摘要

       许多环境宿主导致人类病原体获得性抗生素耐药性问题。一种特别重要的环境宿主是家禽的肠道细菌。抗生素通常用于预防疾病和提高养鸡场的产量。因此，鸡肠道微生物群落作为抗生素抗性基因（ARGs）的储存库受到越来越多的关注。因此，本研究的目的是使用 Illumina 高通量测序研究 ARGs 和移动遗传元件 (MGEs) 的发生、多样性和丰度，以及质粒在蛋鸡和肉鸡粪便中的分布。宏基因组分析表明，变形菌、厚壁菌门、拟杆菌门和放线菌在鸡粪便中占主导地位。在属水平上，大肠杆菌可能在鸡粪中占主导地位，质粒相对丰富。测序读数揭示了蛋鸡粪便和肉鸡粪便微生物群落中质粒分布的差异。在两个社区中都鉴定了编码抗生素抗性的基因。针对抗生素抗性基因数据库 (ARDB) 的 BLAST 分析进一步显示，蛋鸡和肉鸡粪便含有各种高丰度的 ARG，其中万古霉素 (van) 含量最高，占所有 ARG 读数的 36% 以上。 β-内酰胺抗性基因（bl）在肉鸡粪便中高度富集，其中bl2e_cbla含量最高，但在蛋鸡粪便中不存在。在每个粪便样本中检测到超过 20 种类型的插入序列。这些结果突出了鸡粪便中 ARG、质粒和 MGE 的流行，这值得进一步研究以更好地阐明对公共健康的风险。

       Numerous environmental reservoirs contribute to the problem of acquired antibiotic resistance of human pathogens. One environmental reservoir of particular importance is the intestinal bacteria of poultry. Antibiotics are often used to prevent sickness and improve production in chicken farms. Hence, the intestinal microbial community of chickens as a reservoir for antibiotic resistance genes (ARGs) has received increasing attention. Therefore, the aim of this study was to investigate the occurrence, diversity, and abundance of ARGs and mobile genetic elements (MGEs), and the distribution of plasmids in layer and broiler feces using Illumina high-throughput sequencing. Metagenomic analysis showed that Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were predominate in chicken feces. At the genus level, Escherichia coli may be predominant in chicken feces with a relative abundance of plasmids. Sequencing reads revealed differences in the distribution of plasmids in microbial communities between layer and broiler feces. Genes coding for antibiotic resistance were identified in both communities. BLAST analysis against the Antibiotic Resistance Genes Database (ARDB) further revealed that layer and broiler feces contained various ARGs with high abundances, among which vancomycin (van) was the most abundant, accounting for > 36% of all reads of ARGs. Beta-lactam resistance genes (bl) were highly enriched in the broiler feces, among which bl2e_cbla was the most abundant, but was absent in layer feces. Over 20 types of insertion sequences were detected in each fecal sample. These results highlight the prevalence of ARGs, plasmids, and MGEs in chicken feces, which warrants further studies to better elucidate the risk to public health.

https://www.sciencedirect.com/science/article/abs/pii/S2352215117300089