Parameters for one health genomic surveillance of Escherichia coli from Australia
A. Watt, Max L. Cummins, Celeste M. Donato, Wytamma Wirth, Ashleigh F. Porter, Patiyan Andersson, Erica Donner, Australian Pathogen Genomics One Health Working Group, Vitali Sintchenko, Alicia Arnott, Alireza Zahedi, Rowena A. Bull, Jessica R. Webb, Danielle J. Ingle, Kristy Horan, Tuyet Hoang, Angeline Ferdinand, Tehzeeb Zulfiqar, Craig Thompson, Lex E.X. Leong, Bethany J. 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
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.