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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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Results of non-metric multidimensional scaling (NMDS) performed using the presence and absence of (A) pan-genome elements (n = 4,102; identified using Roary), and (B) antimicrobial resistance (AMR) and stress response genes (n = 28; detected using AMRFinderPlus) among 128 bovine-associated Salmonella isolates, plotted in two dimensions. Points represent isolates, while shaded regions and convex hulls correspond to isolate (1) serotypes (ANAT, Anatum; CERO, Cerro; KENT, Kentucky; MELA, Meleagridis; NEWP, Newport; TCOP, Typhimurium Copenhagen; TYPH, Typhimurium), (2) farm, and (3) source (BOV, bovine; ENV, bovine farm environment). For all plots, a Jaccard distance metric was used. For AMR/stress response genes (B), gene names/scores are plotted in dark gray text.