Honey bees as biomonitors of plant pathogens, pesticides and antimicrobial resistance genes

Abstract

The European honey bee (Apis mellifera) can be exposed to pathogens and agrochemicals during foraging; carrying them to the hive where they can be detected and quantified in hive materials: honey, pollen, and wax. Results from our and other laboratories showed the potential of using honey bees as environmental biomonitors. In particular for monitoring a) plant pathogens, b) agrochemicals, and c) antimicrobial resistance (AMR) genes (ARGs). We tested the potential of plant pathogen monitoring (a), by analyzing bees and bee-collected pollen, and we established the presence of plant viruses, fungi, and bacteria using high-throughput sequencing. We analyzed samples for the presence of agrochemicals (b) and identified insecticides, fungicides and herbicides in colonies positioned near and far from blueberry fields; we also studied temporal and spatial patterns of systemic insecticides in bees and flowers. In addition, we identified antimicrobial resistance genes (c) and studied the honey bee gut resistome, i.e. the collection of AMR genes in a microbiome, using metagenomics sequencing. AMR can result in the loss of antibiotic effectiveness and consequently the use of higher doses. This poses an increased risk of residues in honey, gut dysbiosis, and other negative health effects on honey bees, other pollinators, and the ecosystem. We analyzed bee gut microbiome samples from different sites in Ontario, Canada; by processing shotgun metagenomic sequencing results through the AMR++ pipeline producing short-read alignment resistome results classified against the MEGARes database. The same reads were also de novo assembled for ARGs screening against different databases. We found a high relative abundance of tetracycline resistance genes across samples, in accordance with the common use of oxytetracycline for prophylaxis and treatment of bacterial diseases in ON. Sulfonamide and aminoglycoside ARGs were also found consistently across samples. Monitoring AMR genes in apiaries and their surrounding environment can guide decisions towards limited and informed antibiotic use. Bee-based surveillance of ARGs, agrochemicals, and plant pathogens has the potential to be an effective tool in environmental monitoring programs; crucial for protecting human, agriculture, and overall ecosystem health.