The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms. Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms. Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production.

中文翻译：

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抗菌剂的使用和生产系统影响着养猪场的粪便，环境和泥浆抵抗力组

抗菌素耐药性（AMR）的全球威胁是一个人类健康问题，受到人类和牲畜应用抗菌素（AMU）的影响。伊比利亚广泛的养猪生产基于更加可持续和生态友好的管理体系，这提供了极好的机会来评估AMU的持续差异如何不仅影响动物而且影响农场环境，如何影响抵抗力组。在这里，我们通过分析38个农场的105个粪便，环境和泥浆元基因组，评估了与工业化集约化养猪相比，维持了数十年的广泛养猪系统的抵抗力足迹。我们的结果表明，在集约化养殖场中，抗菌素耐药基因（ARG）的丰度明显更高，而且AMU和AMR之间的联系与某些抗菌素种类有关。我们观察到了不同样品类型的电阻组差异，环境样品中ARG的富集度和分散度比粪便或泥浆中的更高。确实，更深入的分析表明，三种样本类型之间的差异是由分类群-ARG关联定义的。有趣的是，动植物分析表明，在集约化农场和粗养农场之间观察到的AMR差异可能与流动遗传元件（MGEs）的丰度差异有关。因此，尽管在集约化畜群和广泛集群之间，与染色体相关的ARG的丰度没有差异，但在集约化养殖场中，无论样品类型如何，在环境和质粒中的整合素的丰度都明显更高。总体而言，这项研究表明了AMU，生产系统和样品类型如何影响