摘要：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
2 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.
