Honey bees as biomonitors of antimicrobial resistance in agricultural systems

Antimicrobial resistance (AMR) is a global threat to agriculture as bacterial infections become increasingly more difficult to treat. In the beekeeping industry, antibiotics are frequently used for prevention and treatment of disease such as American and European foulbrood. However, increasing rates of AMR have limited the effectiveness of antibiotic treatments which has consequences for colony health and the production and stability of pollinator-dependent crops. We studied the honey bee gut resistome, i.e. the collection of AMR genes in a microbiome, using metagenomic 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 high relative abundance of tetracycline resistance genes, in accordance with the common use of oxytetracycline for prophylaxis and treatment of bacterial diseases in Ontario. Sulfonamide and aminoglycoside ARGs were also found consistently. 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.