Expanding the Repertoire of Associations Between Antibiotic Resistance Genes and Putative Mobile Genetic Element Carriers Using Metagenomic Long Reads

Abstract

Antibiotic resistance genes (ARGs) and the mobile genetic elements (MGEs) that mediate their horizontal transfer are central to understanding the mechanisms, evolution, and dissemination of antimicrobial resistance. Although thousands of ARGs have been documented and numerous ARG-MGE associations have been reported, broader questions about the diversity and distribution of these associations remain underexplored. How comprehensive are the current catalogs of ARG-MGE associations? Are certain MGE families preferentially associated with particular ARGs, and vice versa? How are ARG-MGE associations distributed across microbial taxa? Is the environmental abundance of an ARG related to the diversity of its MGE associations? Do ARG-MGE association patterns vary across environments? Here we address these questions by analyzing multiple publicly available long-read metagenomic datasets from various environmental settings, leveraging the ability of long reads to capture ARGs along with their genomic contexts within individual reads. We identified numerous potential ARG-MGE associations not found in existing databases. A few MGE families were putatively associated with nearly all identified ARGs. ARG-MGE associations were unevenly distributed across taxa. ARG abundance was positively associated with both MGE association diversity and the taxonomic spread of those associations. Furthermore, ARG-MGE association patterns varied across environments. Overall, our findings reveal an extensive diversity of ARG-MGE associations that remains largely underrepresented in current knowledge bases.