Biopesticides as Unintentional Reservoirs and Vectors of Antibiotic Resistance Genes and Mobilizable Elements

Antibiotic resistant bacteria generated by agricultural and livestock practices can exchange antibiotic resistance genes (ARG) with soil microbes and generate novel pathogenicity; environmental microbes can then act as reservoirs or vectors of ARG. However, there are many other practices that could be contributing to the generation, spread, and maintenance of antibiotic resistance genes. One industrial agricultural practice that has yet to be investigated for its potential role as a reservoir or vector of antibiotic resistance genes is the use of biopesticides. The use of microorganisms for pest control, frost prevention, and rhizosphere enhancements in agriculture has steadily increased over the last 20 years. Considered safe for consumption, non-toxic, and nonpathogenic, microbial products offer welcome alternatives to traditional chemically synthesized pesticides known to cause damage to human health and the environment. Plasmids bearing antibiotic resistance genes and novel pathogenicity should be considered part of the resistomes when investigating ARG of bacterial biopesticides. The widespread use and application of bacterial biopesticides to crops in high concentrations raises the possibility of unintentional contributions to the movement and generation of antibiotic resistance genes (ARG) in the environment. Are there clinically relevant antibiotic resistance genes present in commercially available bacterial biopesticides? Are the bioinformatically identified antibiotic resistance genes expressed and do they demonstrate resistance to clinically relevant antibiotics? Is there genetic exchange between widely available Bacillus-based bacterial biopesticide products and a bioinformatically informed pathogen? What is the role of plasmids, viruses and other mobile genetic elements in relation to antibiotic resistance genes occurring in commercially available Bacillus-based bacterial biopesticides? This research investigated publicly available genomes sequences for widely used agricultural bacterial biopesticide products in order to identify the presence of antibiotic resistance genes. Commercially available Bacillus-based biopesticides were the basis of antibiotic resistance experiments and whole genome sequencing. I found that biopesticides are reservoirs of clinically relevant antibiotic resistance genes, however, their resistance phenotypes were not matched. Simple contact with carbapenemase positive Klebsiella pneumoniae was enough to change the phenotype from susceptible to resistant for three of the four commercial biopesticide products. A comprehensive look into the viral and integrative and mobile elements showed a likely explanation for the large and diverse suite of genes found in the biopesticides. This work demonstrates the need to include biopesticide use in the cohort of agricultural processes that have been implicated in the generation, spread, and maintenance of ARG in the environment