摘要
      从健康角度来看，来自食用动物及其相关环境的抗微生物耐药性（AMR）和病原体已成为对人类的挑战性威胁，但我们对这些风险及其在当前集约养殖行业的关键预防和控制点的了解仍然很差。通过宏基因组学在四阶段蛋鸡生产链上的粪便、苍蝇、灰尘、污水和土壤中创建耐药性和微生物组的完整组成和风险图谱，我们发现整个生产链是抗微生物耐药性基因（ARGs）的热点，共有374种已知亚型和病原体，包括157种人类致病菌（HPB）。粪便和苍蝇被确定为这些污染的主要风险来源。此外，我们证实了AMR和致病性的双重风险在整个链中普遍存在，但在每个阶段的频率不同；因此，幼鸡期的高风险ARG和鸡期的高度优先HPB分别占AMR总风险的37.33%和致病风险的36.36%，因此这两个阶段是预防的重点。此外，112个装仓的ARG超级载体（例如，携带20个ARG的肺炎克雷伯菌）的流行率沿着生产链被揭示，特别是在粪便、苍蝇和灰尘中，87个潜在宿主表现出高致病风险、高风险AMR或两者兼有，具有262个ARG和816个毒力因子基因。总的来说，这项研究提供了关于密集型蛋鸡生产链中高风险ARG及其致病宿主的第一手综合数据，因此对于制定新措施帮助控制通过动物-环境-人类途径引发的全球AMR危机至关重要。
Abstract
Antimicrobial resistance (AMR) and pathogens derived from food animals and their associated environments have emerged as challenging threats to humans from a health perspective, but our understanding of these risks and their key prevention and control points in the current intensive breeding industry remains poor. By creating an integral composition and risk profile of the resistome and microbiome through metagenomics in feces, flies, dust, sewage, and soil along the four-stage laying hen production chain, we found that the whole production chain is a hotspot for antimicrobial resistance genes (ARGs) with 374 known subtypes and pathogens, including 157 human pathogenic bacteria (HPB). Feces and flies were identified as major risk sources for these contaminations. Also, we confirmed a twin-risk of AMR and pathogenicity prevailing throughout the chain, but with different frequencies in each stage; thus, high-risk ARGs in the young chicken stage and highly prioritized HPB in the chick stage contributed 37.33 % to the total AMR risk and 36.36 % to the pathogenic risks, respectively, thus rendering the two stages to be the key prevention points. Moreover, the prevalence of 112 binned ARG supercarriers (for example, Klebsiella pneumoniae harboring 20 ARGs) was unraveled along the production chain, especially in feces, flies, and dust, and 87 potential hosts exhibited high pathogenic risk, high-risk AMR, or both, with 262 ARGs and 816 virulence factor genes. Overall, this study provides first-hand comprehensive data on high-risk ARGs and their pathogenic hosts in the intensive laying hen production chain, and thus is fundamentally important for developing new measures to help control the global AMR crisis induced through the animal-environment-human pathway.

https://www.sciencedirect.com/science/article/abs/pii/S0048969723004059