Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments

Aquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Here we show that less different E. coli sequence types (STs) are identified in wastewater than in rivers, albeit more resistant to antibiotics, and with significantly more plasmids/cell (6.36 vs 3.72). However, the genomic diversity within E. coli STs in both aquatic environments is similar. Wastewater environments favor the selection of conserved chromosomal structures associated with diverse flexible plasmids, unraveling promiscuous interplasmidic resistance genes flux. On the contrary, the key driver for river E. coli adaptation is a mutable chromosome along with few plasmid types shared between diverse STs harboring a limited resistance gene content.Acknowledgements: The authors acknowledge Isabel Cuesta and Sara Monzon from the Bioinformatics Unit at the Institute of Health Carlos III for their contributions and advice to the study. The authors thank Almudena Casamayor from the Microbial Identification and Characterization Unit at the VISAVET Health Surveillance Centre for her support in the bacterial identification by MALDI-TOF mass spectrometry. The authors acknowledge Iciar Rodriguez-Avial from the Microbiology Unit at the San Carlos Hospital for providing the plazomicin to perform MIC evaluations. Work carried out in the Institute of Biomedicine and Biotechnology (IBBTEC) was funded by the Ministry of Economy and Competitiveness (grant BFU2017-86378-P). The work was supported by the Spanish Ministry of Economy and Competitiveness (MINECO BES-2015-073164) and the European Union’s Horizon 2020 Research and Innovation Programme (grant 773830, OH-EJP-H2020-JRP-AMR-2-WORLDCOM)