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; 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

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. Howden^*

^*Corresponding author for this work

National Centre for Epidemiology and Population Health

Research output: Contribution to journal › Article › peer-review

11 Citations (SciVal)

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.

Original language	English
Article number	17
Pages (from-to)	1-14
Number of pages	14
Journal	Nature Communications
Volume	16
Issue number	1
DOIs	https://doi.org/10.1038/s41467-024-55103-2
Publication status	Published - 2 Jan 2025

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title = "Parameters for one health genomic surveillance of Escherichia coli from Australia",

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.",

author = "Watt, \{Anne E.\} and Cummins, \{Max L.\} and Donato, \{Celeste M.\} and Wytamma Wirth and Porter, \{Ashleigh F.\} and Patiyan Andersson and Erica Donner and Thy Huynh and Aruna Phabmixay and Erin Flynn and Cara Minney-Smith and Tatiana Gonzales and Christina Bareja and Avram Levy and Zoe Bartlett and Angela Donald and Rose Wright and Michelle Wille and Browning, \{Glenn F.\} and Bethany Hoye and Leong, \{Lex E.X.\} and Craig Thompson and Tehzeeb Zulfiqar and Angeline Ferdinand and Tuyet Hoang and Kristy Horan and Danielle Ingle and Webb, \{Jessica R.\} and Rowena Bull and Alireza Zahedi and Alicia Arnott and Vitali Sintchenko and Jennison, \{Amy V.\} and Torsten Seemann and Djordjevic, \{Steven P.\} and Howden, \{Benjamin P.\}",

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AU - Andersson, Patiyan

AU - Donner, Erica

AU - Huynh, Thy

AU - Phabmixay, Aruna

AU - Flynn, Erin

AU - Minney-Smith, Cara

AU - Gonzales, Tatiana

AU - Bareja, Christina

AU - Levy, Avram

AU - Bartlett, Zoe

AU - Donald, Angela

AU - Wright, Rose

AU - Wille, Michelle

AU - Browning, Glenn F.

AU - Hoye, Bethany

AU - Leong, Lex E.X.

AU - Thompson, Craig

AU - Zulfiqar, Tehzeeb

AU - Ferdinand, Angeline

AU - Hoang, Tuyet

AU - Horan, Kristy

AU - Ingle, Danielle

AU - Webb, Jessica R.

AU - Bull, Rowena

AU - Zahedi, Alireza

AU - Arnott, Alicia

AU - Sintchenko, Vitali

AU - Jennison, Amy V.

AU - Seemann, Torsten

AU - Djordjevic, Steven P.

AU - Howden, Benjamin P.

PY - 2025/1/2

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N2 - 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.

AB - 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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Parameters for one health genomic surveillance of Escherichia coli from Australia

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