NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain.
Environ Microbiol. 2021 Dec;23(12):7643-7660. doi: 10.1111/1462-2920.15842. Epub 2021 Nov 18.
In cow farms, the interaction between animal and environmental microbiomes creates hotspots for antibiotic resistance dissemination. 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-amended pasture soil); 6 of them to non-productive heifers and dry cows (faeces, fresh manure, aged manure, aged manure-amended orchard soil, vegetables-lettuces 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 β-lactams, and 9% to macrolide-lincosamide-streptogramin B. All but two of the MGE-associated 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-occurrence 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.
在奶牛养殖场中，动物和环境微生物组之间的相互作用会产生抗生素耐药性传播的热点。本研究采用高通量宏基因组学方法调查了五个奶牛养殖场的耐药组风险。为此，共采集了 10 个环境样本：3 个与产奶牛有关（新鲜粪浆、储存粪浆、粪浆改良的草地土壤）；6 个与非产奶牛和干奶牛有关（粪便、新鲜粪肥、陈粪肥、陈粪肥改良果园土壤、蔬菜生菜和放牧土壤）；最后，还有未改良的对照土壤。使用 MetaCompare 计算了耐药组风险，该方法根据抗生素耐药基因（ARGs）、移动遗传元件（MGEs）和人类病原体之间可能存在的联系对耐药组风险进行评分。耐药组风险从粪浆和粪肥微生物组降低到土壤和蔬菜微生物组。共检测到 18157 个 ARGs：24%与安莎霉素类有关，21%与多药类有关，14%与氨基糖苷类有关，12%与四环素类有关，9%与β-内酰胺类有关，9%与大环内酯类-林可酰胺类-链阳性菌素 B 类有关。除了两个与 MGE 相关的 ARGs 外，所有这些 ARGs都只在动物粪便中发现（不在土壤或蔬菜样本中发现）。确定了一些具有耐药组风险标记物潜力的 ARGs（基于它们在共同出现网络的枢纽中的存在和高传播潜力）。作为预防原则，需要改进牲畜粪便管理，以最大限度地降低抗生素耐药性的风险。
