Abstract
Wastewater treatment plants play an important role in antibiotic resistance development. While it has been shown that wastewater effluents contain resistant bacteria, resistance genes, and antibiotics, there is little knowledge on the link between resistance genotype and phenotype. Here we present the first study, which combines a culture-based phenotypic screen with the analysis of whole genome sequences for the indicator species Escherichia coli of the inflow and outflow of a sewage treatment plant. Our analysis reveals that nearly all isolates are multi-drug resistant and many are potentially pathogenic. This holds in particular for the outflow of the treatment plant. We devise a computational approach correlating genotypic variation and resistance phenotype, which identifies known and candidate resistance genes. The identified genes stem from the pan genome, which is large and thus reflects the genomic heterogeneity of a treatment plant. Overall, the screen and analysis show that sewage treatment plants provide a favourable environment for antibiotic resistance development and that resistant bacteria do not appear to suffer from a competitive disadvantage in wastewater. These findings should find consideration in future improvements of wastewater treatment.