Parameters for one health genomic surveillance of Escherichia coli from Australia

Anne E Watt; Max L Cummins; Celeste M Donato; Wytamma Wirth; Ashleigh F Porter; Patiyan Andersson; Erica Donner; Australian Pathogen Genomics One Health Working Group; Amy V Jennison; Torsten Seemann; Steven P Djordjevic; Benjamin P Howden

doi:10.1038/s41467-024-55103-2

Parameters for one health genomic surveillance of Escherichia coli from Australia

Nat Commun. 2025 Jan 2;16(1):17. doi: 10.1038/s41467-024-55103-2.

Authors

Anne E Watt^#^{1

2}, Max L Cummins^#^{3

4}, Celeste M Donato^#^{2

5}, Wytamma Wirth², Ashleigh F Porter², Patiyan Andersson^{1

2}, Erica Donner^{6

7}; Australian Pathogen Genomics One Health Working Group; Amy V Jennison⁸, Torsten Seemann^{1

2

5}, Steven P Djordjevic^{9

10}, Benjamin P Howden^{11

12

13

14}

Collaborators

Australian Pathogen Genomics One Health Working Group:
Vitali Sintchenko, Alicia Arnott, Alireza Zahedi, Rowena Bull, Jessica R Webb, Danielle Ingle, Kristy Horan, Tuyet Hoang, Angeline Ferdinand, Tehzeeb Zulfiqar, Craig Thompson, Lex E X Leong, Bethany Hoye, Glenn F Browning, Michelle Wille, Rose Wright, Angela Donald, Zoe Bartlett, Avram Levy, Christina Bareja, Tatiana Gonzales, Cara Minney-Smith, Erin Flynn, Aruna Phabmixay, Thy Huynh

Affiliations

¹ Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
² Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
³ Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia.
⁴ The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, New South Wales, Australia.
⁵ Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia.
⁶ Future Industries Institute, University of South Australia, Mawson Lakes, South Australia, Australia.
⁷ Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Mawson Lakes, South Australia, Australia.
⁸ Public Health Microbiology, Public and Environmental Health, Pathology Queensland, Queensland Department of Health, Brisbane, Queensland, Australia.
⁹ Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia. [email protected].
¹⁰ The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, New South Wales, Australia. [email protected].
¹¹ Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia. [email protected].
¹² Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia. [email protected].
¹³ Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia. [email protected].
¹⁴ Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia. [email protected].

^# Contributed equally.

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.

MeSH terms

Animals
Animals, Wild / microbiology
Australia / epidemiology
Disease Outbreaks
Escherichia coli Infections* / epidemiology
Escherichia coli Infections* / microbiology
Escherichia coli Infections* / veterinary
Escherichia coli* / genetics
Escherichia coli* / isolation & purification
Genome, Bacterial*
Genomics* / methods
Humans
Livestock / microbiology
Multilocus Sequence Typing
One Health*
Phylogeny*
Polymorphism, Single Nucleotide*

Grants and funding

GNT1196103/Department of Health | National Health and Medical Research Council (NHMRC)