摘要
      排泄到环境中的牲畜粪便中存在的抗生素抗性基因（ARGs）的传播严重威胁着人类和动物的健康。在这里，我们使用16S rRNA基因图谱和宏基因组分析来表征大型养猪场粪肥储存池中的微生物群落组成和抗生素耐药性。每隔两年采集一次粪便样本。原核群落和抗性组均以厚壁菌门、变形菌门和拟杆菌门为主。对两个样本的宏基因组分析显示，726个和641个ARG分为59个和46个AMR基因家族。除了多药外排泵外，占主导地位的ARGs还可能编码对四环素类、大环内酯类-林可酰胺类-链脲菌素、氨基糖苷类、肽类抗生素、利福霉素、氯霉素和β-内酰胺类的耐药性。在两个样本中都发现了来自所有主要AMR基因家族的基因，表明耐药组的总体长期稳定性。抗生素外排泵是变形杆菌中ARG的主要类型，而抗生素靶点的改变或保护是厚壁菌门、放线菌门和拟杆菌门耐药的主要机制。对4株耐多药菌株的元基因组组装基因组（MAG）进行了组装。第一个属于福氏埃希氏菌的MAG含有46个ARG，包括多药外排泵、修饰孔蛋白、β-内酰胺酶和对肽类抗生素产生耐药性的基因。第二个MAG属于Alcaligenaceae家族，包含18个ARG，编码对大环内酯-林可酰胺-链脲菌素、四环素类、氨基糖苷类和二氨基嘧啶类的耐药性。另外两个MAG代表Atopostipes属和Prevotella属，分别包含4个和7个ARG。所有这些MAG都代表了较小的群落成员，占整个宏基因组的比例不到0.3%。总的来说，一些起源于肠道但在粪肥储存泻湖中相对罕见的谱系是ARGs的主要来源，其中一些具有多种抗性决定因素。
Abstract
The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition and antibiotic resistance in a manure storage lagoon from a large-scale swine finishing facility. Manure samples were collected at intervals of two years. Both the prokaryotic community and the resistome were dominated by the Firmicutes, Proteobacteria and Bacteroidota. Metagenomic analysis of two samples revealed 726 and 641 ARGs classified into 59 and 46 AMR gene families. Besides multidrug efflux pumps, the predominating ARGs potentially encoded resistance to tetracyclines, macrolide–lincosamide–streptogramin, aminoglycosides, peptide antibiotics, rifamycin, chloramphenicol, and beta-lactams. Genes from all predominant AMR gene families were found in both samples indicating overall long-term stability of the resistome. Antibiotic efflux pumps were the primary type of ARGs in the Proteobacteria, while antibiotic target alteration or protection was the main mechanism of resistance in the Firmicutes, Actinobacteriota and Bacteroidota. Metagenome-assembled genomes (MAG) of four multidrug-resistant strains were assembled. The first MAG, assigned to Escherichia flexneri, contained 46 ARGs, including multidrug efflux pumps, modified porins, beta-lactamases, and genes conferring resistance to peptide antibiotics. The second MAG, assigned to the family Alcaligenaceae, contained 18 ARGs encoding resistance to macrolide–lincosamide–streptogramin, tetracyclines, aminoglycosides and diaminopyrimidins. Two other MAGs representing the genera Atopostipes and Prevotella, contained four and seven ARGs, respectively. All these MAGs represented minor community members and accounted for less than 0.3% of the whole metagenome. Overall, a few lineages originated from the gut but relatively rare in the manure storage lagoon, are the main source of ARGs and some of them carry multiple resistance determinants.

https://www.mdpi.com/2076-2607/10/11/2301