Rapid and highly sensitive detection of Salmonella using specific aptamers and nucleic acid enrichment technology
Main Article Content
Keywords
Salmonella, aptamer, Salmonella detection, InvA gene, food safety
Abstract
Salmonella is a significant pathogen that is responsible for foodborne diseases, and the rapid detection of this pathogen is crucial for ensuring food safety. Traditional detection methods are often time-consuming due to the requirement of bacterial enrichment. To address these challenges, this study developed a novel Salmonella enrichment technique utilizing carboxylated magnetic beads and ultrafiltration membranes, and designed and synthesized a specific nucleic acid aptamer targeting the invA gene of Salmonella. By integrating nucleic acid enrichment technology with a specific aptamer, we achieved quantitative detection of low-concentration Salmonella using fluorescence spectrometry without the need for conventional enrichment steps. This method demonstrated a detection limit as low as 1 colony-forming units (CFU)/mL, a linear range from 100 CFU/mL to 103 CFU/mL, and a correlation coefficient of R2 = 0.9864. Compared with conventional methods, this approach exhibited 2.4-fold greater sensitivity accompanied by significant signal amplification. In terms of stability, when the concentration of unknown Salmonella was measured via plate counting methods, a value of 5.76 × 102 CFU/mL was obtained, comparing well with our method, which yielded a concentration of 5.49 × 102 CFU/mL, indicating good performance. Additionally, this method exhibited high specificity, which allowed for the accurate detection of Salmonella even in the presence of multiple interfering bacteria, including Staphylococcus aureus, Escherichia coli, Listeria monocytogenes, and Shigella spp. This novel technique overcomes the limitations of traditional enrichment-based methods, thereby offering an efficient and rapid approach for Salmonella detection in food, with broad potential for practical applications.
References
Aubin, J.E., 1979. Autofluorescence of viable cultured mammalian cells. Journal of Histochemistry and Cytochemistry 27(1): 36–43. 10.1177/27.1.220325
Bai, M., Wang, Y., Zhang, C., et al., 2023. Nanobody-based immunomagnetic separation platform for rapid isolation and detection of Salmonella enteritidis in food samples. Food Chemistry 424: 136416. 10.1016/j.foodchem.2023.136416
Baker, A., Cumberland, S.A., Bradley, C., et al., 2015. To what extent can portable fluorescence spectroscopy be used in the real-time assessment of microbial water quality? Science of The Total Environment 532: 14–19. 10.1016/j.scitotenv.2015.05.114
Besser, J.M., 2018. Salmonella epidemiology: A whirlwind of change. Food Microbiology 71: 55–59. 10.1016/j.fm.2017.08.018
Billah, M.M., Rahman, M.S., 2024) Salmonella in the environment: A review on ecology, antimicrobial resistance, seafood contaminations, and human health implications. Journal of Hazardous Materials Advances 13: 100407. 10.1016/j.hazadv.2024.100407
Buehler, A.J., Wiedmann, M., Kassaify, Z., et al., 2019. Evaluation of invA diversity among Salmonella species suggests why some commercially available rapid detection kits may fail to detect multiple Salmonella subspecies and species. Journal of Food Protection 82(4): 710–717. 10.4315/0362-028X.JFP-18-525
Bülte, M., Jakob, P., 1995. The use of a PCR-generated invA probe for the detection of Salmonella spp. in artificially and naturally contaminated foods. International Journal of Food Microbiology 26(3): 335–344. 10.1016/0168-1605(94)00139-W
Chavan, N., Dharmaraj, D., Sarap, S., et al., 2022. Magnetic nanoparticles–A new era in nanotechnology. Journal of Drug Delivery Science and Technology 77: 103899. 10.1016/j.jddst.2022.103899
Cuypers, W.L., Meysman, P., Weill, F.-X., et al., 2023. A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia. Nature Communications, 14(1): 3517. 10.1038/s41467-023-38902-x
Du, R., Yang, D., Yin, X., 2022. Rapid detection of three common bacteria based on fluorescence spectroscopy. Sensors 22(3).
