The core and variable antimicrobial resistome in pig gut between China and Europe

Monitoring the prevalence of the antimicrobial resistance gene (ARG) is critical to address the global crisis of antibiotic resistant bacterial infections. However, the characterization of ARG and microbiome structure, as well as the indicators for routine ARG monitoring in pig farms, are still lacking under the variation in antimicrobial exposure between countries/regions. Hence, metagenomics and Random Forest machine learning algorithm were used to decipher the ARG profiles, microbiome, and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe. The results showed that Chinese pigs exposed to high level antimicrobials had higher total and plasmid-mediated ARG abundances than European pigs (P < 0.05). ANT(6)-Ib, APH(3')-IIIa, and tet(40) were the shared core ARGs between Chinese and European pigs. The core ARG identified in pigs existed a linkage between corresponding country/regions pigs and humans. Moreover, Lactobacillus and Prevotella were the dominant phyla in the core microbiome of Chinese and European pigs, respectively. Forty ARG markers and 43 biomarkers were found to differentiate Chinese and European pig manure samples with 100% and 98.7% accuracy, respectively. We identified indicators to assess the ARG contamination in Chinese and European pigs with high accuracy (r = 0.72 ~ 0.88). Escherichia flexneri in Chinese and European pigs carried numerous ARGs, ranging from 21 to 37. This study emphasized the importance of global collaboration in reducing antimicrobial resistance (AMR) risk and provided indicators for evaluating the risk of ARG contamination in pig farms.