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Parameters for one health genomic surveillance of Escherichia coli from Australia
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Journal Article
Parameters for one health genomic surveillance of Escherichia coli from Australia
2025
Overview
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.
Methods to demonstrate genomic linkages between pathogens across One Health compartments have not been established. Here, the authors compile a collection of E coli genomes from humans, animals, and the environment in Australia and investigate genomic evidence of cross-source clusters.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ Animals
/ Animals, Wild - microbiology
/ Clusters
/ Context
/ E coli
/ Escherichia coli - isolation & purification
/ Escherichia coli Infections - epidemiology
/ Escherichia coli Infections - microbiology
/ Escherichia coli Infections - veterinary
/ Genomes
/ Genomics
/ Humanities and Social Sciences
/ Humans
/ Linkages
/ Polymorphism, Single Nucleotide
/ Science
