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

Jose F Delgado-Blas,Cristina M Ovejero,David M Aanensen,William Calero-Caceres,William Calero-Caceres,Fernando De La Cruz,Fernando De La Cruz,M Pilar Garcillan-Barcia,Bruno Gonzalez-Zorn,Natalia Montero,Maite Muniesa,Sophia David

doi:10.1038/s42003-021-01949-x

Abstract

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.

Highlights

Aquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance
The intestinal tract of warm-blooded animals, including humans, has long been considered to be the ecological niche of E. coli. This species is thought to be an indicator of fecal contamination[31]. We found that this bacterium is the predominant aminoglycoside-resistant Enterobacteriaceae identified in wastewater treatment plants (WWTPs) of Barcelona, and highly represented in river water samples
The environmental conditions of the sampled rivers and the significant differences found between wastewater E. coli, originated from the human and animal populations of the region, and river E. coli pointed at the natural likely origin of the latter ones

Summary

Introduction

Aquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. Water phases and stages constitute genetic reactors, ecological scenarios where environmental conditions lead bacterial evolution due to biological connection, variation, and selection[2] This situation is especially notorious in wastewater treatment plants (WWTPs), since they collect residual waters from diverse origins and populations where distinct anthropogenic activities occur, including nosocomial environments. ArmA and RmtB are the most prevalent ones worldwide and they completely obliterate the activity of 4,6-DOS aminoglycosides, conferring high resistance levels to the clinically most relevant aminoglycosides[5] These enzymes are even able to abolish the effect of plazomicin, a novel aminoglycoside considered a last resource compound for the treatment of infections caused by multidrug-resistant bacteria[7]. The ecological scenario of 16S-RMTases in different water environments, their epidemiological associations, and their potential implications for public health remain largely ununderstood[3,8]

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