摘要
出身背景
集约化畜牧业中使用的抗生素和抗生素耐药性基因威胁着全世界的人类健康；然而，不同动物粪便和混合肥料中的常见抗性、ARG迁移率和ARG宿主组成尚不清楚。在本研究中，宏基因组组装和交叉样本定位被用于全面解读动物粪便和堆肥中的常见抗性组及其潜在的移动性和宿主。
后果
总共有201个ARGs在不同的动物（蛋鸡、肉鸡、猪、肉牛和奶牛）粪便中共享，占ARGs总相对丰度的86–99%。除了多药、磺酰胺和甲氧苄啶抗性基因外，堆肥中大多数ARGs的相对丰度显著低于动物粪便中的相对丰度。Procrustes分析表明，抗生素残留量与粪肥中ARG成分呈正相关，但与堆肥中的ARG成分无关。在我们的样本中，超过75%的ARG亚型在质粒和染色体之间共享。转座酶在动物粪便和堆肥中不同门之间的ARGs转移中可能发挥关键作用。对携带ARG的重叠群的交叉样本定位表明，粪便中常见抗性组的宿主对动物物种有偏好，并且ARG宿主的优势属从粪便中的肠球菌转移到堆肥中的假单胞菌。广泛的宿主范围和与不同的可移动遗传元件（MGE）的连接是ARGs的两个关键因素，如sul1和aadA，它们可以在堆肥过程中存活。多药耐药基因代表了粪肥中致病性抗生素耐药细菌的主要ARGs，但可以通过堆肥有效控制。
结论
我们的实验揭示了动物粪便中常见的耐药性，对ARG宿主进行了分类和相对量化，并评估了ARG的移动性。堆肥可以通过改变细菌宿主来减轻动物粪便中的ARGs；然而，由于宿主范围和MGE的多样性，持久性ARG可以逃避去除。我们的研究结果为牲畜ARGs的来源追踪、风险评估和控制提供了总体背景。
Abstract
Background
Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts.

Results
In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86–99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting.

Conclusions
Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs.

https://link.springer.com/article/10.1186/s40793-022-00437-x