Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment. null

Background Antimicrobial resistance has been identified as a major threat to global health. The pig food chain is considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of knowledge focusing on the spread dispersion of ARGs from in pig production units to thesystem, including the external environment. Results In the present study, we longitudinally followed two one swine farmsfarm located in Italy from the weaning phase to the slaughterhouse to comprehensively assess the diversity of ARGs, their diffusion, and the bacteria associated with them. We obtained shotgun metagenomic sequences from 294 samples, including pig feces, farm environment, soil around the farm, wastewater, and slaughterhouse environment. We identified a total of 530 species-level genome bins (SGBs), which allowed us to assess the dispersion of microorganisms and their associated ARGs in the farm system. Specifically, wWe identified 309 SGBs being shared able to spread frombetween the the animals gut microbiome, the internal and external farm environments to the soil surrounding the farms. Specifically, these SGBs were characterized by a diverse and complex resistome, with ARGs active against 18 different classes of antibiotic compounds, well matching antibiotic use in the pig food chain in Europe. Conclusions Collectively, our results highlight the urgency to implement more effective countermeasures to limit the spread dispersion of ARGs from in the pig food systems and the relevance of metagenomics-based approaches to monitor the spread of ARGs for the safety of the farm working environment and the surrounding ecosystems. This work was carried out in the context of the “Controlling Microbiomes Circulations for Better Food Systems” (CIRCLES) project, which was funded by the European Union's Horizon 2020 research and innovation program under grant agreement no. 818290.

背景 抗菌药物耐药性已被认定为全球公共卫生的重大威胁。生猪供应链被认为是抗菌药物耐药基因（antimicrobial resistance genes, ARGs）的重要传播源之一。然而目前仍缺乏针对生猪生产单元至包括外部环境在内的全系统内ARGs传播扩散机制的相关研究认知。
结果 本研究对意大利的2个养猪场开展了从断奶阶段至屠宰环节的纵向追踪，以全面解析ARGs的多样性、传播扩散特征及其关联菌群。研究共获取了294份样本的鸟枪宏基因组测序数据，样本类型涵盖猪粪便、猪场内部环境、猪场周边土壤、废水及屠宰场环境。本研究共鉴定得到530个物种水平基因组箱（species-level genome bins, SGBs），借此得以系统评估猪场系统内微生物及其携带ARGs的扩散情况。具体而言，本研究鉴定出309个可在动物肠道菌群、猪场内外环境与猪场周边土壤之间传播共享的SGBs；这些SGBs携带多样且复杂的耐药组（resistome），其所携带的ARGs可靶向18类不同的抗生素化合物，这与欧洲生猪供应链中的抗生素使用情况高度契合。
结论 综上，本研究结果凸显了制定更有效的防控措施以限制生猪供应链内ARGs扩散的紧迫性，同时证实了基于宏基因组学的方法可用于监测ARGs传播，以保障猪场作业环境及周边生态系统的安全。本研究依托“优化食品系统的微生物组循环调控（Controlling Microbiomes Circulations for Better Food Systems, CIRCLES）”项目开展，该项目由欧盟“地平线2020”研究与创新计划资助，资助协议编号为818290。