Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2019

Rapid detection and identification of common Salmonella serovars using target genes selected from comparative genomic analysis (#247)

Xiaomei Zhang 1 , Michael Payne 1 , Qinning Wang 2 , Vitali Sintchenko 2 , Ruiting Lan 1
  1. University of New South Wales, Sydney, NSW, Australia
  2. Centre for Infectious Diseases and Microbiology–Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, NSW, Australia

Salmonella enterica is a highly diverse species with more than 2600 serovars. The ability to distinguish serovars within the species is important for surveillance. With the uptake of whole-genome sequencing technology, serovar determination by traditional serotyping is being to be replaced by inference of serotypes from genome sequences. In this study, we aimed to identify new serovar-specific gene markers for the common Salmonella serovars and to validate the genomic signatures for accurate detection of five most common serovars in Australia. 


A total of 2258 publicly available Salmonella genomes were selected to include serovars with at least 5 genomes available. The genomes were annotated using PROKKA. Pan-genome and core-genome were analyzed by Roary using an 80% sequence identity threshold. The genes specific to each serovar were identified from the pan-genome’s accessory genes using an in-house python script with a cutoff of 20% false negatives and 10% false positives. Multiple Cross Displacement Amplification (MCDA) was employed to develop highly sensitive assay to detect the common serovars.  


Comparative genomics of 2258 Salmonella accessory genomes identified a minimum of 131 serovar-specific gene markers to allow in silico typing of the 106 serovars with 95.1% accuracy. To evaluate the usefulness of gene markers for assay development, we selected seven genes which were specific to the five most common Salmonella serovars in Australia: Typhimurium, Enteritidis, Virchow, Saintpaul, and Infantis. Seven MCDA assays targeting these seven genes for rapid identification of the five Salmonella serovars were developed and evaluated. They demonstrated a sensitivity of 50 fg/ul (10 copies) on the pure DNA and were specific to the target serovars. The assays were also rapid with a result detectable within 8 minutes. 


A new in silico serotyping method based on genomic data of the common Salmonella serovars is described. The gene markers identified in this study have also been used to develop a rapid, accurate and sensitive serotyping MCDA assay which opens the way for culture independent serotyping directly from clinical samples.