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. 2021 Oct 14;12:716182. doi: 10.3389/fmicb.2021.716182

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Copyright © 2021 Truccollo, Whyte, Burgess and Bolton.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Maximum likelihood (ML) tree of the core genome alignments of isolates from Farm 1 and Farm 2 with 500 bootstraps. Branch width corresponds to bootstrap values, where wider branches correspond to higher bootstrap values that ranged from 66 to 100 between MLST types. Genomes are named to indicate farm (a=1 and c=2), broiler age (days), sample type (f=faecal and c=caecal), sample number (1 to 10) and colony number (1 to 5), i.e. ‘a21f62’.