Detection of Salmonella from chicken rinsate with visible/near-infrared hyperspectral microscope imaging compared against RT-PCR

Salmonella is an organism of importance to the poultry industry with increasingly stringent government regulatory standards. Real-time polymerase chain reaction (RT-PCR) and plating procedures on nutrient enriched growth media have been the standard detection methods of Salmonella from broiler chicken carcasses for years. These methods are proven, but offer disadvantages in the amount of time or reoccurring sample cost. Here, we propose the use of a hyperspectral microscope imaging system (HMI) for comparison to standard detection methods. Broiler chicken carcasses were rinsed and plated on Salmonella selective agar. Colonies from plates were picked and RT-PCR was used as a confirmation test to verify plating results, while HMI was collected from the same colonies. Spectral signatures of cells were extracted between 450 and 800 nm from HMI collected with 100x objective. A quadratic discriminant analysis (QDA) was used to classify cells as either Salmonella positive or negative (n = 341). Spectra preprocessing minimized the influence of cellular shape on the spectra, increasing the initial classification accuracy of 81.8-98.5%, yielding a sensitivity of 1.0, and a specificity of 0.963. Results showed the potential as an initial investigation of HMI as a microbial confirmation tool, compared to RT-PCR.