Monitoring the prevalence of antimicrobial resistance genes (ARGs) is vital for addressing the global crisis of antibiotic-resistant bacterial infections. Despite its importance, the characterization of ARGs and microbiome structures, as well as the identification of indicators for routine ARG monitoring in pig farms, are still lacking, particularly concerning variations in antimicrobial exposure in different countries or regions. Here, metagenomics and random forest machine learning were used to elucidate the ARG profiles, microbiome structures, and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe. Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs ( P<0.05). ANT(6)-Ib, APH(3')-IIIa, and tet(40) were identified as shared core ARGs between the two pig populations. Furthermore, the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions. Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs, respectively. Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100% and 98.7%, respectively. Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy ( r=0.72-0.88). Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs. The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.
监测抗菌素耐药基因（Antimicrobial resistance gene，ARG）的流行情况对于解决全球抗生素耐药性细菌感染危机至关重要。然而，在国家/地区间抗菌素暴露差异下，关于ARG和微生物组结构的特征，以及猪场常规ARG监测的指标仍然缺乏。因此，我们采用元基因组学和随机森林机器学习算法来解读中国和欧洲不同抗菌素压力下猪粪中的ARG谱、微生物组和ARG污染指标。结果表明，暴露于高水平抗菌素的中国猪中总ARG和质粒携带的ARG丰度均高于欧洲猪（ P<0.05）。 ANT(6)-Ib、 APH(3')-IIIa和 tet(40)是中国和欧洲猪中共同的核心ARG。在猪身上发现的核心ARG和相应国家/地区的人类之间存在着联系。此外，Lactobacillus和Prevotella分别是中国和欧洲猪的核心微生物组中的主要菌门。40个ARG标志物和43个生物标志物被发现可以区分中国和欧洲的猪粪样本，准确率分别为100%和98.7%。我们确定了评估中国和欧洲猪的ARG污染的指标，高准确率（ r=0.72–0.88）。中国和欧洲猪中的 Escherichia flexneri携带大量的ARG，数量范围为21–37。这项研究强调了全球合作在减少抗菌素耐药性（antimicrobial resistance，AMR）风险方面的重要性，并提供了评估猪场ARG污染风险的指标。.
Keywords: Antimicrobial pressure; Antimicrobial resistance genes; Metagenomic; Microbiome; Pig manure.