{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T02:24:51Z","timestamp":1789698291093,"version":"4.0.1"},"reference-count":64,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T00:00:00Z","timestamp":1743379200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico (CNPq)","award":["001"],"award-info":[{"award-number":["001"]}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","award":["001"],"award-info":[{"award-number":["001"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro (FAPERJ)","award":["001"],"award-info":[{"award-number":["001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Poultry litter is the main waste of poultry farming and is widely used as an agricultural fertilizer. However, owing to the use of antimicrobials in animal production, it can accumulate antimicrobial residues, antimicrobial-resistant bacteria (ARB), and antimicrobial resistance genes (ARGs). This study aimed to evaluate the impact of poultry litter use on the microbiome and resistome of agricultural soils. Methods: Soil samples from fertilized and unfertilized plots were collected from two horticultural farms that intensively use poultry litter. Microbiome composition was assessed using 16S rRNA sequencing. A culture-dependent method was used to isolate resistant strains on CHROMagar plates supplemented with sulfamethoxazole or ciprofloxacin. ARGs and integrase-encoding genes were identified by PCR. Results: Microbiome analysis revealed significant differences in structure and composition between poultry litter-fertilized and unfertilized soils. Fertilized soils exhibited greater alpha diversity and richness. Bacillota, commonly found in the avian gastrointestinal tract, were more abundant in fertilized soils. A total of 62 resistant strains were isolated, and 23 clinically relevant strains harbored ARGs, including fluoroquinolone (qnrA and qnrB) and \u03b2-lactam (blaGES, blaTEM, and blaSHV) resistance genes. Class 1 and 2 integron-associated genes (intI1 and intI2) were also detected. Notably, the rare blaGES gene was detected in Bacillus sp. from unfertilized soil. Similarly, qnrA co-occurred with blaSHV in a Bosea sp. strain from unfertilized soil. Conclusions: These findings highlight the potential for ARB dissemination in agricultural environments, where ARB and ARGs, once introduced into soils, may spread by weathering and other environmental factors, complicating negative control selection in in situ studies.<\/jats:p>","DOI":"10.3390\/antibiotics14040355","type":"journal-article","created":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T08:48:00Z","timestamp":1743410880000},"page":"355","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Microbiome and Resistome in Poultry Litter-Fertilized and Unfertilized Agricultural Soils"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6111-8633","authenticated-orcid":false,"given":"Eliene dos Santos","family":"Lopes","sequence":"first","affiliation":[{"name":"Laboratory of Microbial Genetics, Institute of Microbiology Paulo de G\u00f3es, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Larissa Coutinho Araujo","family":"de Souza","sequence":"additional","affiliation":[{"name":"Laboratory of Microbial Genetics, Institute of Microbiology Paulo de G\u00f3es, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7435-8721","authenticated-orcid":false,"given":"Karen Caroline Ferreira","family":"Santaren","sequence":"additional","affiliation":[{"name":"Laboratory of Microbial Genetics, Institute of Microbiology Paulo de G\u00f3es, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8904-3968","authenticated-orcid":false,"given":"Cl\u00e1udio Ernesto Taveira","family":"Parente","sequence":"additional","affiliation":[{"name":"Olaf Malm Environmental Studies Laboratory, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4992-6395","authenticated-orcid":false,"given":"Lucy","family":"Seldin","sequence":"additional","affiliation":[{"name":"Laboratory of Microbial Genetics, Institute of Microbiology Paulo de G\u00f3es, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Adekiya, A.O., Ejue, W.S., Olayanju, A., Dunsin, O., Aboyeji, C.M., Aremu, C., Adegbite, K., and Akinpelu, O. 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