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Whole-genome sequencing and virulome analysis of Escherichia coli isolated from New Zealand environments of contrasting observed land use

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posted on 2023-05-03, 18:38 authored by Adrian CooksonAdrian Cookson, Jonathan Marshall, Patrick Biggs, Lynn RogersLynn Rogers, Rose CollisRose Collis, Megan Devane, Rebecca Stott, David Wilkinson, Janine Kamke, Gale BrightwellGale Brightwell
Generic Escherichia coli is commonly used as an indicator of fecal contamination to assess water quality and human health risk. Where measured E. coli exceedances occur, the presence of other pathogenic microorganisms, such as Shiga toxin-producing E. coli (STEC), is assumed, but confirmatory data are lacking. Putative E. coli isolates (n = 709) were isolated from water, sediment, soil, periphyton, and feces samples (n = 189) from five sites representing native forest and agricultural environments. Ten E. coli isolates (1.41%) were stx2 positive, 19 (2.7%) were eae positive, and stx1-positive isolates were absent. At the sample level, stx2-positive E. coli (5 of 189, 2.6%) and eae-positive isolates (16 of 189, 8.5%) were rare. Using real-time PCR, these STEC-associated virulence factors were determined to be more prevalent in sample enrichments (stx1, 23.9%; stx2, 31.4%; eae, 53.7%) and positively correlated with generic E. coli isolate numbers (P < 0.05) determined using culture-based methods. Whole-genome sequencing (WGS) was undertaken on a subset of 238 isolates with assemblies representing seven E. coli phylogroups (A, B1, B2, C, D, E, and F), 22 Escherichia marmotae isolates, and 1 Escherichia ruysiae isolate. Virulence factors, including those from extraintestinal pathogenic E. coli, were extremely diverse in isolates from the different locations and were more common in phylogroup B2. Analysis of the virulome from WGS data permitted the identification of gene repertoires that may be involved in environmental fitness and broadly align with phylogroup. Although recovery of STEC isolates was low, our molecular data indicate that they are likely to be widely present in environmental samples containing diverse E. coli phylogroups.


Rights statement

Copyright © 2022 Cookson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.


  • English

Does this contain Māori information or data?

  • No


American Society for Microbiology

Journal title

Environmental Microbiology




Cookson, A. L., Marshall, J. C., Biggs, P. J., Rogers, L. E., Collis, R. M., Devane, M., Stott, R., Wilkinson, D. A., Kamke, J., & Brightwell, G. (2022). Whole-genome sequencing and virulome analysis of Escherichia coli isolated from New Zealand environments of contrasting observed land use. Environmental Microbiology, 88(9), e00277–22.

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