Whole genome sequencing and protein structure analyses of target genes for the detection of Salmonella

Abstract

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 Phyre2 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.

Antimicrobial resistance genes, virulence markers and prophage sequences in Salmonella enterica serovar Enteritidis isolated in Tunisia using whole genome sequencing

“…These sequences can carry virulence genes, toxins and antimicrobial resistance genes ( Mottawea et al., 2018 ; Wahl et al., 2019 ). Previous studies reported that Salmonella enterica are characterized by high degree of variability of prophage profiles ( Gymoese et al., 2019 ; Hu et al., 2021 ). This is consistent with our results that prophage profiles are variable among S. Enteritidis.…”

“…In our study, all tested isolates were positive for pho P and pho Q genes which are essential for the regulation of type III secretion systems. Pho Q is the transmembrane sensor histidine kinase of the bacterial and pho P is cytoplasmic regulatory protein ( Hu et al., 2021 ).…”

“…During the last two decades, whole-genome sequencing (WGS) has become the affordable tool that has the capacity to revolutionize different domains including genetics, microbiology, epidemiology and public health surveillance. The evolution of the current WGS technologies allowed to rapidly increase the realization of bacterial genome sequencing projects ( Hu et al., 2021 ; Punina et al., 2015 ) . Since the entire genome is readily available for analysis, WGS has the capacity to replace traditional methods for characterizations such as serotyping, virulotyping and antimicrobial resistance which can easily be predicted from the genome.…”

“…These genes are located on various elements of the genome including Salmonella pathogenicity islands (SPIs) ( Gupta et al., 2019 ; Zhao et al., 2020 ). Different strains of S. Enteritidis have mobile genetic elements such as plasmids, prophages and transposon that can carry virulence or antimicrobial resistance genes ( Hu et al., 2021 ).…”

Genomic Characterization of Cronobacter spp. and Salmonella spp. Strains Isolated From Powdered Infant Formula in Chile

“…The SPI-2 gene encodes genes such as ssaR and ssrA that promote survival and replication within the macrophages and their dissemination in the host ( Barilli et al, 2018 ). The spvC gene enables the survival and rapid growth of Salmonella in the host ( Hu et al, 2021 ), while the spvB gene is known as an intracellular toxin that encodes an enzyme that ADP-ribosylates actin and destabilizes the cytoskeleton of eukaryotic cells ( Lesnick et al, 2001 ).…”