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A shotgun metagenomic approach was used to survey the resistome risk in five dairy cow farms. To this purpose, 10 environmental compartments were sampled: 3 of them linked to productive cows (fresh slurry, stored slurry, slurry\u2010amended pasture soil); 6 of them to non\u2010productive heifers and dry cows (faeces, fresh manure, aged manure, aged manure\u2010amended orchard soil, vegetables\u2010lettuces and grazed soil); and, finally, unamended control soil. The resistome risk was assessed using MetaCompare, a computational pipeline which scores the resistome risk according to possible links between antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and human pathogens. The resistome risk decreased from slurry and manure microbiomes to soil and vegetable microbiomes. In total (sum of all the compartments), 18,157 ARGs were detected: 24% related to ansamycins, 21% to multidrugs, 14% to aminoglycosides, 12% to tetracyclines, 9% to \u03b2\u2010lactams, and 9% to macrolide\u2013lincosamide\u2013streptogramin B. All but two of the MGE\u2010associated ARGs were only found in the animal dejections (not in soil or vegetable samples). Several ARGs with potential as resistome risk markers (based on their presence in hubs of co\u2010occurrence networks and high dissemination potential) were identified. As a precautionary principle, improved management of livestock dejections is necessary to minimize the risk of antibiotic resistance.<\/jats:p>","DOI":"10.1111\/1462-2920.15842","type":"journal-article","created":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T06:29:04Z","timestamp":1637216944000},"page":"7643-7660","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Reduction of the resistome risk from cow slurry and manure microbiomes to soil and vegetable microbiomes"],"prefix":"10.1111","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5388-2375","authenticated-orcid":false,"given":"Leire","family":"Jauregi","sequence":"first","affiliation":[{"name":"NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA) Parque Cient\u00edfico y Tecnol\u00f3gico de Bizkaia  P812, E\u201048160 Derio Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4624-4946","authenticated-orcid":false,"given":"Lur","family":"Epelde","sequence":"additional","affiliation":[{"name":"NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA) Parque Cient\u00edfico y Tecnol\u00f3gico de Bizkaia  P812, E\u201048160 Derio Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aitor","family":"Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA) Parque Cient\u00edfico y Tecnol\u00f3gico de Bizkaia  P812, E\u201048160 Derio Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Luis","family":"Lav\u00edn","sequence":"additional","affiliation":[{"name":"NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA) Parque Cient\u00edfico y Tecnol\u00f3gico de Bizkaia  P812, E\u201048160 Derio Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos","family":"Garbisu","sequence":"additional","affiliation":[{"name":"NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA) Parque Cient\u00edfico y Tecnol\u00f3gico de Bizkaia  P812, E\u201048160 Derio Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,11,18]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2020.00201"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2319"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics6020012"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.3402\/iee.v5.28564"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms4010014"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro753"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.2134\/jeq2008.0128"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1007\/s42832-019-0011-0"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.est.7b01420"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1120800"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2012.07.004"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12941-015-0100-6"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1109326109"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.3389\/fsufs.2018.00044"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00053"},{"key":"e_1_2_7_17_1","unstructured":"EMA(2020) Sales of veterinary antimicrobial agents in 31 European countries in 2018. 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