Characterization of known and novel clinically important antibiotic resistance genes and novel microbes from wastewater-impacted high Arctic fjord sediments

Abstract

Arctic microbiota is enigmatic and highly underexplored. With the aim of understanding the resistome and microbiota of high-Arctic fjord sediments and the effect of wastewater discharge on sediment microbiota, we analyzed sediments from Advent fjord in Svalbard using metagenomics. We show the presence of 888 clinically relevant antibiotic resistance genes including genes coding resistance against last-resort antibiotics such as carbapenems, colistin, vancomycin, linezolid and tigecycline in the sediment microbiota. Using computational models, 478 novel β-lactamases belonging to 217 novel β-lactamase families were revealed in the sediment microbiota. Further, we identified hosts for 69 novel families and showed that these genes are widespread in the Arctic environment. We assembled 644 metagenome-assembled genomes (MAGs) from sediment metagenomes. Of these >97 % belonged to novel taxa with 89 bacterial MAGs representing seven putative novel phyla. These MAGs encoded important functions like nutrient cycling and methane metabolism etc. Our study demonstrated mixing of human associated bacteria and Arctic sediment microbiota. It provides the first comprehensive dataset of the distribution and diversity of novel microbes and β-lactamases in the wastewater-impacted high Arctic fjord sediments.