A comparative study of invA and ttrC-based real-time PCR assays for the genus-specific molecular identification of Salmonella enterica

Aims: The reliability of the invA gene, a gold-standard target for PCR-based diagnosis of Salmonella, has been questioned due to false-negative results reported by some authors. Thus, evaluation of the inclusivity features of invA and ttrC-based real-time PCR assays and comparison of the specificity performance of both targets for the genus-specific molecular identification of Salmonella enterica has been carried out on a wide strain panel. Methods and results: Genus-specific identification using two real-time PCR-based assays targeting invA and ttrC gene fragments was performed on Salmonella strains (n = 421) of 50 different serovars isolated in Central Italy between 2002 and 2023 from: food and veterinary samples during poultry chain surveillance, human clinical samples, and surface water samples collected from rivers. A 99% inclusivity was recorded for both the ttrC-based and the invA-based real-time PCR assays, with perfect agreement (Cohen's Kappa = 0.991) with the ISO/TR 6579-3:2014 and with each other. Conclusions: Our findings suggest that both the ttrC-based and invA-based PCR assays are equally reliable for the genus-specific identification of a wide Salmonella enterica strain panel of epidemiological relevance and are in complete agreement. However, considering the genomic variability in some Salmonella serovars, a dual-target PCR approach is recommended to potentially improve diagnostic accuracy.