Occurrence of sulfonamide class of antibiotics resistance in Korean paddy soils under long-term fertilization practices

Bacteria and genes that can resist antibiotics are emerging as environmental pollutants, and they need to be dealt with. While a few reports have been published, on veterinary antibiotic resistant bacteria and genes, none has been done on the soils in Korea, where the use of sulfonamides in veterinary antibiotics is prevalent. This is the first study to investigate the prevalence and distribution of sulfonamide (sulfamethoxazole, sulfamethazine, and sulfathiazole)-resistant bacteria and genes in both natural and long-term fertilized (inorganic fertilizer and pig and cattle manure composts) soils in Korea. Three long-term (47 years) fertilized (NPK, pig or cattle manure composts) paddy field soils along with an unfertilized, natural wetland soil of a mountain site collected from South Korea were examined in this study. Antibiotic resistance rates of bacteria in the collected samples were calculated for different concentrations of the sulfonamide class of antibiotics. The antibiotic-resistant bacteria were identified using the matrix-assisted laser desorption/ionization-time of flight or MALDI-TOF identification method at genus and species levels. Soil DNA was extracted, and PCR coupled with gel electrophoresis was done in order to detect sulfonamide resistant genes. Results showed that amendment of antibiotics containing animal manures, particularly from pig farms, may be a prime root cause for the spread and abundance of antibiotic resistance in Korean agricultural soils (cumulative resistance rate of 40 to 95% in the order sulfathiazole > sulfamethazine > sulfamethoxazole). Of the 2444 antibiotic-resistant isolates identified, about 80-95% belonged to Bacillus followed by Arthrobacter and Pseudomonas. Of the 56-58 distinct bacterial species detected in the long-term manure-amended Korean paddy soils, the known endospore-forming B. megatherium was predominant and it is suggested that they contribute to the observed high antibiotic resistance. Further, the sulfonamide-resistant genes [sul(I) and sul(II)] were prevalent in both natural and fertilized soils, confirming the widespread prevalence of the sulfonamide-resistant community in Korean soils. This study demonstrates that applying livestock manure compost to agricultural fields does have a large impact on the occurrence of sulfonamide-resistant bacteria and genes, particularly the ability to increase their prevalence in the environment. This outcome highlights the necessity to regulate the usage of veterinary antibiotics in Korea.