Overview of the microbiome and resistome of swine manure in commercial piglet farms and its application in grazing soils

The environmental spread of antimicrobial resistance genes (ARGs) through the use of animal manure in agriculture has become a significant concern. This study investigated the impact of applying swine manure treated through biodigestion on the spread of ARGs in agricultural soils in the Midwest region of Brazil. Samples of untreated and treated manure, fertilized soil, and unfertilized soil were collected from three piglet production units. Bacterial communities and ARGs were characterized through metagenomic sequencing and bioinformatics. Bacterial profiles in fertilized and unfertilized soils were highly similar across all farms. In contrast, biodigestion reduced the total number of ARGs in treated manure. Of the 399 ARGs detected in fertilized soils, 67% were also found in unfertilized soils, and 12% were shared exclusively with treated manure. The presence of numerous ARGs in unfertilized soils highlights the role of environmental dissemination routes, such as runoff, dust, or wildlife, in shaping soil resistomes even in areas without manure application. These findings suggest a stable bacterial and resistome profile in soils, regardless of manure application. Although antimicrobial residues were not evaluated, the results reinforce the need for responsible antibiotic use and effective manure management to minimize environmental ARG dissemination.

农业生产中施用动物粪便导致抗菌药物抗性基因（antimicrobial resistance genes, ARGs）的环境传播，已成为备受关注的重大问题。本研究聚焦于经生物消化处理的猪粪施用对巴西中西部农业土壤中ARGs传播的影响。研究人员从3个仔猪生产场采集了未经处理与经处理的猪粪、施肥土壤及未施肥土壤样本。通过宏基因组测序与生物信息学技术，对细菌群落及ARGs进行了表征分析。结果显示，所有受试猪场的施肥土壤与未施肥土壤的细菌群落谱均高度相似。与之相对，生物消化处理可降低经处理猪粪中ARGs的总数量。在施肥土壤中检出的399种ARGs中，67%同时存在于未施肥土壤中，另有12%仅与经处理猪粪共享。未施肥土壤中存在大量ARGs这一发现，凸显了径流、扬尘或野生动物等环境传播途径在未施用粪肥区域的土壤抗性组（resistome）塑造过程中发挥的重要作用。上述研究结果表明，无论是否施用猪粪，土壤中的细菌群落与抗性组均呈现稳定的特征。尽管本研究未对抗菌药物残留进行评估，但结果仍强调了需负责任地使用抗生素，并采取有效的粪肥管理策略，以最大限度减少环境中ARGs的传播。