Metagenomic Characterization of Antibiotic Resistance Genes, Mobile Genetic Elements and Virulence Factors in the Surface Water of the Baotou Section of the Yellow River

Antibiotic resistance genes (ARGs) have been widely recognized as emerging environmental contaminants due to their potential threats to public health and ecosystems. Owing to the extensive use of antibiotics in clinical, agricultural, and aquaculture settings, large quantities of ARGs are continuously introduced into the natural environment. As a result, aquatic environments—particularly surface waters—act as important reservoirs and transmission pathways for ARGs. However, despite the Yellow River being a major surface river in northern China, the occurrence and sources of ARGs in this river remain poorly understood. In this study, shotgun metagenomic sequencing was applied to investigate the composition of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs) in three water sources in the Baotou section of the Yellow River. A total of 35 types of ARGs, 3 types of MGEs, and 14 categories of VFs were identified across all samples. Among them, multidrug resistance genes, peptide resistance genes and glycopeptide resistance genes exhibited relatively high abundances, indicating their widespread distribution in the study area. In terms of MGEs, recombinases and transposases were dominant, suggesting their important roles in gene mobilization. Meanwhile, VFs were mainly associated with metabolic functions, immune modulation, and adherence, reflecting the potential pathogenic risks in the aquatic environment. Co-occurrence networks revealed extensive associations between ARGs and MGEs, as well as ARGs and VFs. Many positive correlations were observed, suggesting possible ecological associations between ARGs and MGEs and potential co-selection between ARGs and VFs. Overall, this study provides valuable insights into the distribution patterns and co-occurrence patterns of ARGs, MGEs, and VFs in the Yellow River and offers a scientific basis for the management and control of antibiotic resistance pollution in large river systems.