title: Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing.
abstract: Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing foodborne infections in Australia and many other countries. Twenty-one S. Typhimurium strains from Salmonella reference 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 available S. Typhimurium genomes, the S. Typhimurium core genes (STCG) were determined. The STCG consist of 3,846 genes, a set that is much larger than that of the 2,882 Salmonella core genes (SCG) found previously. The STCG together with 1,576 core intergenic regions (IGRs) were defined as the S. Typhimurium core genome. Using 93 S. Typhimurium genomes from 13 epidemiologically confirmed community outbreaks, we demonstrated that typing based on the S. 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 of S. 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 the S. Typhimurium core genome allows standardization of genes/regions to be used for high-resolution epidemiological typing and genomic surveillance of S. Typhimurium.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
authors.forename: Songzhe
authors.initials: S
authors.lastname: Fu
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
authors.forename: Sophie
authors.initials: S
authors.lastname: Octavia
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
authors.forename: Mark M
authors.initials: MM
authors.lastname: Tanaka
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia.
authors.forename: Vitali
authors.initials: V
authors.lastname: Sintchenko
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia r.lan@unsw.edu.au.
authors.forename: Ruiting
authors.initials: R
authors.lastname: Lan
mesh_terms: D000818:Animals; D004196:Disease Outbreaks; D062665:Epidemiological Monitoring; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D005838:Genotype; D014943:Global Health; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058889:Molecular Typing; D020641:Polymorphism, Single Nucleotide; D012480:Salmonella Infections / Q000453:epidemiology / Q000382:microbiology; D012481:Salmonella Infections, Animal / Q000453:epidemiology / Q000382:microbiology; D012486:Salmonella typhimurium / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification