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PLoS One 16(6)_e0235066 - RCollis et al 250620.pdf (2.64 MB)

Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies

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posted on 2023-05-04, 09:59 authored by Rose CollisRose Collis, Patrick Biggs, Anne Midwinter, Springer Browne, David Wilkinson, Hamid Irshad, Nigel French, Gale BrightwellGale Brightwell, Adrian CooksonAdrian Cookson
Shiga toxin-producing Escherichia coli (STEC) are a leading cause of foodborne outbreaks of human disease, but they reside harmlessly as an asymptomatic commensal in the ruminant gut. STEC serogroup O145 are difficult to isolate as routine diagnostic methods are unable to distinguish non-O157 serogroups due to their heterogeneous metabolic characteristics, resulting in under-reporting which is likely to conceal their true prevalence. In light of these deficiencies, the purpose of this study was a twofold approach to investigate enhanced STEC O145 diagnostic culture-based methods: firstly, to use a genomic epidemiology approach to understand the genetic diversity and population structure of serogroup O145 at both a local (New Zealand) (n = 47) and global scale (n = 75) and, secondly, to identify metabolic characteristics that will help the development of a differential media for this serogroup. Analysis of a subset of E. coli serogroup O145 strains demonstrated considerable diversity in carbon utilisation, which varied in association with eae subtype and sequence type. Several carbon substrates, such as D-serine and D-malic acid, were utilised by the majority of serogroup O145 strains, which, when coupled with current molecular and culture-based methods, could aid in the identification of presumptive E. coli serogroup O145 isolates. These carbon substrates warrant subsequent testing with additional serogroup O145 strains and non-O145 strains. Serogroup O145 strains displayed extensive genetic heterogeneity that was correlated with sequence type and eae subtype, suggesting these genetic markers are good indicators for distinct E. coli phylogenetic lineages. Pangenome analysis identified a core of 3,036 genes and an open pangenome of >14,000 genes, which is consistent with the identification of distinct phylogenetic lineages. Overall, this study highlighted the phenotypic and genotypic heterogeneity within E. coli serogroup O145, suggesting that the development of a differential media targeting this serogroup will be challenging.

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Copyright: © 2020 Collis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Language

  • English

Does this contain Māori information or data?

  • No

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PLOS

Journal title

PLoS ONE

ISSN

1932-6203

Citation

Collis, R. M., Biggs, P. J., Midwinter, A. C., Browne, A. S., Wilkinson, D. A., Irshad, H., … Cookson, A. L. (2020). Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies. PLoS ONE, 15(6), e0235066. doi:10.1371/journal.pone.0235066

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