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

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.

Dissemination Routes of Carbapenem and Pan-Aminoglycoside Resistance Mechanisms in Hospital and Urban Wastewater Canalizations of Ghana

“…Concurrently to the genetic dissemination caused by clonal expansion of bacterial hosts, other carbapenemase genes were associated with multiple MGEs, demonstrating a high competence to be mobilized, transferred, and coselected. In fact, the genetic dissemination via horizontal gene transfer is one of the main AMR drivers in Enterobacteriaceae species inhabiting wastewater environments ( 21 ). This is the case for bla NDM-1 , identified in diverse plasmid structures but generally sharing a common gene-flanking region.…”

Geography shapes the genomics and antimicrobial resistance of Salmonella enterica Serovar Enteritidis isolated from humans

“…All the plasmids with the same pHN7A8 origin of replication were isolated in Asia, especially China 38 . Recently, two pHN7A8-like plasmids were detected in clinical isolates of K. pneumonia e from Bolivia 39 and E. coli from a wastewater treatment plant (WWTP) from Barcelona, Spain 40 , respectively, with most variation associated with ARGs, demonstrating a possible intercontinental dissemination. In the U. S., pHN7A8 was detected in E. coli isolated from a forest in North Carolina without carrying any ARGs.…”

Genomic Insights into the Mobilome and Resistome of Sentinel Microorganisms Originating from Farms of Two Different Swine Production Systems

“…The mobilome was particularly complex in E. coli , with a great diversity of TEs identified, suggesting that MGE transposition is relatively common in this species ( 30 ). The plasmidome, considered to be a determinant for AMR dissemination ( 31 ), was also especially relevant in terms of ARD carriage in E. coli genomes, evidencing its role in the AMR mobilization ( 15 , 32 ). Indeed, most of the constituents of the E. coli resistome were predicted to be associated with MGEs, and about half of them, with plasmids, either exclusively or coupled with TEs and/or integrons.…”