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Parameters for one health genomic surveillance of Escherichia coli from Australia

Author

Listed:
  • Anne E. Watt

    (Melbourne
    Melbourne)

  • Max L. Cummins

    (University of Technology Sydney, Ultimo
    University of Technology Sydney, Ultimo)

  • Celeste M. Donato

    (Melbourne
    The University of Melbourne, Melbourne)

  • Wytamma Wirth

    (Melbourne)

  • Ashleigh F. Porter

    (Melbourne)

  • Patiyan Andersson

    (Melbourne
    Melbourne)

  • Erica Donner

    (University of South Australia
    Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE))

  • Amy V. Jennison

    (Queensland Department of Health)

  • Torsten Seemann

    (Melbourne
    Melbourne
    The University of Melbourne, Melbourne)

  • Steven P. Djordjevic

    (University of Technology Sydney, Ultimo
    University of Technology Sydney, Ultimo)

  • Benjamin P. Howden

    (Melbourne
    Melbourne
    The University of Melbourne, Melbourne
    Austin Health, Heidelberg)

Abstract

Genomics is a cornerstone of modern pathogen epidemiology yet demonstrating transmission in a One Health context is challenging, as strains circulate and evolve within and between diverse hosts and environments. To identify phylogenetic linkages and better define relevant measures of genomic relatedness in a One Health context, we collated 5471 Escherichia coli genome sequences from Australia originating from humans (n = 2996), wild animals (n = 870), livestock (n = 649), companion animals (n = 375), environmental sources (n = 292) and food (n = 289) spanning over 36 years. Of the 827 multi-locus sequence types (STs) identified, 10 STs were commonly associated with cross-source genomic clusters, including the highly clonal ST131, pandemic zoonotic lineages such as ST95, and emerging human ExPEC ST1193. Here, we show that assessing genomic relationships at ≤ 100 SNP threshold enabled detection of cross-source linkage otherwise obscured when applying typical outbreak-oriented relatedness thresholds ( ≤ 20 SNPs) and should be considered in interrogation of One Health genomic datasets.

Suggested Citation

  • Anne E. Watt & Max L. Cummins & Celeste M. Donato & Wytamma Wirth & Ashleigh F. Porter & Patiyan Andersson & Erica Donner & Amy V. Jennison & Torsten Seemann & Steven P. Djordjevic & Benjamin P. Howde, 2025. "Parameters for one health genomic surveillance of Escherichia coli from Australia," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-024-55103-2
    DOI: 10.1038/s41467-024-55103-2
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