Bees, bugs and antibiotics – the interactions of veterinary and agricultural antibiotics with the gut microbiome, resistome and health of bees

Abstract

Human use and misuse of antibiotics puts pressure on bacteria, including metazoan microbiomes, to evolve or acquire antibiotic resistance genes (ARGs). Moreover, antibiotic use can have off-target effects on the health of organisms with host-adapted microbiota, by causing dysbiosis. I investigate the impact of veterinary and agricultural antibiotics on the health, gut microbiota composition and resistome of honeybee and bumblebee species: Apis mellifera and Bombus terrestris, which are globally in decline. Firstly, I used an agent-based simulation model and empirical data to assess colony-level effects of antibiotic-induced honeybee worker bee mortality, mimicking treatment for a common honeybee disease, American foulbrood disease. Strikingly, I found that with antibiotic-induced mortality of bees from just 60 days per year, the colony size is reduced to the degree that tetracycline treatment would not meet the European Food Safety Authority’s honeybee protection goals. Secondly, I experimentally exposed B. terrestris workers to concentrations of streptomycin and oxytetracycline, mimicking exposure they are likely to experience while foraging in orchards treated for Fireblight. This exposure severely reduced microbial abundance and impacted the community composition of the core microbiota, in a dose-dependent manner. At a critical threshold, the microbiota shifted from being dominated by core species, to non-core and opportunistic species. This threshold was much lower for oxytetracycline than streptomycin. Through use of a new Cas9-based enrichment methodology, I characterised the gut resistome of these bees and found them to contain dozens of ARGs. The antibiotic treatments selected for 7 ARGs and many metal resistance genes, including a tetracycline resistance gene. Through a culture-based study I showed that the presence of these ARGs in the microbiomes was congruent with shifts in the phenotypic 3 resistance. Finally, I characterised the microbiota and resistomes of commercial and wild British B. terrestris from farmland and heathland conservation sites. I showed that wild bees have a greater diversity and richness of bacteria and resistance genes within their microbiota. Interestingly, bees from farmland habitats had a higher proportion of multidrug resistance gene arcB than their heathland counterparts. arcB confers resistance to many antimicrobials used in agriculture. Importantly, wild bees’ resistomes contained antibiotic resistance genes which have been labelled as a “current threat” to human health. Overall, this thesis shows the broad and detrimental impacts of antibiotic exposure on bee health, gut microbiota and gut resistome. Our results highlight the importance of examining the resistomes of insect microbiota, when assessing the antibiotic resistance crisis from a One Health perspective.