Quantification of Salmonella in raw poultry using droplet digital PCR with a whole cell, enrichment-free approach

Authors: Armstrong, Cheryl; Chen, Chin Yi; XIE, YICHENG - Bio-Rad Laboratories; ATENCIA, JAVIER - Pathotrak Inc; PIERRE, SOPHIE - Bio-Rad Laboratories; He, Yiping; Lee, Joseph; Dykes, Gretchen; Johnson, Kathleen; FROMENT, BRICE - Bio-Rad Laboratories; MARTINOS, SEAN - Pathotrak Inc; Capobianco Jr, Joseph

Submitted to: Journal of Food Protection
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/20/2025
Publication Date: 3/24/2025
Citation: Armstrong, C.M., Chen, C., Xie, Y., Atencia, J., Pierre, S., He, Y., Lee, J., Dykes, G.E., Johnson, K.M., Froment, B., Martinos, S., Capobianco Jr, J.A. 2025. Quantification of Salmonella in raw poultry using droplet digital PCR with a whole cell, enrichment-free approach. Journal of Food Protection. https://doi.org/10.1016/j.jfp.2025.100498.
DOI: https://doi.org/10.1016/j.jfp.2025.100498

Interpretive Summary: Salmonella contamination in poultry remains a significant public health concern. Traditional detection methods rely on bacterial growth in specialized media, which can inaccurately estimate contamination levels by favoring certain bacterial strains and failing to detect stressed bacteria, resulting in false negatives. This study introduces a new approach that eliminates the need for enrichment. Researchers utilized the Pathotrak system to directly separate and concentrate bacteria from poultry samples, followed by droplet digital PCR (ddPCR) for precise quantification of Salmonella levels, avoiding the errors and biases inherent in traditional methods. This faster, more accurate method provides clearer insights into Salmonella contamination, supporting regulatory compliance and improving food safety. By delivering reliable data, the approach contributes to protecting public health and ensuring safer poultry products for consumers.

Technical Abstract: Salmonella contamination in poultry remains a persistent public health challenge, despite ongoing regulatory efforts to reduce its presence. Traditional culture-based enrichment methods commonly employed for detecting Salmonella have inherent limitations, such as biases in bacterial growth and inaccurate quantification of initial contamination levels. This study introduces an enrichment-free approach for quantifying Salmonella in raw poultry, utilizing the Pathotrak system for bacterial separation and concentration, followed by Droplet Digital PCR (ddPCR) for absolute quantification. Our findings highlight that whole-cell preparations within ddPCR droplets yield significantly higher detection efficiency compared to extracted DNA, likely due to the reduced loss of genetic material during processing. The method was validated by correlating theoretical inoculation levels with ddPCR measurements, resulting in a strong linear relationship (R² = 0.903) and a slope of 0.99, indicating high accuracy. Residuals from the regression model were normally distributed, confirming its validity. This platform offers a robust, rapid, and precise tool for detecting low levels of Salmonella in poultry products without enrichment, making it a more accurate and efficient approach to bacterial quantification in complex food matrices.