摘要
      鸡肠道微生物群作为抗生素耐药性基因（ARGs）的宿主，对全世界的人类和动物构成了高风险。然而，对鸡肠道抗生素耐药性的全面探索仍不完整。在这项研究中，我们通过对629个鸡肠道样本的宏基因组分析，建立了迄今为止最大的鸡肠道抗性基因目录。我们发现中国鸡肠道中ARGs的丰度明显高于欧洲。在中国鸡的肠道中检测到了tetX、mcr和blaNDM这三种对人类和动物健康的抗生素具有耐药性的基因。ARGs的丰度与移动遗传元件的丰度呈线性相关。宿主追踪分析确定大肠杆菌、肠球菌、葡萄球菌、克雷伯菌和乳酸杆菌是ARG的主要宿主。尤其是乳酸杆菌，一种肠道益生菌，携带多种耐药基因，与ISLhe63成比例，突出了其在农业生产过程中的潜在风险。我们首先建立了鸡肠道抗生素耐药性的参考基因目录。我们的研究有助于提高对鸡肉抗生素耐药性的认识和理解，以实现基于知识的可持续鸡肉生产。
重要性鸡肠道环境中抗生素耐药性基因的流行对人类健康构成严重威胁；然而，我们缺乏对鸡肠道环境中抗生素耐药性和微生物组的全面探索。本研究的结果证明了鸡肠道环境中抗生素抗性基因和菌群的多样性和丰度，并鉴定了携带抗生素抗性基因的各种潜在宿主。进一步的分析表明，流动遗传元素与抗生素抗性基因丰度呈线性相关，这意味着我们应该注意流动遗传元素在抗生素抗性基因传播中所起的作用。我们建立了鸡肠道抗生素耐药性基因的参考基因组，这将有助于合理化家禽养殖中的药物使用。
ABSTRACT
The chicken gut microbiota, as a reservoir of antibiotic resistance genes (ARGs), poses a high risk to humans and animals worldwide. Yet a comprehensive exploration of the chicken gut antibiotic resistomes remains incomplete. In this study, we established the largest chicken gut resistance gene catalogue to date through metagenomic analysis of 629 chicken gut samples. We found significantly higher abundance of ARGs in the Chinese chicken gut than that in the Europe. tetX, mcr, and blaNDM, the genes resistant to antibiotics of last resort for human and animal health, were detected in the Chinese chicken gut. The abundance of ARGs was linearly correlated with that of mobile genetic elements (MGEs). The host-tracking analysis identified Escherichia, Enterococcus, Staphylococcus, Klebsiella, and Lactobacillus as the major ARG hosts. Especially, Lactobacillus, an intestinal probiotic, carried multiple drug resistance genes, and was proportional to ISLhe63, highlighting its potential risk in agricultural production processes. We first established a reference gene catalogue of chicken gut antibiotic resistomes. Our study helps to improve the knowledge and understanding of chicken antibiotic resistomes for knowledge-based sustainable chicken meat production.
IMPORTANCE The prevalence of antibiotic resistance genes in the chicken gut environment poses a serious threat to human health; however, we lack a comprehensive exploration of antibiotic resistomes and microbiomes in the chicken gut environment. The results of this study demonstrate the diversity and abundance of antibiotic resistance genes and flora in the chicken gut environment and identify a variety of potential hosts carrying antibiotic resistance genes. Further analysis showed that mobile genetic elements were linearly correlated with antibiotic resistance genes abundance, implying that we should pay attention to the role played by mobile genetic elements in antibiotic resistance genes transmission. We established a reference genome of gut antibiotic resistance genes in chickens, which will help to rationalize the use of drugs in poultry farming.

https://journals.asm.org/doi/full/10.1128/spectrum.01907-21