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Parameters for one health genomic surveillance of Escherichia coli from Australia

A. WattDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, AustraliaMax L. CumminsAustralian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, AustraliaCeleste M. DonatoDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, AustraliaWytamma WirthPeter Doherty InstituteAshleigh F. PorterDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, AustraliaPatiyan AnderssonDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, AustraliaErica DonnerCooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Mawson Lakes, South Australia, AustraliaAustralian Pathogen Genomics One Health Working GroupCentre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, AustraliaVitali SintchenkoVictorian Infectious Diseases Reference LaboratoryAlicia ArnottVictorian Infectious Diseases Reference LaboratoryAlireza ZahediPublic Health Microbiology, Public and Environmental Health, Pathology Queensland, Queensland Department of Health, Brisbane, Queensland, AustraliaRowena A. BullSchool of Biomedical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, AustraliaJessica R. WebbPeter Doherty InstituteDanielle J. IngleDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, AustraliaKristy HoranDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, AustraliaTuyet HoangDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, AustraliaAngeline FerdinandPeter Doherty InstituteTehzeeb ZulfiqarPublic Health Microbiology, Public and Environmental Health, Pathology Queensland, Queensland Department of Health, Brisbane, Queensland, AustraliaCraig ThompsonPublic Health Microbiology, Public and Environmental Health, Pathology Queensland, Queensland Department of Health, Brisbane, Queensland, AustraliaLex E.X. LeongSA Pathology, Adelaide, South Australia, AustraliaBethany J. HoyeEnvironmental Futures, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, AustraliaGlenn F. BrowningDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, AustraliaMichelle WilleAustralian GovernmentRose WrightDepartment of Health and Aged CareAngela DonaldDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, AustraliaZoe BartlettFood Standards Australia and New Zealand, Canberra, Australian Capital Territory, AustraliaAvram LevyQueen Elizabeth II Medical CentreChristina BarejaAustralian GovernmentTatiana GonzalesDepartment of Health and Aged CareCara Minney‐SmithPathwest Laboratory MedicineErin FlynnAustralian GovernmentAruna PhabmixayAustralian GovernmentThy HuynhDepartment of Health and Aged CareAmy V. JennisonCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, AustraliaTorsten SeemannDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, AustraliaSteven P. DjordjevicAustralian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia. [email protected]Benjamin P. HowdenCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia. [email protected]

2025en

ABI

Annotatsiya

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.

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DOI: 10.1038/s41467-024-55103-2

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