Natural antibiotic resistance has been found in ancient microbes in permafrost that predates the discovery of antibiotics. As climate change thaws the permafrost, antibiotic resistant microbes may have a significant negative impact on the health of Alaskans. Identifying specific antibiotic resistant microbes is essential for quick and appropriate treatment of Alaskans. Using culture-based methods, we found widespread antibiotic resistance in local boreal forest soils effected by thawing permafrost. Using analysis of long read DNA sequence data, I have developed a novel analysis pipeline to complete metagenomic assemblies. Using these genomes, we identify individual resistance genes and the associated organisms. Importantly, these methods allow us to better understand the environmental reservoir of antibiotic resistance in Alaska.
Initial data collection for this project was completed by a BLaST funded undergraduate. Our first paper from this project was published in Spring 2019 (Haan T, McDougall S, and Drown DM. 2019. DOI: 10.1128/MRA.00507-19). This brief paper demonstrates our expertise using third generation DNA sequencing methods to understand environmental reservoirs of antibiotic resistance. The authors include both undergraduate and graduate students from my lab.