The presence of pathogenic bacteria is a major health risk factor in food 
samples and the commercial food supply chain is susceptible to bacterial 
contamination. Thus, rapid and sensitive identification methods are in demand 
for the food industry. Quantitative polymerase chain reaction (PCR) is one of 
the reliable specific methods with reasonably fast assay times. However, many 
constituents in food samples interfere with PCR, resulting in false results and 
thus hindering the usability of the method. Therefore, we aimed to develop an 
aptamer-based magnetic separation system as a sample preparation method for 
subsequent identification and quantification of the contaminant bacteria by 
real-time PCR. To achieve this goal, magnetic beads were prepared via suspension 
polymerization and grafted with glycidylmethacrylate (GMA) brushes that were 
modified into high quantities of amino groups. The magnetic beads were decorated 
with two different aptamer sequences binding specifically to Escherichia coli or 
Salmonella typhimurium. The results showed that even 1.0% milk inhibited PCR, 
but our magnetic affinity system capture of bacteria from 100% milk samples 
allowed accurate determination of bacterial contamination at less than 2.0 h 
with limit of detection around 100 CFU/mL for both bacteria in spiked-milk 
samples.