Background: Salmonella enterica is the most common cause of food-borne diseases and responsible for considerable morbidity. The case rate in Australia is 67.9 per 100,000, with 16,441 cases being notified in 2017 based on data in the National Notifiable Diseases Surveillance System (NNDSS). S. Typhimurium was the most frequently isolated serovar in Australia followed by S. Enteritidis, S. Virchow, S. Saintpaul, and S. infantis. There are over 120,000 Salmonella genomes available from public databases. In this study we used this resource to identify serovar specific genes for rapid detection of the five most commonly reported serovars in Australia.
Methods: A selected set of 2988 publicly available genome assemblies from 5 target serovars and 27 non-target serovars were analysed in this study. The genomes were annotated using PROKKA. Pan-genome and core-genome were analysed by roary. The genes unique to each target serovar were identified using in-house python scripts.
Results: STM4494, SEN1384, SESV_RS06060, SeSPB_A1749/SeSPA_A1352 and L287_11788 were determined as serovar-specific genes to Typhimurium, Enteritidis, Virchow, Saintpaul and Infantis respectively. STM4494 was absent in 2/879 Typhimurium genomes, SEN1384 was absent in 4/724 Enteritidis genomes and L287_11788 was absence in 1/107 Infantis genomes. The number of non-target serovars’ genomes that contained the target gene were 8, 2, 6 to STM4494, SEN1384 and SeSPB_A1749 respectively. STM4494 located in region tRNAleuX was only present in Typhimurium, while SEN1384 was in the region GEI/SE14 unique to Enteritidis and SESV_RS06060 was in GI-leuX region only present in Virchow. Conventional PCR confirmed the specificities of these target genes.
Conclusion: Using Bioinformatic analysis, genes specific to each of five of Australia’s most frequently isolated serovars were identified. These serovar specific genes are suitable for developing rapid real time PCR based serovar detection and identification.