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Salmonella enterica serovar Indiana (S. Indiana) is a newly emerging pathogen with high levels of drug resistance. It has become one of the most common Salmonella serovars in China with a worldwide distribution, posing significant public health concerns. Detection of S. Indiana by traditional bacteriological methods is time-consuming and laborious, which prevents timely surveillance and effective control of the pathogen. In this study, comparative genomics was used to identify an A7P63_13850 gene that is uniquely present in S. Indiana, but not in other Salmonella serovars or any non-Salmonella bacteria. Then, a polymerase chain reaction (PCR) assay targeting this serovar-specific gene was established for specific detection of S. Indiana. The detection limit of this method is 10 pg per reaction for bacterial genomic DNA, being equivalent to 100 colony-forming units (CFU) per reaction. The established PCR amplifies all S. Indiana strains (n = 56), but none of other Salmonella serovars (n = 146) and non-Salmonella species (n = 14). The assay established in this study was also used to detect clinical samples from poultry, showed a positivity of 14.7% (23/156) for S. Indiana, which were verified by bacteriological methods. The highly sensitive and serovar-specific PCR for S. Indiana established in this study is suitable and convenient for detection of S. Indiana which aids in surveillance and control of the pathogen.

Salmonella spp. pose a threat to both human and animal health, with more than 2600 serovars having been reported to date. Salmonella serovars are usually identified by slide agglutination tests, which are labor intensive and time consuming. In an attempt to develop a more rapid screening method for the major poultry Salmonella serovars, we developed a loop-mediated isothermal amplification (LAMP) assay, which directly detected the sefA gene, a fimbrial operon gene existing in several specific serovars of Salmonella enterica including the major poultry serovars, namely Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) and Salmonella enterica serovar Gallinarum (Salmonella Gallinarum). With the 177 bacterial strains we tested, positive reactions were only observed with 85 strains of serovar Salmonella Enteritidis and Salmonella Gallinarum. The detection limit of the LAMP assay was 4 CFU/reaction with genomic DNAs of Salmonella Enteritidis (ATCC 13076) from pure culture and 400 CFU/ reaction with DNA extracted from spiked chicken feces. The LAMP assay was more sensitive than conventional culture, especially without enrichment, in detecting Salmonella Enteritidis (CMCC 50041) in the spiked fecal samples. The results show the sefA LAMP method is a rapid, sensitive, specific, and practical method for directly detection of Salmonella Enteritidis and Salmonella Gallinarum in chickens. The sefA LAMP assay can potentially serve as new on-site diagnostics in the poultry industry.