Elucidating the scope and dynamics of microbiomes and resistomes in earth, wind and water

Antibiotic resistance (AR) has considerable epidemiological ramifications, predicted to reach pandemic proportions in the next few decades. Although AR is traditionally linked to hospitals and the community, there is growing evidence that it is also associated with the environment. Nonetheless, our understanding of environmental "resistomes" and their connection to AR in humans is currently an enigma. This lecture will focus on three comprehensive studies that targeted AR in the environment. The first assessed the scope of AR in treated wastewater effluents, and attempted to elucidate the impact of treated wastewater irrigation on the dissemination of antibiotic resistance in terrestrial and food-associated microbiomes. It combined culture-based and quantitative PCR based approaches, including a novel amplicon sequencing approach that specifically targeted antibiotic resistance genes carried on integron gene cassettes. The second study explored the abundance and diversity of microbial communities and antibiotic resistance genes in aerial ecosystems, comparing ambient air to dust storms tracked using back trajectory calculations. Finally, the third study applied complex network analyses to investigate correlations between antibiotic resistance genes from metagenomic data to elucidate potential mobilization of antibiotic resistance genes between different ecosystems. Collectively, these studies demonstrate that antibiotic resistance dynamics and the dissemination of antibiotic resistance genes in the environment is highly complex and is associated with a broad spectrum of multifactorial biotic and abiotic constraints that we are just beginning to understand.