Expression of resistance genes instead of gene abundance are correlated with trace levels of antibiotics in urban surface waters.

In this study, antibiotic resistance to macrolide-lincosamide-streptogramin B (MLSB) antibiotics in total microbial community in surface water in a coastal urban city was measured using a modified fluorescence in situ hybridization (FISH) technique. This FISH technique quantified the rate of antibiotic resistance to MLSB antibiotics through targeting methylation site of A2058 of 23S rRNAs resulting from expressed erythromycin ribosome methylation (erm) genes. Correlations between the rates of MLSB resistance measured by FISH and macrolide concentrations was stronger than that between the relative abundance of erm genes and macrolide concentrations, especially in residential areas where the main detected antibiotics were macrolides. These results suggest that trace levels of antibiotics in environmental waters, which was as low as 40 ng L-1, may still play important roles in the development and spread of antibiotic resistance. Additionally, methylation as a result of erm gene expression, instead of erm gene abundance, was a better indicator of selective pressure of trace level macrolides. The rates of MLSB resistance varied significantly among land use types, suggesting that anthropogenic activities are important factors to select for erm gene expression in the environment. Microbial community analysis of representative surface water samples showed that relatively high rates of MLSB resistance were observed in Alphaproteobacteria (42%), Acidobacteria (36%), Bacteroidaceae (32%), Chloroflexi (27%), and Betaproteobacteria (20.2%).