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. 2023 Nov 18;12(11):1637. doi: 10.3390/antibiotics12111637

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© 2023 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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(A) Rarefaction curves for core (3436) and pan-genes (8384) of the 78 isolates. The x-axis represents the number of genomes. (B) Pie chart showing the pan-genome composition of the isolates. Core genes are present in 100% of isolates, with soft-core genes in 95–99%, shell genes in 15–99%, and cloud genes in <15% of isolates. (C) Whole-genome core SNP-based phylogeny of Salmonella enterica isolates (n = 78), with samples (tips) colored by serotype. Each isolate is color-coded differently in five different circles based on the isolation year, isolation source, farm type, MLST, and serogroup.