摘要

        粪便衍生的改良剂通常应用于土壤，引发了有关在牲畜中使用抗生素是否会影响土壤抵抗力（集体抗生素抗性基因（ARGs））并最终导致食品生产过程中抗生素抗性向人类传播的疑问。在这里，我们检查了土壤的基因组学，这些土壤的基因组与未经改良的土壤相比，土壤中的基因组由原奶或经堆肥处理的粪肥产生，这些粪肥是由施用吡霉素和头孢氨苄（抗生素）或不使用抗生素（对照）的奶牛产生的。用肥料或堆肥进行的最初改良（第1天）显着增加了土壤中ARGs的多样性（丰富度）（p <0.01），并导致了各个ARG类型的明显不同。值得注意的是，对抗生素肥料的初步改良显着提高了土壤（每个16S rRNA基因）的总ARG相对丰度（2.21××未改良土壤，p ＜＜ 0.001）。孵育120天后，为了模拟作物收获前的等待时间，在修正的抗生素肥料中，282个ARGs降低了4.33倍（中位数），最高可达307倍，而210个ARGs增加了2.89倍（中位数），最高可达76倍。土壤，导致总的ARG相对丰度降低，与未改良的土壤相当。我们进一步汇总了宏基因组学数据并计算了抵抗力组风险评分，最近将其定义为比较在同一支架上对应于ARGs，移动遗传元件和推定病原体的序列共现的相对指数。最初的粪肥改良显着增加了土壤抵抗力风险评分，尤其是当母牛施用抗生素后产生的风险评分，而堆肥降低了其影响，导致土壤抵抗力风险与背景更加相似。 120天后，粪便改良土壤的风险评分降低到与未经改良土壤相当的水平。总的来说，这项研究对先前的抗生素使用，堆肥以及粪便改良后对土壤抗药性的120天等待期的影响进行了综合，高分辨率的检验，表明所有三种管理措施均具有可衡量的作用，应予以控制。在制定缓解抗生素耐药性扩散的政策和实践时考虑到这一点。

        Manure-derived amendments are commonly applied to soil, raising questions about whether antibiotic use in livestock could influence the soil resistome (collective antibiotic resistance genes (ARGs)) and ultimately contribute to the spread of antibiotic resistance to humans during food production. Here, we examined the metagenomes of soils amended with raw or composted manure generated from dairy cows administered pirlimycin and cephapirin (antibiotic) or no antibiotics (control) relative to unamended soils. Initial amendment (Day 1) with manure or compost significantly increased the diversity (richness) of ARGs in soils (p < 0.01) and resulted in distinct abundances of individual ARG types. Notably, initial amendment with antibiotic-manure significantly increased the total ARG relative abundances (per 16S rRNA gene) in the soils (2.21 × unamended soils, p < 0.001). After incubating 120 days, to simulate a wait period before crop harvest, 282 ARGs reduced 4.33-fold (median) up to 307-fold while 210 ARGs increased 2.89-fold (median) up to 76-fold in the antibiotic-manure-amended soils, resulting in reduced total ARG relative abundances equivalent to those of the unamended soils. We further assembled the metagenomic data and calculated resistome risk scores, which was recently defined as a relative index comparing co-occurrence of sequences corresponding to ARGs, mobile genetic elements, and putative pathogens on the same scaffold. Initial amendment of manure significantly increased the soil resistome risk scores, especially when generated by cows administered antibiotics, while composting reduced the effects and resulted in soil resistomes more similar to the background. The risk scores of manure-amended soils reduced to levels comparable to the unamended soils after 120 days. Overall, this study provides an integrated, high-resolution examination of the effects of prior antibiotic use, composting, and a 120-day wait period on soil resistomes following manure-derived amendment, demonstrating that all three management practices have measurable effects and should be taken into consideration in the development of policy and practice for mitigating the spread of antibiotic resistance.

        https://www.sciencedirect.com/science/article/pii/S0160412019301874?via%3Dihub