Duan, N., Shen, M., Qi, S., et al., 2020. A SERS aptasensor for simultaneous multiple pathogens detection using gold decorated PDMS substrate. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 230: 118103. 10.1016/j.saa.2020.118103
Duan, N., Wu, S., Zhu, C., et al., 2012. Dual-color upconversion fluorescence and aptamer-functionalized magnetic nanoparticles-based bioassay for the simultaneous detection of Salmonella Typhimurium and Staphylococcus aureus. Analytica Chimica Acta 723: 1–6. 10.1016/j.aca.2012.02.011
Fuentes-García J.A., Diaz-Cano, A.I., Guillen-Cervantes, A., et al., 2018. Magnetic domain interactions of Fe3O4 nanoparticles embedded in a SiO2 matrix. Scientific Reports 8(1): 5096. 10.1038/s41598-018-23460-w
Gautam, A., 2022. Magnetic bead-based nucleic acid isolation. In A. Gautam (Ed.), DNA and RNA Isolation Techniques for Non-Experts (pp. 111–117). Springer International Publishing. 10.1007/978-3-030-94230-4_15
Gonçalves-Tenório, A., Silva, B.N., Rodrigues, V., et al., 2018. Prevalence of pathogens in poultry meat: A meta-analysis of European oublished surveys. Foods 7(5). 10.3390/foods7050069
Gong, L., Wang, K., Liang, J., et al., 2023. Enhanced sensitivity and accuracy via gold nanoparticles based multi-line lateral flow immunoassay strip for Salmonella typhimurium detection in milk and orange juice. Talanta 265: 124929. 10.1016/j.talanta.2023.124929
He, D., Wu, Z., Cui, B., et al., 2019. Building a fluorescent aptasensor based on exonuclease-assisted target recycling strategy for one-step detection of T-2 toxin. Food Analytical Methods 12(2): 625–632. 10.1007/s12161-018-1392-x
He, Y., Yuan, J., Khan, I. M., et al., 2023. Research progress of aptasensor technology in the detection of foodborne pathogens. Food Control 153: 109891. 10.1016/j.foodcont.2023.109891
Jin, N., Xue, L., Ding, Y., et al., 2023. A microfluidic biosensor based on finger-driven mixing and nuclear track membrane filtration for fast and sensitive detection of Salmonella. Biosensors and Bioelectronics 220: 114844. 10.1016/j.bios.2022.114844
Khalid, A., Ahmed, R.M., Taha, M., et al., 2023. Fe3O4 nanoparticles and Fe3O4 @SiO2 core-shell: Synthesize, structural, morphological, linear, and nonlinear optical properties. Journal of Alloys and Compounds 947: 169639. 10.1016/j.jallcom.2023.169639
Khamlamoon, A., Nawattanapaiboon, K., Srikhirin, T., 2023. A magnetic nanoparticles-based method for nucleic acid extraction from specimen collection. Materials Today: Proceedings. 10.1016/j.matpr.2023.05.542
Lee, W., Hwang, B.H., 2020. Plasmonic biosensor controlled by DNAzyme for on-site genetic detection of pathogens. Biotechnology Journal 15(5): e1900329. 10.1002/biot.201900329
Li, L., Zeng, Y., Yang, G., et al., 2025. Aptamer-functionalized magnetic blade spray coupled with a nucleic acid dye-based mass tag strategy for miniature mass spectrometry analysis of endoglin. Talanta 283: 127142. 10.1016/j.talanta.2024.127142
Li, P., Li, M., Zhang, F., et al., 2021. High-efficient nucleic acid separation from animal tissue samples via surface modified magnetic nanoparticles. Separation and Purification Technology 262: 118348. 10.1016/j.seppur.2021.118348
Lin, L., Zheng, Q., Lin, J., et al., 2020. Immuno-and nucleic acid-based current technique for Salmonella detection in food. European Food Research and Technology 246(3): 373–395. 10.1007/s00217-019-03423-9
Liu, L., Zhao, G., Li, X., et al., 2022. Development of rapid and easy detection of Salmonella in food matrics using RPA-CRISPR/Cas12a method. LWT (Food Science and Technology) 162: 113443. 10.1016/j.lwt.2022.113443
Liu, Z., Lei, M., Zeng, W., et al., 2023. Synthesis of magnetic Fe3O4@SiO2-(-NH2/-COOH) nanoparticles and their application for the removal of heavy metals from wastewater. Ceramics International 49(12): 20470–20479. 10.1016/j.ceramint.2023.03.177
Materón, E.M., Miyazaki, C.M., Carr, O., et al., 2021. Magnetic nanoparticles in biomedical applications: A review. Applied Surface Science Advances 6: 100163. 10.1016/j.apsadv.2021.100163
Montesinos-Cruz, V., Somerville, G.A., 2024. Shining a light on spectrophotometry in bacteriology. Antibiotics 13(12).
Myers, J.A., Curtis, B.S., Curtis, W.R., 2013. Improving accuracy of cell and chromophore concentration measurements using optical density. BioMed Central Biophysics 6(1): 4. 10.1186/2046-1682-6-4
Nakar, A., Schmilovitch, Z.E., Vaizel-Ohayon, D., et al., 2020. Quantification of bacteria in water using PLS analysis of emission spectra of fluorescence and excitation-emission matrices. Water Research 169: 115197. 10.1016/j.watres.2019.115197
Pan, Y.-L., 2015. Detection and characterization of biological and other organic-carbon aerosol particles in atmosphere using fluorescence. Journal of Quantitative Spectroscopy and Radiative Transfer 150: 12–35. 10.1016/j.jqsrt.2014.06.007
Paniel, N., Noguer, T., 2019. Detection of Salmonella in food matrices, from conventional methods to recent aptamer-sensing technologies. Foods 8(9): 371. https://www.mdpi.com/2304-8158/8/9/371
Pgi, D., Rathnayaka, R.M.U.S.K., 2018. Fluorescence in situ hybridization (FISH) in food pathogen detection. International Journal of Molecular Biology.
