Multiple selection of resistance genes in arable soil amended with cephalosporin fermentation residue

Abstract

Abstract Cephalosporin fermentation residue (CFR) is a byproduct of the pharmaceutical industry that may be disposed through land application. While this organic residue can improve soil physico-chemical properties, the possibility of CFR-induced antibiotic resistance in the native soil microbial community still needs to be investigated. In a lab-based incubation study, the CFR-induced selection for antibiotic resistance genes (ARGs), including changes in the structure of native soil bacterial populations, antibiotic-induced selection and lateral transfer potential, was determined with quantitative PCR array and 16S amplicon sequencing. CFR amendment of soil increased the abundance of β-lactam resistance genes over time. There were higher abundance of β-lactam resistance genes in soil receiving raw CFR than treated CFR, indicating that antibiotics or metabolites contained in raw CFR contributed to the selection of resistant microorganisms. There were more mobile genetic elements in the raw CFR-amended soil, which is further evidence that bacterial responses contributed to the dissemination of antibiotic resistance genes within species in the bacterial community. Marked shifts in the native soil bacterial community composition were observed and several specific genera probably contributed to the resistance as representatives of corresponding phyla Bacteroidetes, Actinobacteria, Proteobacteria and Firmicutes, suggesting a phylogenetic basis for the increase of resistance genes in CFR-amended soil. These results imply the selection for β-lactam resistance genes at multiple levels following the application of CFR to arable soil.