Parameters for one health genomic surveillance of Escherichia coli from Australia
Abstract
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.
Article Details
Authors (36)
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
Public and Environmental Health, Pathology Queensland, Queensland Health, Brisbane, Australia
Torsten Seemann
Steven P. Djordjevic
Benjamin P. Howden