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<p>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 <i>Escherichia coli</i> genome sequences from Australia originating from humans (<i>n</i> = 2996), wild animals (<i>n</i> = 870), livestock (<i>n</i> = 649), companion animals (<i>n</i> = 375), environmental sources (<i>n</i> = 292) and food (<i>n</i> = 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.</p>

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Parameters for one health genomic surveillance of Escherichia coli from Australia

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年1月2日

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  • Anne E. Watt,
  • Max L. Cummins,
  • Celeste M. Donato,
  • Wytamma Wirth,
  • Ashleigh F. Porter,
  • Patiyan Andersson,
  • Erica Donner,
  • 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,
  • Amy V. Jennison,
  • Torsten Seemann,
  • Steven P. Djordjevic,
  • Benjamin P. Howden

摘要

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.