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抗生素使用和堆肥对接受粪肥改良土壤的抗生素抗性基因丰度和抗性组风险的影响

发布者:抗性基因网 时间:2021-09-17 浏览量:528

摘要

       粪便衍生的改良剂通常应用于土壤,引发了关于牲畜使用抗生素是否会影响土壤抗性组(集体抗生素抗性基因 (ARG))并最终在食品生产过程中导致抗生素抗性向人类传播的问题。在这里,我们检查了相对于未经改良的土壤,用施用吡利霉素和头孢匹林(抗生素)或不施用抗生素(对照)的奶牛产生的生粪或堆肥改性的土壤的宏基因组。用粪肥或堆肥进行初始修正(第 1 天)显着增加了土壤中 ARG 的多样性(丰富度)(p<0.01),并导致各个 ARG 类型的丰度不同。值得注意的是,抗生素肥料的初始修正显着增加了土壤中总 ARG 相对丰度(每 16S rRNA 基因)(2.21×未修正土壤,p<0.001)。培养 120 天后,为了模拟作物收获前的等待期,282 个 ARGs 减少了 4.33 倍(中位数)至 307 倍,而 210 个 ARGs 增加了 2.89 倍(中位数)至 76 倍在抗生素粪便修正土壤,导致总 ARG 相对丰度降低,相当于未改良土壤的总 ARG 相对丰度。我们进一步组装了宏基因组数据并计算了抵抗组风险评分,该评分最近被定义为比较对应于同一支架上的 ARG、移动遗传元件和推定病原体的序列的共同出现的相对指数。粪便的初始修正显着增加了土壤抵抗组风险评分,特别是当奶牛施用抗生素时产生的,而堆肥降低了影响并导致土壤抵抗组与背景更相似。粪便改良土壤的风险评分在 120 天后降低到与未改良土壤相当的水平。总体而言,这项研究提供了对先前使用抗生素、堆肥和 120 天等待期对粪便衍生改良剂后土壤抗性组的影响的综合、高分辨率检查,证明所有三种管理做法都具有可衡量的效果,应该在制定减少抗生素耐药性传播的政策和实践时考虑在内。

       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