Culture-independent detection of Salmonella enterica in cattle feces via digital PCR without pre-enrichment

Salmonella enterica is a significant cause of foodborne illness globally, and pre-harvest methods for detection are key to preventing downstream product contamination. Culture-based methods of detection are time and labor intensive. Real-time PCR assays are faster and less cumbersome but require a pre-enrichment step that can potentially bias detection results. To address these shortcomings, a digital PCR protocol, using invA and pagC as target genes,​ was developed to detect Salmonella DNA in cattle feces without the need for pre-enrichment. The average Salmonella DNA concentration for all samples was 42.1 ng/µL and was, on average, 15.8 ng/µL lower without pre-enrichment (P < 0.001). Prevalence using invA was 53.3% with and 46.7% without pre-enrichment, whereas prevalence with pagC was 38.3 and 28.3%, respectively. Salmonella prevalence using invA and pagC in parallel was 63.3% with and 57.5% without pre-enrichment, respectively, while prevalence calculated in series was 28.3 and 17.5%, respectively. Gwet’s AC1 coefficients showed that Salmonella prevalence in series without pre-enrichment had the highest agreement with prevalence in culture at 82.5% (probabilistic benchmark interval: 60–80%). Our results indicate that this platform is an effective tool for the detection of Salmonella in cattle feces without the need for pre-enrichment.