Título:	From farm to environment: the microbiome and the silent spread of antimicrobial resistance genes in soil despite manure management in swine farms.
Autor:	BREYER, G. M. TORRES, M. C. REBELATTO, R. WUADEN, C. R. PASTORE, J. LAZZAROTTI, M. NICOLOSO, R. da S. DORN, M. KICH, J. D. SIQUEIRA, F. M.
Afiliación:	GABRIELA MERKER BREYER, UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL; MARIANA COSTA TORRES, UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL; RAQUEL REBELATTO, CNPSA; CAMILA ROSANA WUADEN; JANAINA PASTORE; MATEUS LAZZAROTTI, CNPSA; RODRIGO DA SILVEIRA NICOLOSO, CPACT; MÁRCIO DORN, UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL; JALUSA DEON KICH, CNPSA; FRANCIELE MABONI SIQUEIRA, UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL.
Año:	2026
Referencia:	Journal of Environmental Management, v. 400, p.128747, 2026.
Descripción:	Abstract: The swine industry generates large amounts of organic waste containing antimicrobial residues, requiring efficient manure management to reduce environmental risks. Covered lagoon biodigesters (CLBs) and waste stabilization ponds (WSPs) are commonly used digestion systems, with digestates subsequently applied as organic fertilizers. Although these systems successfully reduce pathogenic bacteria, their effectiveness in removing antimicrobial resistance genes (ARGs) remains unclear. In this study, we compared microbiome and resistome profiles from CLB- (n = 23) and WSP-farms (n = 20) using shotgun metagenomic sequencing of raw and digested manure, as well as fertilized and non-fertilized soils. Our findings indicate that digestate application slightly shifted soil microbial communities and significantly increased bacterial diversity, suggesting the introduction of diverse manure-derived bacteria. Reads from taxonomic markers associated with clinically important pathogens, including Enterobacterales, streptococci (groups A and B), Enterococcus faecium, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella enterica were still detected in digestates and fertilized soils, regardless of the digestion system. Moreover, DNA sequences associated with ARGs against critical antimicrobials, such as carbapenems, cephalosporins, and glycopeptides persisted. Notably, WSPs exhibited greater accumulation of some ARGs, including OXA-347 and vanG. Overall, although CLBs exerted a lower impact on soil microbial communities and resistomes compared to WSPs, neither system effectively eliminated ARGs. These findings highlight the potential for environmental dissemination of ARGs through manure fertilization and underscore the urgent transition toward more sustainable production practices, including eliminating non-therapeutic antimicrobial use in the swine industry, as well as the need for improved digestion technologies and continuous monitoring under the One Health framework.
Thesagro:	Pecuária Bactéria
NAL Thesaurus:	Livestock Metagenomics
Palabras clave:	Metagenômica Sequenciamento aleatório Shotgun
DOI:	https://doi.org/10.1016/j.jenvman.2026.128747
Tipo de Material:	Artigo de periódico
Acceso:	openAccess
Aparece en las colecciones:	Artigo em periódico indexado (CNPSA)