Co-occurrence of microbial source tracking markers and antibiotic resistance genes in the Chishui River, China

Fecal contamination is an important source for the emergence of antibiotic resistance genes (ARGs) worldwide. Identifying the host sources of ARG contamination and distinguishing whether the increased abundance of ARGs in the environment is due to on-site selection or the result of fecal contamination can effectively protect water quality and predict human health risks. In this study, the occurrence of 5 ARGs (sul1, sul2, tetO, tetW, and ermF), 1 mobile element intI1 and 7 microbial source tracker (MST) markers (CPQ_064, BacHum, Rum-2-Bac, BacCow, P.ND5, Pig-1-Bac, and GFD) was analyzed in the Chishui River watershed of Southwest China. The results showed that the detection frequencies of most ARGs exceeded 90% except for tetO. The abundance of the ARGs was higher in sediments than those in water. There was no significant difference in the ARG abundance in the sediments between the dry season and wet season, but the abundance of most ARGs in water during the dry season was significantly higher than those of the wet season. For MST markers, the abundance was also higher in sediments than that in water. Temporal distribution analysis showed that the abundance of most MST markers in water during the dry season was higher than that of the wet season, but the opposite result was found in sediments. Correlation analysis revealed that the prevalence of most ARGs in water was largely attributed to human fecal contamination. The results suggested that ruminant fecal contamination was a significant contributor to the distribution of tetW and ermF in water. In contrast, ARGs showed poor correlation with most MST markers in the sediments. Considering the lower specificity of Pig-1-Bac and ruminant-associated markers (Rum-2-Bac and BacCow), as well as the different decay rates between two human-associated markers (CPQ_064 and BacHum), the accuracy of ARG source tracking may be affected. Thus, this study suggested that multiple MST markers should be applied simultaneously to characterize ARGs sources. These findings provide critical guidance for mitigating ARG dissemination in agricultural and rural regions reliant on surface water, where fecal contamination poses dual threats to drinking safety and livestock productivity.