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

FIGURE 5.

FIGURE 5

Rooted, time-scaled maximum clade credibility (MCC) phylogeny constructed using core SNPs identified among 15 Salmonella Anatum 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 and absence of plasmid replicons (detected using ABRicate/PlasmidFinder and minimum nucleotide identity and coverage thresholds of 80 and 60%, respectively; blue); (iii) presence and absence 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 strict 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 median 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.