA, and rbpA were detected in environmental compartments outside of poultry litter, suggesting broader dissemination. Plasmidome analysis revealed plasmids carrying multiple resistance genes, frequently associated with clinically relevant bacterial genera such as Staphylococcus, Enterococcus, Escherichia, and Pseudomonas. Among the results, the presence of the tet(L) gene was observed in a mobilizable plasmid similar to pBC16 of Bacillus cereus, detected in poultry litter, soil, and the rhizosphere, and the tet(X4) gene in a non-mobilizable plasmid similar to pER24y-8ksm of Escherichia coli, identified in the rhizosphere. The findings of this thesis demonstrate the dissemination and persistence of resistance genes in poultry and agricultural production systems, with a potential risk of these elements entering the food chain through the soil–plant system and the use of contaminated water for irrigation and poultry hydration. Furthermore, this study contributes to understanding the mechanisms of environmental dissemination of AMR and reinforces the need for integrated monitoring strategies, safe waste management practices, and risk mitigation measures in animal production systems.