Data associated with "A metagenomic survey reveals widespread antibiotic resistance genes in honey bee (Apis mellifera) gut bacteria across the United States"

Antibiotic use has contributed to antibiotic resistance genes (ARGs) accumulating in many environments, including host-associated microbiomes. Managed honey bees may accumulate ARGs, as they are sometimes treated with antibiotics and often live in agricultural landscapes that could be contaminated with antibiotics. We describe the occurrence and distribution of ARGs in honey bee bacterial gut symbionts from 13 apiaries in a transect across the USA from Washington to Virginia. Using metagenomic sequencing, we detected 55 unique ARGs conferring resistance to 14 classes of antibiotics. Of these, 11 ARGs encoded multidrug resistance. ARGs varied across sites but did not correlate with longitude. We compared ARG occurrence among core honey bee gut bacterial genera to determine whether any taxa act as ARG reservoirs. ARG occurrence did vary among honey bee gut symbionts, with Gilliamella and Frischella containing the highest proportions of ARGs despite their low relative abundance in the gut community. As tetracycline is the most commonly used antibiotic in beekeeping, we compared the frequency and abundance of tetracycline resistance genes across apiaries. All hives contained tetracycline resistance genes, with tetB and tetM present at all apiaries. Based on qPCR, tetB and tetM abundance varied significantly among apiaries. TetB was higher overall and negatively correlated with longitude. We demonstrate honey bee gut bacteria possess a diversity of ARGs, not all of which are consistent antibiotic use in beekeeping, ARG frequency varies among bacterial genera in the honey bee gut, and certain ARGs are associated with hive geographic location.