Abstract Genes prot6E and sefA are used as targets for detection of Salmonella enterica subsp. enterica serovar Enteritidis (Salmonella ser. Enteritidis). We investigated variations in these genes across 64 different Salmonella ser. Enteritidis strains isolated from egg and chicken samples, then used Whole Genome Sequence (WGS) data to model the structures of their protein products. Isolates were sequenced using Illumina technologies. Based on the resulting phylogenetic tree, our isolates clustered in 2 distinct clades. All isolates carried prot6E and sefA. Comparative genomic analyses indicated two non-synonymous mutations (Glycine → Serine and Valine → Isoleucine) of prot6E in 11 isolates (9 egg samples, 2 chicken samples). However, SWISS-MODEL was unable to clearly model the protein structure of these two mutations. We identified one non-synonymous mutation (Valine → Glutamic Acid) in the sefA gene in 4 isolates from egg samples. The model for the protein structure of this mutant gene was clearly different from that of the other isolates studied herein. Circular maps of plasmid genomes from two PacBio platform-sequenced Salmonella ser. Enteritidis isolates revealed prot6E gene was located on the tail of the plasmid. Based on the biosynthesis of amino acids - Reference pathway in the KEGG pathway Database, the transition of amino acid from sefA Var. was a transversion from essential amino acid to non-essential amino acid, while that of prot6E Var.1 happened between the conditionally non-essential amino acid, and prot6E Var. 2 occurred between essential amino acids. Properties of these mutated amino acids, such as side-chain polarity or charge, may contribute to the occurrence and rate of mutations in prot6E and sefA. These insights can be used to improve detection methods for Salmonella ser. Enteritidis.

中文翻译：

---

沙门氏菌的 prot6E 和 sefA 基因的 DNA 序列和预测的蛋白质结构。肠炎检测

摘要 基因 prot6E 和 sefA 被用作检测沙门氏菌亚种的靶标。肠炎沙门氏菌血清型肠炎沙门氏菌（Salmonella ser. Enteritidis）。我们研究了 64 种不同沙门氏菌系列中这些基因的变异。从鸡蛋和鸡肉样本中分离出肠炎菌株，然后使用全基因组序列 (WGS) 数据对其蛋白质产物的结构进行建模。使用 Illumina 技术对分离物进行测序。基于由此产生的系统发育树，我们的分离株聚集在 2 个不同的进化枝中。所有分离株都携带 prot6E 和 sefA。比较基因组分析表明 prot6E 在 11 个分离株（9 个鸡蛋样本，2 个鸡样本）中有两个非同义突变（甘氨酸→丝氨酸和缬氨酸→异亮氨酸）。然而，SWISS-MODEL 无法清楚地模拟这两个突变的蛋白质结构。我们在来自鸡蛋样品的 4 个分离株的 sefA 基因中发现了一个非同义突变（缬氨酸→谷氨酸）。该突变基因的蛋白质结构模型明显不同于本文研究的其他分离株的模型。来自两个 PacBio 平台测序的沙门氏菌序列的质粒基因组的圆形图谱。肠炎分离株显示 prot6E 基因位于质粒尾部。基于氨基酸的生物合成 - KEGG 通路数据库中的参考通路，氨基酸从 sefA Var 的转变。是必需氨基酸向非必需氨基酸的颠换，而prot6E Var.1的颠换发生在条件非必需氨基酸和prot6E Var之间。2 发生在必需氨基酸之间。这些突变氨基酸的特性，例如侧链极性或电荷，可能有助于 prot6E 和 sefA 突变的发生和发生率。这些见解可用于改进沙门氏菌系列的检测方法。肠炎。