Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing

Abstract

Salmonella entericaserovar Typhimurium is the most commonSalmonellaserovar causing foodborne infections in Australia and many other countries. Twenty-oneS. Typhimurium strains fromSalmonellareference collection A (SARA) were analyzed using Illumina high-throughput genome sequencing. Single nucleotide polymorphisms (SNPs) in 21 SARA strains ranged from 46 to 11,916 SNPs, with an average of 1,577 SNPs per strain. Together with 47 strains selected from publicly availableS. Typhimurium genomes, theS. Typhimurium core genes (STCG) were determined. The STCG consist of 3,846 genes, a set that is much larger than that of the 2,882Salmonellacore genes (SCG) found previously. The STCG together with 1,576 core intergenic regions (IGRs) were defined as theS. Typhimurium core genome. Using 93S. Typhimurium genomes from 13 epidemiologically confirmed community outbreaks, we demonstrated that typing based on theS. Typhimurium core genome (STCG plus core IGRs) provides superior resolution and higher discriminatory power than that based on SCG for outbreak investigation and molecular epidemiology ofS. Typhimurium. STCG and STCG plus core IGR typing achieved 100% separation of all outbreaks compared to that of SCG typing, which failed to separate isolates from two outbreaks from background isolates. Defining theS. Typhimurium core genome allows standardization of genes/regions to be used for high-resolution epidemiological typing and genomic surveillance ofS.Typhimurium.