High genomic diversity of multi-drug resistant wastewater Escherichia coli

Abstract

Wastewater treatment plants play an important role in the release of antibiotic resistance into the environment. It has been shown that wastewater contains multi-drug resistant Escherichia coli, but information on strain diversity is surprisingly scarce. Here we present an exceptionally large dataset on multidrug resistant Escherichia coli, originating from wastewater, over a thousand isolates were phenotypically characterized for twenty antibiotics and for 103 isolates whole genomes were sequenced. To our knowledge this is the first study documenting such a comprehensive diversity of multi-drug resistant Escherichia coli in wastewater. The genomic diversity of the isolates was unexpectedly high and contained a high number of resistance and virulence genes. To illustrate the genomic diversity of the isolates we calculated the pan genome of the wastewater Escherichia coli and found it to contain over sixteen thousand genes. To analyse this diverse dataset, we devised a computational approach correlating genotypic variation and resistance phenotype, this way we were able to identify not only known, but also candidate resistance genes. Finally, we could verify that the effluent of a wastewater treatment plant will contain multi-drug resistant Escherichia coli belonging to clinically important clonal groups.