PRJDB2338
Persistence or attenuation of antibiotic resistance genes during full-scale swine manure vermicomposting via housefly larvae (Musca domestica)
The widespread use of antibiotics in the swine industry has the potential to exert selective pressure for antibiotic resistance genes (ARGs) in both swine-associated microbiota and the bacterial communities in associated environments, posing a potential threat to public health. Full-scale vermicomposting utilizes housefly larvae (Musca domestica) to remove water and aid decomposition of swine manure. Here we determined the prevalence and persistence of ARGs in larvae-associated bacterial communities undergoing ecological succession. The concentrations of four classes of antibiotics, comprising 17 different compounds, and the abundance of their corresponding ARGs, were assessed. Most tetracyclines and sulfadiazine compounds were significantly (p< 0.05) attenuated, while quinolones showed no degradation and were the dominant antibiotics detected in unprocessed manure. Correspondingly, genes encoding tetracycline resistance (tetM, tetO, tetQ, and tetW) were depleted over the course of the study, while two quinolone resistance genes (qnrA and qnrS) were persistent. Interestingly, while sulfonamide was barely detected in late stages of vermicomposting, 2genes encoding sulfonamide resistance (sul1 and sul2) were shown to increase in abundance. While no significant difference in phylum-level bacterial community structure was observed, diversity and species richness did significantly decrease as a result of an increase in abundance of certain taxa, e.g. the relative abundance of a Flavobacteriaceae genus increased 100x, probably representing an excreted intracellular larval symbiont. The persistence of qnrA and qnrS maybe closely related an increase in the relative abundance of certain genera, which responded to shifts in the physicochemical characteristics of the manure (water content, total nitrogen, temperature and pH). The observed sustained bacterial sulfonamide resistance in manure should be a major concern as treated manure is applied to farmland as fertilizer.