Rare Taxa Are Key Links in Regional Antimicrobial Resistance Profiles in Dusts Across Diverse North American Regions

Abstract

The role of bioaerosols in the dispersal of antimicrobial resistance genes (ARGs) and resistant microorganisms is poorly understood. In addition, bioaerosols are powerful composite samples representative of the surrounding environment and can be used as sentinels of many local habitats. Evidence suggests that using environmental DNA from dust collected on vehicle cabin air filters can define regional resistance profiles. Here, this method was used to investigate differences in resistance gene profiles, their underlying bacterial communities, and their links to anthropogenic and environmental variables across Canada. In total, 477 car filter samples were collected, with every province and territory being represented. DNA was extracted from filter dust. High-throughput qPCR was used to detect and quantify a panel of 36 ARGs and 3 mobile genetic elements. Bacterial biomass was assessed using standard qPCR methods of the 16S rRNA gene, which was also used to assess bacterial biodiversity via metabarcoding. Results indicated that qepA dominates antimicrobial resistance profiles across Canada. However, after they were removed from the dataset, regional profiles were evident based on gene type and richness. Factors positively linked to total numbers of ARGs included human and livestock populations; whereas mean annual precipitation was negatively linked to resistance gene quantities. Measures of α-diversity were generally greater in the western regions of Canada than in the east and the north. Community composition analyses showed similarities between the prairies and territories, which were separated from other regions. Finally, network analyses revealed a relatively stable group of core ARGs across regions, which were largely correlated with low-abundance genera. Such findings suggest that rare taxa are key links in the diffusion of antimicrobial resistance in environmental contexts. Furthermore, this study highlights the potential application of vehicle air filters in building long-term monitoring capacity of outdoor bioaerosols.