Pui, C.F., Wong, W.C., Chai, L.C., et al., 2011. Simultaneous detection of Salmonella spp., Salmonella Typhi and Salmonella Typhimurium in sliced fruits using multiplex PCR. Food Control 22(2): 337–342. 10.1016/j.foodcont.2010.05.021
Qiao, Z., Xue, L., Sun, M., et al., 2023. Highly sensitive detection of Salmonella based on dual-functional HCR-mediated multivalent aptamer and amplification-free CRISPR/Cas12a system. Analytica Chimica Acta 1284: 341998. 10.1016/j.aca.2023.341998
Qiu, S., Liu, B., Leng, Y., et al., 2023. A label-free fiber ring laser biosensor for ultrahigh sensitivity detection of Salmonella Typhimurium. Biosensors and Bioelectronics 234: 115337. 10.1016/j.bios.2023.115337
Ranjbar, M., Nedaeinia, R., Goli, M., et al., 2022. Evaluation of the thermal processes on changing the phenotypic characteristics of Escherichia coli strains from ice cream compared to non-pasteurized milk. Fermentation 8(12): 730. https://www.mdpi.com/2311-5637/8/12/730
Shin, W.R., Sekhon, S.S., Kim, S.G., et al., 2018. Aptamer-based pathogen monitoring for Salmonella enterica ser. Typhimurium. Journal of Biomedical Nanotechnology 14(11): 1992–2002. 10.1166/jbn.2018.2634
Simões, J., Dong, T., 2018. Continuous and real-time detection of drinking-water pathogens with a low-cost fluorescent optofluidic sensor. Sensors 18(7).
Stevenson, K., McVey, A.F., Clark, I.B.N., et al., 2016. General calibration of microbial growth in microplate readers. Scientific Reports 6(1): 38828. 10.1038/srep38828
Su, Y., Chu, H., Tian, J., et al., 2021. Insight into the nanomaterials enhancement mechanism of nucleic acid amplification reactions. Trends in Analytical Chemistry 137: 116221. 10.1016/j.trac.2021.116221
Tas, Z., Ciftci, F., Icoz, K., et al., 2025. Emerging biomedical applications of surface-enhanced Raman spectroscopy integrated with artificial intelligence and microfluidic technologies. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 339: 126285. 10.1016/j.saa.2025.126285
Wang, M., Zhang, Y., Tian, F., et al., 2021. Overview of rapid detection methods for Salmonella in foods: Progress and challenges. Foods 10(10): 2402. https://www.mdpi.com/2304-8158/10/10/2402
Wei, S., Su, Z., Bu, X., et al., 2022. On-site colorimetric detection of Salmonella typhimurium.npj (Nature Partner Journals) Science of Food 6(1): 48. 10.1038/s41538-022-00164-0
Wei, Y., Han, B., Hu, X., et al., 2012. Synthesis of Fe3O4 nanoparticles and their magnetic properties. Procedia Engineering 27: 632–637. 10.1016/j.proeng.2011.12.498
Xie, M., Chen, T., Xin, X., et al., 2022. Multiplex detection of foodborne pathogens by real-time loop-mediated isothermal amplification on a digital microfluidic chip. Food Control 136: 108824. 10.1016/j.foodcont.2022.108824
Yue, H., Shin, J.M., Tegafaw, T., et al., 2020. Magnetic separation of nucleic acids from various biological samples using silica-coated iron oxide nanobeads. Journal of Nanoparticle Research 22(12): 366. 10.1007/s11051-020-05101-4
Zha, L., Garrett, S., Sun, J., 2019. Salmonella infection in chronic inflammation and gastrointestinal cancer. Diseases 7(1). 10.3390/diseases7010028
Zhang, J., Zhou, M., Li, X., et al., 2023. Recent advances of fluorescent sensors for bacteria detection: A review. Talanta 254: 124133. 10.1016/j.talanta.2022.124133
Zhang, L., Jiang, H., Zhu, Z., et al., 2022. Integrating CRISPR/Cas within isothermal amplification for point-of-care assay of nucleic acid. Talanta 243: 123388. 10.1016/j.talanta.2022.123388
Zhao, F., Yan, H., Zheng, Y., et al., 2023. Joint concanavalin A-aptamer enabled dual recognition for anti-interference visual detection of Salmonella typhimurium in complex food matrices. Food Chemistry 426: 136581. 10.1016/j.foodchem.2023.136581
Zhao, L., Li, L., Liu, Z., et al., 2024. Aptamer functionalized magnetic hydrophobic polymer with synergetic effect for enhanced adsorption of alternariol from wheat. Food Chemistry 435: 137556. 10.1016/j.foodchem.2023.137556
Zhou, C., Zhao, Y., Guo, B., et al., 2024. Establishment of a simple, sensitive, and specific Salmonella detection method based on recombinase-aided amplification combined with dsDNA-specific nucleases. Foods 13(9): 1380. https://www.mdpi.com/2304-8158/13/9/1380
