Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater

Shuai Zhi; Graham Banting; Paul Stothard; Nicholas J. Ashbolt; Sylvia Checkley; Kelsey Meyer; Simon Otto; Norman F. Neumann

doi:10.1016/j.watres.2019.03.024

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Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater

Journal article

Open access

Peer reviewed

Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater

Shuai Zhi, Graham Banting, Paul Stothard, Nicholas J. Ashbolt, Sylvia Checkley, Kelsey Meyer, Simon Otto and Norman F. Neumann

Water research (Oxford), Vol.156, pp.208-222

01/06/2019

DOI: https://doi.org/10.1016/j.watres.2019.03.024

PMID: 30921537

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Abstract

Cryptic

Enteric

Escherichia coli

Naturalized

Stress-resistance

wastewater

We previously demonstrated the existence of naturalized strains of E. coli in wastewater and herein perform an in-depth comparative whole genome analysis of these strains (n = 17). Fourteen of the Canadian E. coli strains, isolated from geographically separated wastewater treatment plants, were virtually identical at the core genome and were ≥96% similar at the whole genome level, suggesting clonal-relatedness among these isolates. Remarkably, these strains were shown to be extremely similar to the genome of an E. coli isolated from wastewater in Switzerland, suggesting a global distribution of these strains. The genomes of three other Canadian wastewater strains were more diverse but very similar to the genomes of E. coli isolates collected from U.S. wastewater samples. Based on maximum likelihood phylogenetic analysis, wastewater strains from Canada, the U.S. and Switzerland formed a clade separate from other known enteric phylogroups (i.e., A, B1, B2, D, E) and the cryptic clades. All Canadian, Swiss and U.S. wastewater strains possessed a common SNP biomarker pattern across their genomes, and a sub-population (i.e., 14 Canadian and 1 Swiss strain) also possessed a previously identified wastewater-specific marker known as uspC-IS30-flhDC element. Biochemical heat mapping of 518 categories of genes recapitulated phylogeny, with wastewater strains phenotypically clustering separately from enteric and cryptic clades. Wastewater strains were enriched for stress-response genes (i.e., nutrient acquisition/deprivation, DNA repair, oxidative stress, and UV resistance) - elements reflective of their environmental survival challenges. Wastewater strains were shown to carry a plethora of known antibiotic resistance (AR) genes, the patterns of which were remarkably similar among all Canadian, U.S. and Swiss wastewater strains. Virulence gene composition was also similar among all the wastewater strains, with an abundant representation of virulence genes commonly associated with urinary pathogenic E. coli (UPEC) as well as enterohemorrhagic (EHEC) E. coli. The remarkable degree of similarity between all wastewater strains from Canada, Switzerland and the U.S. suggests the evolution and global-dissemination of water treatment-resistant clone of E. coli. These finding, along with others, raise some important concerns about the potential for emergence of E. coli pathotypes resistant to water-treatment.

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Title: Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater
Creators: Shuai Zhi - University of Alberta
Graham Banting - University of Alberta
Paul Stothard - University of Alberta
Nicholas J. Ashbolt - University of Alberta
Sylvia Checkley - University of Calgary
Kelsey Meyer - University of Calgary
Simon Otto - University of Alberta
Norman F. Neumann - University of Alberta
Publication Details: Water research (Oxford), Vol.156, pp.208-222
Publisher: Elsevier Ltd
Identifiers: 991013098099102368
Academic Unit: Faculty of Science and Engineering
Language: English
Resource Type: Journal article

Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater

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