Ecological specificity and interconnectivity in Danish environmental resistomes

The environment plays a critical role in "One Health", facilitating the evolution, persistence, and dissemination of antibiotic resistance genes (ARGs). However, environmental resistomes have primarily been characterized through scattered studies of individual habitats, limiting our understanding of baseline resistome structure and connectivity across landscapes at a national level. Here, we analyzed metagenomes from 7,000 Danish environmental samples (24 Tbp), collected from 21 distinct habitats including soils, sediments, aquatic environments and wastewater treatment plants (WWTPs). We identified core ARGs for establishing the environmental baseline, and habitat-associated indicator ARGs for facilitating source tracking. Using an additional 110 deep long-read metagenomes (9 Tbp data), we found a subset of cross-habitat commonly abundant ARGs was carried by diverse hosts and associated with mobile genetic elements, suggesting their potential role in resistome connectivity across ecosystems. Additionally, although natural habitats had much lower resistome relative abundance and transferability than human-associated habitats, some mobile environmental ARGs exhibited links to those in human pathogens. Our results support the implementation of environmental resistome surveillance by providing an environmental ARG baseline, enabling future ARG source-tracking and cross-habitat ARG dissemination assessment.