PDF(Pubmed)
Abstract：
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 on the dispersion of ARGs in pig production system, including the external environment.
RESULTS: In the present study, we longitudinally followed one swine farm 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. We identified 309 SGBs being shared between the animals gut microbiome, the internal and external farm environments. 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 dispersion of ARGs 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.
RESULTS: In the present study, we longitudinally followed one swine farm 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. We identified 309 SGBs being shared between the animals gut microbiome, the internal and external farm environments. 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 dispersion of ARGs 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.
摘要：
背景：抗菌素耐药性已被确定为对全球健康的主要威胁。猪食物链被认为是抗微生物抗性基因(ARGs)的重要来源。然而,对ARGs在生猪生产系统中的分散仍然缺乏了解，包括外部环境。
结果：在本研究中，我们从断奶阶段到屠宰场纵向跟踪了位于意大利的一个猪场，以全面评估ARGs的多样性，他们的扩散，以及与之相关的细菌。我们从294个样本中获得了鸟枪宏基因组序列，包括猪的粪便,农场环境,农场周围的土壤，废水,和屠宰场环境。我们确定了总共530个物种水平的基因组箱（SGB），这使我们能够评估微生物及其相关ARG在农场系统中的分散情况。我们确定了309个SGB在动物肠道微生物组之间共享，内部和外部农场环境。具体来说,这些SGB的特征是多样化和复杂的抗性组，ARGs对18种不同类型的抗生素化合物有活性，与欧洲猪食物链中抗生素的使用非常匹配。
结论：总的来说，我们的研究结果强调了实施更有效的对策以限制ARGs在猪食物系统中的分散的紧迫性,以及基于宏基因组学的方法监测ARGs的传播对农场工作环境和周围生态系统安全的相关性.
结果：在本研究中，我们从断奶阶段到屠宰场纵向跟踪了位于意大利的一个猪场，以全面评估ARGs的多样性，他们的扩散，以及与之相关的细菌。我们从294个样本中获得了鸟枪宏基因组序列，包括猪的粪便,农场环境,农场周围的土壤，废水,和屠宰场环境。我们确定了总共530个物种水平的基因组箱（SGB），这使我们能够评估微生物及其相关ARG在农场系统中的分散情况。我们确定了309个SGB在动物肠道微生物组之间共享，内部和外部农场环境。具体来说,这些SGB的特征是多样化和复杂的抗性组，ARGs对18种不同类型的抗生素化合物有活性，与欧洲猪食物链中抗生素的使用非常匹配。
结论：总的来说，我们的研究结果强调了实施更有效的对策以限制ARGs在猪食物系统中的分散的紧迫性,以及基于宏基因组学的方法监测ARGs的传播对农场工作环境和周围生态系统安全的相关性.
