High Prevalence of Human-Associated Escherichia coli in Wetlands Located in Eastern France.

Daniel Martak,Marion Richard,Didier Hocquet,Gudrun Bornette,Charlotte Couchoud,Benoit Valot,Xavier Bertrand,Julie Couchot,Marion Broussier,Charles P Henriot

doi:10.3389/fmicb.2020.552566

Abstract

Escherichia coli that are present in the rivers are mostly brought by human and animal feces. Contamination occurs mostly through wastewater treatment plant (WWTP) outflows and field amendment with sewage sludge or manure. However, the survival of these isolates in river-associated wetlands remains unknown. Here, we assessed E. coli population structure in low-anthropized wetlands located along three floodplains to identify the major source of contamination of wetlands, whose functioning is different from the rivers. We retrieved 179 E. coli in water samples collected monthly from 19 sites located in eastern France over 1 year. Phylogroups B1 and B2 were dominant in the E. coli population, while phylogroup A was dominant in isolates resistant to third-generation cephalosporins, which harbored the extended-spectrum β-lactamase (ESBL) encoding genes blaCTX–M–15 and blaCTX–M–27 in half of the cases. The high proportion of isolates from human source can be attributed to WWTP outflows and the spread of sewage sludge. We analyzed the distribution of the isolates belonging to the most human-associated phylogroups (B2 and D) on a phylogenetic tree of the whole species and compared it with that of isolates retrieved from patients and from WWTP outflows. The distribution of the three E. coli populations was similar, suggesting the absence of a specific population in the environment. Our results suggest that a high proportion of E. coli isolates that reach and survive in low-anthropized environments such as wetlands are from human source. To the best of our knowledge, this is the first study assessing E. coli contamination and resistance genes in natural freshwater wetlands.

Highlights

Escherichia coli is a facultative anaerobic organism commensal of the vertebrate gut microbiota
We found 29 isolates belonging to the Escherichia cryptic clades (Clermont et al, 2013)
We divided 125 E. coli isolates into phylogroups and found a high proportion of isolates belonging to phylogroups A and B2, representing half of the isolates retrieved (48.8%)

Summary

Introduction

Escherichia coli is a facultative anaerobic organism commensal of the vertebrate gut microbiota. It can be responsible of infections and is one of the main pathogens responsible for hospital- and community-acquired infections (Tenaillon et al, 2010). Humans widely contribute to the dissemination of E. coli in the environment through wastewaters. In developed countries, these wastewaters are treated in wastewater treatment plants (WWTPs). Agriculture contributes to E. coli dissemination through practices such as spreading manure or sewage sludge (Cabral, 2010; Niu and Phanikumar, 2015; Hocquet et al, 2016). E. coli contaminates most environments, with both human-associated or not human-associated E. coli present in rivers, lakes, groundwater, plants, and soils (Brookes et al, 2004; John and Rose, 2005; Park et al, 2016)

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Results

Conclusion