Automatic detection of Salmonella enterica in sprout irrigation water using a nucleic acid sensor

A nucleic acid sensor capable of automated sample and reagent loading, real-time PCR, automated detection, and sample line cleaning was tested. Real-time PCR reactions were performed with Salmonella enterica in autoclaved and spent alfalfa sprout irrigation water. S. enterica boiled cells were detected over a range of approximately 104 to 108 CFU/reaction (rxn). It was possible to generate enough PCR product to visualize a band on a gel at the expected size over approximately five orders of magnitude from 3.2 × 103 to 108 CFU/rxn. Automated detection experiments yielded correct identification of 9/9 positive control reactions over a range of 104 to 108 CFU/rxn, correctly identified a negative control reaction, and a sample of 3.2 × 103 CFU/rxn was incorrectly identified as negative. Primer dimers were not seen in positive or negative control reactions with sprout irrigation water, suggesting that it may be possible to improve the detection limit simply by increasing the number of thermal cycles or by lowering the annealing temperature. The system required no interpretation of real-time PCR data by the operator. The entire process of loading, running the PCR, automated data interpretation, and sample line cleaning was completed in under 2 h and 20 min, significantly faster than it would take to ship a sample and have it tested by an independent laboratory.