Qiu Tianlei, Huo Linhe, Guo Yajie, Gao Min, Wang Guoliang, Hu Dong, Li Cheng, Wang Zhanwu, Liu Guiming, Wang Xuming
Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
Institute of Agro-Resources and Environment, Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, Hebei, People's Republic of China.
Environ Microbiome. 2022 Aug 11;17(1):42. doi: 10.1186/s40793-022-00437-x.
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.
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.
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.
集约化养殖中使用的抗生素和抗生素抗性基因（ARGs）对全球人类健康构成威胁；然而，不同动物粪便和混合粪便堆肥中的常见抗性组、ARG 流动性和 ARG 宿主组成仍不清楚。在本研究中，利用宏基因组组装和跨样本映射全面解析动物粪便和堆肥中的常见抗性组及其潜在流动性和宿主。
总共 201 种 ARGs 在不同动物（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%。除多药、磺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。Procrustes 分析表明，抗生素残留与粪便中的 ARG 组成呈正相关，但与堆肥中的无关。我们的样本中超过 75% 的 ARG 亚型在质粒和染色体之间共享。转座酶在介导动物粪便和堆肥中不同门类之间 ARGs 的转移中可能起关键作用。对携带 ARGs 的重叠群进行跨样本映射表明，粪便中常见抗性组的宿主对动物物种有偏好，ARG 宿主的优势属从粪便中的肠球菌转变为堆肥中的假单胞菌。广泛的宿主范围以及与多种移动遗传元件（MGEs）的关联是 ARGs（如 sul1 和 aadA）在堆肥过程中得以存活的两个关键因素。多药抗性基因是粪便中致病性抗生素抗性细菌中的主要 ARGs，但可通过堆肥有效控制。
我们的实验揭示了动物粪便中的常见抗性组，对 ARG 宿主进行了分类和相对定量，并评估了 ARGs 的流动性。堆肥可通过改变细菌宿主来减轻动物粪便中的 ARGs；然而，由于宿主范围广泛和 MGEs，持久性 ARGs 可能逃避去除。我们的研究结果为家畜 ARGs 的来源追踪、风险评估和控制提供了总体背景。
