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. 2021 Oct 18;12:763669. doi: 10.3389/fmicb.2021.763669

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Copyright © 2021 Carroll, Buehler, Gaballa, Siler, Cummings, Cheng and Wiedmann.

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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Rooted, time-scaled maximum clade credibility (MCC) phylogeny constructed using core SNPs identified among 36 Salmonella Kentucky genomes isolated from subclinical bovine sources and the surrounding bovine farm environment. Tip label colors denote the ID of the farm from which each strain was isolated. Branch labels denote posterior probabilities of branch support. Time in years is plotted along the X-axis, and branch lengths are reported in years. The heatmap to the right of the phylogeny denotes (i) the susceptible-intermediate-resistant (SIR) classification of each isolate for each of 15 antimicrobials (obtained using phenotypic testing and NARMS breakpoints; orange); (ii) presence of plasmid replicons (detected using ABRicate/PlasmidFinder and minimum nucleotide identity and coverage thresholds of 80 and 60%, respectively; blue); (iii) presence of antimicrobial resistance (AMR) and stress response genes (identified using AMRFinderPlus and default parameters; green). Core SNPs were identified using Snippy. The phylogeny was constructed using the results of ten independent runs using a relaxed lognormal clock model, the Standard_TVMef nucleotide substitution model, and the Coalescent Bayesian Skyline population model implemented in BEAST version 2.5.1, with 10% burn-in applied to each run. LogCombiner-2 was used to combine BEAST 2 log files, and TreeAnnotator-2 was used to construct the phylogeny using common ancestor node heights. Abbreviations for the 15 antimicrobials are: AMK, amikacin; AMC, amoxicillin-clavulanic acid; AMP, ampicillin; FOX, cefoxitin; TIO, ceftiofur; CRO, ceftriaxone; CHL, chloramphenicol; CIP, ciprofloxacin; GEN, gentamicin; KAN, kanamycin; NAL, nalidixic acid; STR, streptomycin; SXT, sulfamethoxazole-trimethoprim; SUL, sulfisoxazole; TET, tetracycline.