Development and Evaluation of the Effectiveness of a PCR Test System for Identifying Salmonella Bacteria in Clinical and Epidemiological Materials

BackgroundReliable detection of Salmonella remains a major challenge for public health surveillance and food safety due to the growing diversity of circulating serovars and the limitations of existing molecular targets. This study aimed to identify an optimal molecular target and develop a TaqMan real-time PCR assay for the detection of Salmonella spp. MethodsBased on the results screening for Salmonella genes suitability as molecular markers, a TaqMan real-time PCR assay targeting the hilA gene was developed and validated. Analytical sensitivity, analytical specificity, and performance on bacterial isolates and artificially contaminated food samples were assessed. ResultsAmong all candidate targets, hilA demonstrated the broadest coverage and was detected in all tested Salmonella isolates, including representatives of rare serological groups, whereas invA conventionally used for this pathogen detection, was absent in a subset of strains. The assay exhibited a limit of detection of 100 bacterial cells/mL and 100 fg/L of genomic DNA. No cross-reactivity was observed with DNA from Shigella flexneri, Shigella sonnei, Yersinia pestis, Y. pseudotuberculosis, Y. enterocolitica, Y. kristensenii, Bacillus anthracis, Vibrio cholerae, or Francisella tularensis. The assay successfully detected Salmonella DNA in all artificially contaminated food samples tested. Evaluation using a collection of 25 bacterial isolates demonstrated positive amplification in all 24 confirmed Salmonella strains, while a strain initially identified by conventional bacteriology as Salmonella but subsequently confirmed by whole-genome sequencing as Proteus mirabilis yielded a negative result. ConclusionsThe hilA gene represents a highly conserved and reliable molecular target for the detection of Salmonella spp. The developed TaqMan real-time PCR assay demonstrated high analytical sensitivity, excellent specificity, and broad serovar coverage, supporting its application in laboratory detection of Salmonella, food safety monitoring, and epidemiological surveillance.