DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. Enteritidis detection

Hu, Lijun; Stones, Robert; Brown, Eric W.; Allard, Marc W.; M., Li; Zhang, Guodong

doi:10.1016/j.foodcont.2018.09.018

Cited by 3 publications

(2 citation statements)

References 38 publications

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“…We selected 143 Salmonella isolates from chicken/duck eggs (including raw egg whites, raw egg yolks, raw whole eggs, pecked eggs, egg slurry, egg salad, frozen liquid egg, cooked quail eggs, salted duck eggs, duck egg yolks, frozen salted duck yolks) and chicken (chicken, chicken jerky, chicken breast): 64 Salmonella ser. Enteritidis isolates were collected from 1995 to 2016 (Supplementary Table 1 ) as described previously 57 ; 40 Salmonella ser. Typhimurium isolates were collected from 2001 to 2010 (Supplementary Table 2 ); and 39 Salmonella ser.…”

Section: Methodsmentioning

confidence: 99%

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

Cao

Brown

et al. 2021

Sci Rep

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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.

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Section: Methodsmentioning

confidence: 99%

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

Cao

Brown

et al. 2021

Sci Rep

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“…To validate the effectiveness of MRTFP, we designed and integrated strand exchange 3WJ structures into a four-angle probe (FP) and a hexagonal probe (HP; Scheme ) for the detection of two or three target genes, including the general Salmonella invA gene, the specific Prot6e gene of Salmonella enteritidis (SE), and the specific MDH gene of Salmonella typhimurium (ST). , In Scheme B, the FP is formed by concatenating the strand exchange 3WJ structures designed for invA and Prot6e . The presence of ROX fluorescence output indicates the Salmonella infection, while the simultaneous presence of ROX and FAM signals suggests the coexistence of Salmonella and SE.…”

Section: Introductionmentioning

confidence: 99%

Advancing Multiple Detection in RT-LAMP with a Specific Probe Assembled from Plural Three-Way-Junction Structures

Sun,

Zhang,

et al. 2023

Anal. Chem.

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The timely detection of diseases and the accurate identification of pathogens require the development of efficient and reliable diagnostic methods. In this study, we have developed a novel specific multivariate probe termed MRTFP (multivariate real-time fluorescent probe) by assembling strand exchange threeway-junction (3WJ) structures. The 3WJ structures were incorporated into a four-angle probe (FP) and a hexagonal probe (HP), to target the multivariate genes of Salmonella. The FP and HP enable single-step and multiplexed detection in RT-LAMP (real-time loop-mediated isothermal amplification) with exceptional sensitivity and specificity. Encouragingly, real food samples contaminated with Salmonella (Salmonella enteritidis and Salmonella typhimurium) can be readily identified and distinguished with a minimum detectable concentration (MDC) of 10 3 CFU/mL without the need for further culture. The introduction of MRTFP allows for simultaneous detection of dual or three targets in a single tube for LAMP, thereby improving detection efficiency. The MRTFP simplifies the design of robust multivariate probes, exhibits excellent stability, and avoids interference from multiple probe units, offering significant potential for the development of specific probes for efficient and accurate disease detection and pathogen identification.

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Validation of isolation and polymerase chain reaction of Salmonella species and Escherichia coli bacteria for developing a prototype kit for detecting foodborne pathogens diseases

Nurjayadi,

Maulana,

Pramudiyasih

et al. 2023

International Conference on Applied Computational Intelligence and Analytics (Acia-2022)

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DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. Enteritidis detection

Cited by 3 publications

References 38 publications

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

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

Advancing Multiple Detection in RT-LAMP with a Specific Probe Assembled from Plural Three-Way-Junction Structures

Validation of isolation and polymerase chain reaction of Salmonella species and Escherichia coli bacteria for developing a prototype kit for detecting foodborne pathogens diseases

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