Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, USA.
Institute for Biosecurity and Microbial Forensics, Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74074, USA.
Sci Rep. 2021 Oct 22;11(1):20887. doi: 10.1038/s41598-021-00224-7.
Rapid and sensitive detection of Salmonella is a critical step in routine food quality control, outbreak investigation, and food recalls. Although various genes have been the targets in the design of rapid molecular detection methods for Salmonella, there is limited information on the diversity of these target genes at the level of DNA sequence and the encoded protein structures. In this study, we investigated the diversity of ten target genes (invA, fimA, phoP, spvC, and agfA; ttrRSBCA operon including 5 genes) commonly used in the detection and identification of Salmonella. To this end, we performed whole genome sequencing of 143 isolates of Salmonella serotypes (Enteritidis, Typhimurium, and Heidelberg) obtained from poultry (eggs and chicken). Phylogenetic analysis showed that Salmonella ser. Typhimurium was more diverse than either Enteritidis or Heidelberg. Forty-five non-synonymous mutations were identified in the target genes from the 143 isolates, with the two most common mutations as T ↔ C (15 times) and A ↔ G (13 times). The gene spvC was primarily present in Salmonella ser. Enteritidis isolates and absent from Heidelberg isolates, whereas ttrR was more conserved (0 non-synonymous mutations) than ttrS, ttrB, ttrC, and ttrA (7, 2, 2, and 7 non-synonymous mutations, respectively). Notably, we found one non-synonymous mutation (fimA-Mut.6) across all Salmonella ser. Enteritidis and Salmonella ser. Heidelberg, C → T (496 nt postion), resulting in the change at AA 166 position, Glutamine (Q) → Stop condon (TAG), suggesting that the fimA gene has questionable sites as a target for detection. Using Phyre and SWISS-MODEL software, we predicted the structures of the proteins encoded by some of the target genes, illustrating the positions of these non-synonymous mutations that mainly located on the α-helix and β-sheet which are key elements for maintaining the conformation of proteins. These results will facilitate the development of sensitive molecular detection methods for Salmonella.
快速灵敏地检测沙门氏菌是常规食品质量控制、疫情调查和食品召回的关键步骤。尽管各种基因已被用于设计沙门氏菌快速分子检测方法，但有关这些靶基因在 DNA 序列和编码蛋白结构水平上的多样性的信息有限。在这项研究中，我们研究了十种常用的检测和鉴定沙门氏菌的靶基因（invA、fimA、phoP、spvC 和 agfA；包括 5 个基因的 ttrRSBCA 操纵子）的多样性。为此，我们对从家禽（鸡蛋和鸡肉）中获得的 143 株沙门氏菌血清型（肠炎、鼠伤寒和海德堡）进行了全基因组测序。系统发育分析表明，鼠伤寒沙门氏菌比肠炎或海德堡沙门氏菌更为多样化。在 143 个分离株的靶基因中鉴定出 45 个非同义突变，最常见的两种突变是 T ⇔ C（15 次）和 A ⇔ G（13 次）。基因 spvC 主要存在于肠炎沙门氏菌分离株中，不存在于海德堡沙门氏菌分离株中，而 ttrR 比 ttrS、ttrB、ttrC 和 ttrA 更为保守（0 个非同义突变）（分别为 7、2、2 和 7 个非同义突变）。值得注意的是，我们在所有肠炎沙门氏菌和海德堡沙门氏菌血清型中发现了一个非同义突变（fimA-Mut.6），C → T（496 nt 位置），导致 AA 166 位置的变化，谷氨酰胺（Q）→终止密码子（TAG），表明 fimA 基因作为检测靶点存在可疑位点。使用 Phyre 和 SWISS-MODEL 软件，我们预测了一些靶基因编码蛋白的结构，说明了这些非同义突变的位置，这些突变主要位于维持蛋白质构象的关键元件α-螺旋和β-折叠上。这些结果将有助于开发灵敏的沙门氏菌分子检测方法。
