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The authors report on a surface-enhanced Raman scattering (SERS) nanoprobe for the specific detection of Escherichia coli O157:H7 (E. coli O157:H7). Gold nanoparticles (AuNPs) were coated with a thick silica shell, and the Raman reporter (4,4'-dipyridyl) was embedded between gold nanoparticle and silica shell. This technique prevents any external effects on the AuNPs from the environment and avoids any interaction between the Raman reporter and possible impurities. Compared to the SERS nanoprobe of the conventional AuNP/AgNP type, the present nanoprobe can be applied in complex biochemical circumstances without aggregation because of its excellent stability. The SERS nanoprobeis stable for up to 50 h. The probe was applied to the SERS detection of E. coli O157:H7 by exploiting the Raman band peaking at 1612 cm of 4,4'-dipyridyl (DP). The limit of detection is as low as 10 CFU·mL. The technique was successfully employed to the detection of E. coli O157:H7 in real samples, achieving recoveries between 95.5 and 114.8%. Graphical abstract A novel surface-enhanced Raman scattering (SERS) nanoprobe based on the silica encapsulated gold nanoparticles (SEGNs) combining with the functionalized magnetic nanoparticles (MNPs), detecting E. coli O157:H7 with high sensitivity and specificity.